Merge branch 'knepley/fix-plex-highorder-coords' into 'main'

Cleanup coordinate mappings for high order

See merge request petsc/petsc!7207

Use PetscTryTypeMethod when possible

Plex: Rework coordinate maps
- Add DMPlexCoordMap and some default maps
- Allow mapping to be done from DMSetFromOptions()
- Reimplemented DMPlexShearGeometry()
- Added affine fallback to DMPlexRemap

Plex: Rework coordinate maps
- Add DMPlexCoordMap and some default maps
- Allow mapping to be done from DMSetFromOptions()
- Reimplemented DMPlexShearGeometry()
- Added affine fallback to DMPlexRemapGeometry()

show more ...

Merge remote-tracking branch 'origin/release'

Merge branch 'stefanozampini/smallfixes' into 'release'

small release fixes

See merge request petsc/petsc!7182

DMCopyAuxiliaryVec: must take reference on the vectors

Merge branch 'knepley/fix-plex-create-and-view' into 'main'

Fixes for Plex creation and viewing

See merge request petsc/petsc!7159

DM: Correct misspelling

Merge branch 'MarDiehl/backport-DS-fix' into 'release'

Plex: Should set DS from options after creation

See merge request petsc/petsc!7097

Plex: Should set DS from options after creation

Backport from main (cf1363e4f1a257c8e2d557b3d09599624a61d010)

Merge branch 'barry/2023-11-21/fix-thread-safety-petscoptionsgetviewer' into 'main'

Fix PetscOptionsGetViewer() so it works in a thread-safe way

See merge request petsc/petsc!7047

Fix PetscOptionsGetViewer() so it works in a thread-safe way

When PetscOptionsGetViewer() returns, for example, PETSC_VIEWER_STDOUT_SELF the same object is shared
by all threads that call PetscOptio

Fix PetscOptionsGetViewer() so it works in a thread-safe way

When PetscOptionsGetViewer() returns, for example, PETSC_VIEWER_STDOUT_SELF the same object is shared
by all threads that call PetscOptionsGetViewer(). In the previous code PetscObjectReference() and
dereference (via PetscViewerDestroy() where called on the viewer by multiple threads after the viewer
was accessed thus corrupting the object.

This branch introduces a PetscOptionsRestoreViewer() that allows not doing the referencing and dereferencing
on persistant viewers, thus removing the specific race condition above.

Other possible solutions include

Use a lock on each PetscObjectReference/Dereference() just in case they are shared. Could be time consuming so one
could mark each object as either threadshared or independent and only do the locks on threadshared objects. This lowers
the cost but would require more extensive changes to PETSc infrastructure. And I do not know if this shared/not shared model
is what we need in the long run, though it might be.

show more ...

Merge branch 'knepley/fix-exodusii-check' into 'main'

Knepley/fix exodusii check

See merge request petsc/petsc!6985

DM: Fix DMSetVecType() and DMSetMatType() - Freeing the string first could cause the strange effects on FreeBSD

Merge branch 'knepley/fix-plex-tmp-space' into 'main'

Plex: Improve calculation of temp space

See merge request petsc/petsc!6989

Merge branch 'knepley/fix-ds-setup' into 'main'

Plex: Should set DS from options after creation

See merge request petsc/petsc!6986

Plex: Introducting new DMPolytopeType for arbitrary faces and cells, allowing to create and distribute arbitrary polygonal/polyhedral meshes (e.g. voronoi meshes)

Co-Authored-By: Fabien Evard <fabie

Plex: Introducting new DMPolytopeType for arbitrary faces and cells, allowing to create and distribute arbitrary polygonal/polyhedral meshes (e.g. voronoi meshes)

Co-Authored-By: Fabien Evard <fabien.evrard@ovgu.de>

show more ...

Plex: Should set DS from options after creation

Merge branch 'knepley/fix-plex-setup' into 'main'

Plex: Fix setup for RDycore

See merge request petsc/petsc!6877

Plex: Updates for FVM
- Add DMPlexInsertBoundaryValuesFVM()
- Add -dm_plex_print_fvm
- Fix copy of diagnostic flags

DM: Fix destroy

Merge branch 'knepley/fix-plex-ceed' into 'main'

Plex: More work adding in CEED backend

See merge request petsc/petsc!6870

Plex: More work adding in CEED backend
- Add DMPlexGetUseCeed() and DMPlexSetUseCeed()
- Need to propagate useCeed flag
- When using CEED, make tensor order the default, but shut it off for matrix in

Plex: More work adding in CEED backend
- Add DMPlexGetUseCeed() and DMPlexSetUseCeed()
- Need to propagate useCeed flag
- When using CEED, make tensor order the default, but shut it off for matrix insertion since this is still done by Plex kernels
- DMPlexMatSetClosureGeneral() now takes flag for closure permutation
- Add DMPlexMatSetClosure_Internal() which takes flag for closure permutation
- Add DMPlexVecGetClosure_Internal() with flag to turn off closure permutation - Turn off closure permutation in L2 diff calculation
- Add DMUseTensorOrder()
- Add DMPlexSNESComputeResidualCEED() - Cleanup SNES ex13 - Do not give CEED negative offsets

show more ...

Merge branch 'knepley/fix-swarm-layout' into 'main'

Swarm: Reworked Swarm projection interface and fixed some particle layout

See merge request petsc/petsc!6856

DM: Added DMPrintCellIndices() for debugging