Start to introduce zstart/zend and change loops (updated) #1713
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Most robust approach is to replace nested loops with BOUT_FOR loops as this defers the zp/zm offsetting to the SpecificInd code
Doesn't use global `mesh`, instead uses `Field::getMesh()`, and constructs return fields using this `localmesh`. Loops in Z use `zstart`/`zend`, or changed to use `BOUT_FOR`
Updating the cxx file functions to use these new features.
* next: (1066 commits) Fix more typos in BoutMesh boundary Region y-ranges Add implementation of Field2D::applyBoundary(BoutReal time) Fix typos in BoutMesh boundary Region y-ranges Fixes for FV::Div_a_Laplace_perp Add Options::withDefault(Options&) to manual Set y-direction of FieldPerp results in ParallelTransformIdentity Do not calculate parallel slices for field-aligned fields Allow default value of Options to be set from another Options object Unit test ParallelTransformIdentity::toFieldAligned/fromFieldAligned Set y-direction of results in ParallelTransformIdentity Correct Field3D->FieldPerp in error message RGN_NOBNDRY in FieldPerp unit tests toFieldAligned and fromFieldAligned Unit tests for FieldPerp toFieldAligned and fromFieldAligned Add support for shifting a FieldPerp toFieldAligned/fromFieldAligned More tests for case sensitivity/insensitivity in options unit tests Convert Options::isSection() argument to lower case Update required Jinja2 version to avoid CVE-2019-10906 Move Gridfile::get implementations for Field3D/Field2D to .cxx typo Warn about random failures in test ...
* next: (26 commits) Make manual entry on file I/O for FieldPerps clearer Rename safeAtReverse to safeAt Use BoutComm::rank() in datafile.cxx Add FieldPerp to File I/O documentation Throw in unimplemented 'int' version of GridFromOptions::get Make sure yindex_global is invalid in DataFormat::writeFieldAttributes HDF5 version of I/O test with reading from restart files I/O test with reading from restart files Make restart.redistribute work for FieldPerps Add FieldPerp to test-io and test-io_hdf5 More FieldPerp support in datafile.py Add FieldPerp support to collect.py Loading FieldPerp from grid, only communicate and checkData if valid Don't allocate in Mesh::get GridFromFile: only allocate FieldPerp when actually reading Read attributes when getting Fields from grid-file Add FieldPerp version of Mesh::get() Implement FieldPerp capability in FieldFactory Don't use DataFormat::mesh when it might be nullptr Move readFieldAttributes/writeFieldAttributes to DataFormat ...
* next: (80 commits) Deprecate Karniadakis solver Remove Laplace3D Don't specify boundary regions in D2DXDY Use function_traits<T>::arg_t<N> in SUNDIALS wrappers Add some tests for function_traits Provide function_traits<T>::arg_t<0> for ease of use Remove autoconf macros for handling SUNDIALS integer types Replace SUNDIALS int types with `function_traits` or sunindextype Add traits class to get types of function arguments fix nc-format Manual section on mixed second derivatives In D2DXDY take y-derivative first, apply boundary condition before DDX Take z-derivative before x-derivative in D2DXDZ Simplify location-setting in D2DYDZ Handle attributes for missing variables Revert "Hypnotoad: 'H' is derivative of integral" Default initialise member variables Fix return type on empty Petsc Laplace solve Add LaplacianNaulin::resetMeanIterations Replace old-style C casts with static_cast in PetscSolver ...
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What is the best way to move this forward? Also, should this be split in several PRs, to make it easier (and thus faster) to review? |
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We have a new RSE starting next week, this will be on their to-do list, but it might be awhile before they actually get to it. I haven't looked at how bad the conflicts are, but I suspect that will determine how we actually proceed. Multiple PRs might be better, but the hope with the new RSE is that we'll have a bit more bandwidth to review PRs and get them merged faster. |
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#1448 + next
The merge commit had a lot of conflicts, hence new PR.
I think maybe we should undo the changes to
ShiftedMetric-- at least for now, we probably want to transform all of Z.