Merge branch 'knepley/fix-plex-exodus-surfaces' into 'master'

Knepley/fix plex exodus surfaces

See merge request petsc/petsc!2997

Plex: Turn on some options for extrusion

Merge branch 'jacobf/fix-dmplex-ints' into 'master'

int -> PetscInt, double -> PetscReal/PetscScalar in DMPlex API for various front facing functions

See merge request petsc/petsc!2512

Add DMPlexCreateFromCellList[Parallel]Petsc and marked previous namesake as
deprecated. New function accpets only petsc datatypes, old function performs types conversions within. Affects tetgen, ctet

Add DMPlexCreateFromCellList[Parallel]Petsc and marked previous namesake as
deprecated. New function accpets only petsc datatypes, old function performs types conversions within. Affects tetgen, ctetgen, and any createfromcelllist[parallel] interfaces.

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Merge branch 'knepley/feature-plex-ball' into 'master'

Knepley/feature plex ball

See merge request petsc/petsc!2977

Plex: Fixed sphere and ball meshes, and cleaned up refinement
- Added function to DMPlex to remap new coordinates
- Refinement must copy coordinate discretization
- Fixed sphere mesh to be the unit s

Plex: Fixed sphere and ball meshes, and cleaned up refinement
- Added function to DMPlex to remap new coordinates
- Refinement must copy coordinate discretization
- Fixed sphere mesh to be the unit sphere
- DMPlexCheckGeometry() cannot check surfaces

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Merge branch 'knepley/feature-swarm-fortran' into 'master'

Knepley/feature swarm fortran

See merge request petsc/petsc!2680

Plex: Move FEM assembly from dmplexsnes.c to plexfem.c, and fix DMCreateMassMatrix()
- Create regular mass matrix if we pass in the same DM to DMCreateMassMatrix()
- Changed DMPlexSNESGetGeometryFVM(

Plex: Move FEM assembly from dmplexsnes.c to plexfem.c, and fix DMCreateMassMatrix()
- Create regular mass matrix if we pass in the same DM to DMCreateMassMatrix()
- Changed DMPlexSNESGetGeometryFVM() to DMPlexGetGeometryFVM()
- Changed DMPlexSNESGetGradientDM() to DMPlexGetGradientDM()

Co-authored-by: Mark Adams <mfadams@lbl.gov>

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Merge branch 'dalcinl/partitioner' into 'master'

PetscPartitioner: Reorganize code in a proper package subtree

See merge request petsc/petsc!2941

PetscPartitioner: Reorganize code in a proper package subtree

Merge branch 'knepley/feature-plex-project-point' into 'master'

Plex: Have projection report the point it is currently working on

See merge request petsc/petsc!2865

Plex: Have projection report the point it is currently working on

Merge branch 'jacobf/feature-dmplex-orth-qual' into 'master'

Compute cell-wise orthogonal quality

See merge request petsc/petsc!2808

Compute cell-wise orthogonal quality, optionally tagging cells below absolute tolerance with
DM_ADAPT_REFINE in DMLabel for refinement

Merge branch 'knepley/fix-plex-projection-label' into 'master'

Plex: This fixes a pernicious bug with projection - When setting points along...

See merge request petsc/petsc!2773

Plex: Allow projection between bases on the same mesh

Plex: Abstract getting dof indices on closure
- Added DMPlexMatSetClosureGeneral()
- Changed interface for existing DMPlexGetClosureIndices()

Merge branch 'knepley/fix-plex-subpoint-is' into 'master'

Plex: Now subpointIS is managed by the DM

See merge request petsc/petsc!2687

Plex: Now subpointIS is managed by the DM

Merge branch 'knepley/feature-dm-boundary-function-projection' into 'master'

DM: Added DMProjectBdFieldLabelLocal()

See merge request petsc/petsc!2667

DM: Added DMProjectBdFieldLabelLocal()
- Called from DMPlexInsertBoundaryValuesEssentialBdFIeld()
- Added projectbdfieldlabelLocal() to DM
- Added Plex impl
- Added more documentation of the InsertBo

DM: Added DMProjectBdFieldLabelLocal()
- Called from DMPlexInsertBoundaryValuesEssentialBdFIeld()
- Added projectbdfieldlabelLocal() to DM
- Added Plex impl
- Added more documentation of the InsertBoundaryValues*() methods

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Merge branch 'knepley/feature-dm-remove-hybrid' into 'master'

Knepley/feature dm remove hybrid

See merge request petsc/petsc!2614

DMPlex: Fixed cell reordering and namespaced cell type names
- Namespaced DMPlexCellRefinerType enum items
- Added DMPlexReorderCell() and refactored DMPlexInvertCell()
- Update Gmsh reader to han

DMPlex: Fixed cell reordering and namespaced cell type names
- Namespaced DMPlexCellRefinerType enum items
- Added DMPlexReorderCell() and refactored DMPlexInvertCell()
- Update Gmsh reader to handle tet+tri-prism meshes

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DM+Plex: Removed the idea of hybrid and ghost cells, in favor of cell type
- Improved Plex tests to work for other cell types
- Plex creation, interpolation, submesh, and refinement routines now set

DM+Plex: Removed the idea of hybrid and ghost cells, in favor of cell type
- Improved Plex tests to work for other cell types
- Plex creation, interpolation, submesh, and refinement routines now set the cell type
- Distribution sorts strata by cell type
- Fixed orientation of prisms from input formats
- Added Plex ex40 to test regular refinement
- CellRefiner is a PetscObject
- dm_plex_cell_refiner chooses the refinement strategy
- Removed SimplexToTensor stuff in favor of ToHex refiner
- Most functions take DMPolytopeType instead of CellRefiner
- CellRefinerInCellTest_Internal()
- CellRefinerGetAffineTransforms_Internal()
- CellRefinerGetAffineFaceTransforms_Internal()
- DMForest now responds to DMPlexGetOverlap() and propagates its overlap to the underlying Plex
- Use DMPlexComputeCellType_Internal() to classify a cell based only on topology
- Added DMPlexGetSimplexOrBoxCells() to replace DMPlexGetInteriorCellStratum()
- Added DM_POLYTOPE_POINT_PRISM_TENSOR
- Added DMPolytopTypeGetDim() and DMPolyTopeTypeGetConeSize()
- Added DMLabelSetStratumBounds()
- Added DMPlexSetCellType()
- Added celltypes to DMView()
- Added DMPolytopeTypeGetNumVertices()
- Added DMPlexCreateReferenceCellByType()
- Added DMPolytopeTypeFromGmsh()
- Made DMPlexRefineUniform() public

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Merge branch 'knepley/feature-plex-exodusii-viewer' into 'master'

Knepley/feature plex exodusii viewer

See merge request petsc/petsc!2535