Boundary conditions fixes - #1319

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johnomotani wants to merge 84 commits into

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boundary-conditions-fixes

Commits on Mar 23, 2018

AX_LIB_HDF5: fix order of flags
ZedThree
committed
2909334
Merge pull request #962 from boutproject/bugfix-961
ZedThree
authored
8389878

Commits on Oct 3, 2018

Use input field/vector location for CELL_DEFAULT in vecops
ZedThree
committed
bdd81a1

Commits on Oct 8, 2018

add simple test for squashoutput
dschwoerer
committed
a9fcbf9
Fix append mode
dschwoerer
committed
f7d5117
Fix for Field2D
dschwoerer
committed
de6ffad
Fix: glob not correctly imported
dschwoerer
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25cfad4
add dump_on_restart=false sub test
dschwoerer
committed
5006006
Fix formatting
dschwoerer
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a555391

Commits on Oct 9, 2018

Ensure CELL_DEFAULT and CELL_VSHIFT are forbidden in calls to
d7919
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291b9f6
Bump version number to 4.2.0
ZedThree
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f02880b
Include caveats on OpenMP parallelisation in documentation
ZedThree
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8d68443
Merge branch 'master' into v4.2-rc
ZedThree
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a5ce343
Remove mixed field-aligned/non-field-aligned derivatives
johnomotani
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e9e0008
Add missing fromFieldAligned calls
johnomotani
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90648ba
Fix f->f_fa
johnomotani
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54494d4
Set location of result as soon as it is declared in index_derivs.cxx
johnomotani
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1342d87
Merge branch 'next' into v4.2-rc
ZedThree
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feb65a4
Add ASSERTs for checking requested location is unambigous/consistent.
d7919
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791ebc7
Ensure Vector copy and assignment copies the location
d7919
committed
5a079d4

Commits on Oct 10, 2018

Expand unit tests to check that vector copy/assignment copies location
d7919
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2f39306
Handle CELL_DEFAULT in vector setLocation
d7919
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b3b756e
Add unit tests for vector setLocation
d7919
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04f0eca
Fix for vector non-staggered setLocation unit tests
d7919
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96dc8ab
Add staggered flag check in vector setLocation
d7919
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ba80a08
Remove duplicated ASSERT
d7919
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546ca78
Remove setLocation calls that are not required
d7919
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8c571e9
Improvements after feedback
dschwoerer
committed
fce307d
Adding support for CELL_VSHIFT to Grad(Field2D)
d7919
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1c4f9b9
Deprecating three arg version of Grad(Field3D)
d7919
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83d6b82
Ensure Grad_perp only works at location of input field
d7919
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993968c
Updating treatment of location in Curl. Forbid use of CELL_VSHIFT
d7919
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93330d0
Attempt to fix asserts in V_dot_grad
d7919
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0669941
Move depecrated into header
d7919
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db34fd6
Clear up language about parallelisation directions
ZedThree
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2c863fa
Rename Mesh::coordinates -> Mesh::getCoordinates; deprecate old name
ZedThree
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f9ea8ba
Adding some Doxygen comments to mention allowed locations
d7919
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a11951c

Commits on Oct 11, 2018

Merge pull request #1306 from boutproject/bugfixes-from-shiftedmetric-update
ZedThree
authored
23930d1
Remove output location argument from V_dot_Grad
ZedThree
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573b1aa
Use launch_safe in order set nproc and mthread
ZedThree
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cbe4688
Use minimal number of timesteps
ZedThree
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627179a
Add docstrings, simplify error message handling
ZedThree
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ef396a1
Throw error messages for non-python collect routines
ZedThree
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3c7f806
Merge pull request #1303 from boutproject/squash-test
ZedThree
authored
002d30c
Remove support for CELL_VSHIFT in V_dot_Grad
ZedThree
committed
7fd82e9
Add some text on setting the openmp schedule
ZedThree
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d5a9f21
Fix some sphinx whitespace/code blocks
ZedThree
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1493312

Commits on Oct 12, 2018

Merge pull request #1307 from boutproject/openmp-docs
ZedThree
authored
cbd4da3
Merge pull request #1308 from boutproject/vecops-consistent-cell-default-more-pass-through
d7919
authored
77dd5bb
Provide `getRegion` method on Fields to return the requested Region from fieldmesh
d7919
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836abfb
Add const(_iterator) overload of Region::begin/end
d7919
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00dfc5f
Make mesh::getRegion?? const
d7919
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a1b8dee
Remove unnecessary interp_to in Grad2_par2
johnomotani
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cba520f
Tidying up more location setting in derivatives
johnomotani
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b54aef9
Remove bracket_location() function, replace with ASSERT1
johnomotani
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3be5334
Remove const on arguments passed by value
johnomotani
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ac984b8
Add method argument to Grad2_par2
johnomotani
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2bef4ec
Merge pull request #1312 from boutproject/fix-issue-394
ZedThree
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89e4110
Merge pull request #1316 from boutproject/field_get_region
ZedThree
authored
8bb7ce6
Use std::map::emplace to avoid naming complicated type with insert
ZedThree
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8757d9c
Fix V_dot_Grad documentation
ZedThree
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fce8979
Use curly braces with if statements
johnomotani
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49247a3

Commits on Oct 13, 2018

Set yup/ydown fields for Div_par_flux()
johnomotani
committed
6ef003f

Commits on Oct 15, 2018

Fix locations of Jacobian in Div
ZedThree
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c9acb64
Deprecate Curl overloads that take a location
ZedThree
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afe353c
Fix whitespace in vecops header
ZedThree
committed
df49dd1
Remove output location from Curl properly
ZedThree
committed
64e24b7
Merge pull request #1317 from boutproject/fix-coordsmap-emplace-type
ZedThree
authored
b34d0cc
Merge pull request #1293 from boutproject/vecops-consistent-cell-default
ZedThree
authored
c7014c2
Check TwistShift==true in ShiftedMetric
johnomotani
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20a4cc1
Make test-yupdown work with new test for TwistShift=true
johnomotani
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0d57cb7
Invert conditional in Div_par and Div_par_flux
johnomotani
committed
0575997

Commits on Oct 16, 2018

Merge pull request #1318 from boutproject/derivatives-more-tidyup
ZedThree
authored
f586fbd
Merge pull request #1323 from boutproject/shiftedmetric-test-twistshift-global-option
ZedThree
authored
c353ef9
Merge branch 'v4.2-rc' into rename-mesh-coordinates
ZedThree
committed
69b9455
Merge pull request #1310 from boutproject/rename-mesh-coordinates
ZedThree
authored
7516b23
Handle CELL_ZLOW case in boundary_standard.cxx
johnomotani
committed
3fe02cb
Remove uses of global mesh from boundary conditions
johnomotani
committed
3657ce8
Tidy up location checking in boundary_standard.cxx
johnomotani
committed
bfcf30f
Make FieldData() backward compatible, no virtual on getDataMesh()
johnomotani
committed
ea613e1
Move FieldData::fielddatamesh init into init list

ZedThree
authored and
johnomotani
committed
38f4161
Check Mesh*'s are the same in Field3D operator=(Field2D)
johnomotani
committed
2de6e1d
Copy or check fielddatamesh in Field3D/Field2D operator=
johnomotani
committed
2f36229
Check consistency of fieldmesh and fielddatamesh
johnomotani
committed
df110a0