Patch v1.3.1

.github/workflows/build-macos.yml

@@ -0,0 +1,41 @@
+name: macOS build
+
+on:
+  push:
+    branches: [ "master", "develop" ]
+  pull_request:
+    branches: [ "master", "develop" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build-and-test:
+    name: Apple Silicon with OpenVDB
+    runs-on: macos-26
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Verify runner architecture
+        run: |
+          test "$(uname -m)" = "arm64"
+          clang++ --version
+
+      - name: Install dependencies
+        run: brew install cmake tclap boost openvdb tbb pkgconf cppunit eigen xz zstd c-blosc
+
+      # Keep these commands aligned with the macOS reproduction in issue #14.
+      - name: Configure CMake with OpenVDB
+        run: |
+          mkdir build
+          cd build
+          cmake -DMOD_OPENVDB=1 ../src
+
+      - name: Build
+        working-directory: build
+        run: make -j5
+
+      - name: Run unit tests
+        working-directory: build
+        run: ctest --output-on-failure

src/CMakeLists.txt

@@ -19,7 +19,7 @@
  #*************************************************************************/
 
 cmake_minimum_required(VERSION 3.16)
-project(den2obj VERSION 1.3.0 LANGUAGES CXX)
+project(den2obj VERSION 1.3.1 LANGUAGES CXX)
 
 option(USE_GCOV "Build with gcov coverage instrumentation" OFF)
 option(MOD_OPENVDB "Enable OpenVDB support" OFF)
@@ -65,8 +65,35 @@ endif()
 
 set(OPENVDB_LIBS "")
 if(MOD_OPENVDB)
-    set(OPENVDB_LIBS openvdb tbb PkgConfig::BLOSC ZLIB::ZLIB)
-    message(STATUS "Compiling with OpenVDB module")
+    # OpenVDB currently installs a Find-module rather than a Config package.
+    # Locate that module relative to its headers so this works with Homebrew's
+    # /opt/homebrew prefix as well as Linux multiarch installations.
+    find_package(OpenVDB CONFIG QUIET)
+    if(NOT TARGET OpenVDB::openvdb)
+        find_path(OpenVDB_INCLUDE_DIR NAMES openvdb/openvdb.h)
+        if(NOT OpenVDB_INCLUDE_DIR)
+            message(FATAL_ERROR "Could not locate the OpenVDB headers")
+        endif()
+
+        get_filename_component(_OPENVDB_INSTALL_PREFIX "${OpenVDB_INCLUDE_DIR}" DIRECTORY)
+        find_path(OpenVDB_CMAKE_MODULE_DIR
+            NAMES FindOpenVDB.cmake
+            HINTS "${_OPENVDB_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH}
+            PATH_SUFFIXES
+                lib/cmake/OpenVDB
+                "lib/${CMAKE_LIBRARY_ARCHITECTURE}/cmake/OpenVDB"
+                share/cmake/OpenVDB
+        )
+        if(NOT OpenVDB_CMAKE_MODULE_DIR)
+            message(FATAL_ERROR "Could not locate OpenVDB's FindOpenVDB.cmake module")
+        endif()
+
+        list(PREPEND CMAKE_MODULE_PATH "${OpenVDB_CMAKE_MODULE_DIR}")
+        find_package(OpenVDB REQUIRED)
+    endif()
+
+    set(OPENVDB_LIBS OpenVDB::openvdb)
+    message(STATUS "Compiling with OpenVDB module: ${OpenVDB_VERSION}")
 endif()
 
 file(GLOB SOURCES CONFIGURE_DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/*.cpp")

src/d2o_format.h

@@ -38,7 +38,7 @@
 #include <boost/iostreams/filter/bzip2.hpp>
 #include <boost/iostreams/filtering_streambuf.hpp>
 
-#include "math.h"
+#include "den2obj_math.h"
 
 namespace D2OFormat {
 

src/math.h → src/den2obj_math.h

@@ -18,8 +18,8 @@
  *                                                                        *
  **************************************************************************/
 
-#ifndef _MATRICES_H
-#define _MATRICES_H
+#ifndef DEN2OBJ_MATH_H
+#define DEN2OBJ_MATH_H
 
 #include <Eigen/Dense>
 
@@ -33,4 +33,4 @@ template <typename T> T sgn(T val) {
     return (T(0) < val) - (val < T(0));
 }
 
-#endif // _MATRICES_H
+#endif // DEN2OBJ_MATH_H

src/generator_benzene_data.h

@@ -21,7 +21,7 @@
 #ifndef _GENERATOR_BENZENE_DATA_H
 #define _GENERATOR_BENZENE_DATA_H
 
-#include "math.h"
+#include "den2obj_math.h"
 
 namespace GeneratorData {
 

src/generator_sto3g_data.h

@@ -21,7 +21,7 @@
 #ifndef _GENERATOR_STO3G_DATA_H
 #define _GENERATOR_STO3G_DATA_H
 
-#include "math.h"
+#include "den2obj_math.h"
 
 namespace GeneratorData {
 

src/isosurface.h

@@ -29,7 +29,7 @@
 #include "edgetable.h"
 #include "triangletable.h"
 #include "scalar_field.h"
-#include "math.h"
+#include "den2obj_math.h"
 
 #define PRECISION_LIMIT 0.000000001
 

src/isosurface_mesh.cpp

@@ -20,6 +20,30 @@
 
 #include "isosurface_mesh.h"
 
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+namespace {
+
+size_t get_max_thread_count() {
+#ifdef _OPENMP
+    return static_cast<size_t>(omp_get_max_threads());
+#else
+    return 1;
+#endif
+}
+
+size_t get_thread_number() {
+#ifdef _OPENMP
+    return static_cast<size_t>(omp_get_thread_num());
+#else
+    return 0;
+#endif
+}
+
+} // namespace
+
 /**
  * @brief      build isosurface mesh object
  *
@@ -176,14 +200,16 @@ void IsoSurfaceMesh::write_obj(const std::string& filename, const std::string& h
     outfile << "o " << name << std::endl;
 
     // calculate number of threads
-    size_t nrthreads = omp_get_max_threads();
-    omp_set_num_threads(nrthreads); // always allocate max threads
-    std::stringstream local[nrthreads];
+    const size_t nrthreads = get_max_thread_count();
+#ifdef _OPENMP
+    omp_set_num_threads(static_cast<int>(nrthreads)); // always allocate max threads
+#endif
+    std::vector<std::stringstream> local(nrthreads);
 
     // parallel writing vertices
     #pragma omp parallel
     {
-        size_t threadnum = omp_get_thread_num();
+        const size_t threadnum = get_thread_number();
 
         // calculate size
         size_t rem = this->vertices.size() % nrthreads;
@@ -215,7 +241,7 @@ void IsoSurfaceMesh::write_obj(const std::string& filename, const std::string& h
 
     #pragma omp parallel
     {
-        size_t threadnum = omp_get_thread_num();
+        const size_t threadnum = get_thread_number();
 
         // calculate size
         size_t rem = this->normals.size() % nrthreads;
@@ -249,7 +275,7 @@ void IsoSurfaceMesh::write_obj(const std::string& filename, const std::string& h
 
     #pragma omp parallel
     {
-        size_t threadnum = omp_get_thread_num();
+        const size_t threadnum = get_thread_number();
 
         // calculate size
         size_t rem = (this->indices.size() / 3) % nrthreads;

src/isosurface_mesh.h

@@ -24,10 +24,9 @@
 #include <fstream>
 #include <set>
 #include <vector>
-#include <omp.h>
 #include <boost/filesystem.hpp>
 
-#include "math.h"
+#include "den2obj_math.h"
 #include "isosurface.h"
 #include "check_endian.h"
 

src/scalar_field.h

@@ -40,7 +40,7 @@
 #include <boost/iostreams/filter/lzma.hpp>
 #include <boost/iostreams/filtering_streambuf.hpp>
 
-#include "math.h"
+#include "den2obj_math.h"
 #include "float_parser.h"
 #include "periodic_table.h"
 #include "d2o_format.h"

src/test/CMakeLists.txt

@@ -21,6 +21,7 @@
 pkg_check_modules(CPPUNIT REQUIRED IMPORTED_TARGET cppunit)
 add_library(unittest STATIC unittest.cpp)
 target_compile_features(unittest PUBLIC cxx_std_17)
+target_link_libraries(unittest PRIVATE PkgConfig::CPPUNIT)
 
 set(EXECUTABLES TestIsosurface TestScalarField TestD2OFileFormat TestGenerator)
 

src/test/test_file_creation.cpp

@@ -20,6 +20,10 @@
 
 #include "test_file_creation.h"
 
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
 CPPUNIT_TEST_SUITE_REGISTRATION( TestFileCreation );
 
 void TestFileCreation::setUp() {
@@ -44,8 +48,10 @@ void TestFileCreation::test_obj_file() {
 }
 
 TestFileCreation::MeshReference TestFileCreation::generate_mesh() const {
+#ifdef _OPENMP
     // set number of threads to 1
     omp_set_num_threads(1);
+#endif
 
     // read scalar field
     ScalarField sf("co_2pi_x.cub", ScalarFieldInputFileType::SFF_CUB);