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

Knepley/feature dm remove hybrid

See merge request petsc/petsc!2614

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

show more ...

Merge branch 'knepley/feature-plex-bc-highorder' into 'master'

Knepley/feature plex bc highorder

See merge request petsc/petsc!2536

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

Knepley/feature plex exodusii viewer

See merge request petsc/petsc!2535

Merge branch 'jed/fix-dmplexclosureindices-local-section' into 'master'

DMPlexGetClosureIndices: fix indexing for local section

See merge request petsc/petsc!2526

Merge remote-tracking branch 'origin/maint'

Plex: Added ExodusII viewer

Plex: Fix for setting boundary conditions on some components with high order discretizations

Merge branch 'jolivet/fix-dmplexcreaterankfield' into 'maint'

Segfault in DMPlexCreateRankField()

See merge request petsc/petsc!2534

DMPlexGetIndicesPointFieldsSplit_Internal: remove setBC argument

This function uses global indices, thus setBC=TRUE is invalid.

Also make function static.

DMPlexGetIndicesPointFields_Internal: add islocal argument and docs

This fixes a serious bug in DMPlexGetClosureIndices (and likely many
other places) that returns corrupt local indices in case a co

DMPlexGetIndicesPointFields_Internal: add islocal argument and docs

This fixes a serious bug in DMPlexGetClosureIndices (and likely many
other places) that returns corrupt local indices in case a constrained
component is not last. See example in new comment for
DMPlexGetIndicesPointFields_Internal. The prior behavior was correct
for global sections, but many/all uses were with local sections.

The same bug applies to DMPlexGetIndicesPoint_Internal, which is also
updated in this commit.

Thanks-to: Matthew Knepley <knepley@gmail.com>

show more ...

Segfault in DMPlexCreateRankField()

Merge branch 'jed/dmplex-boundary-clperm' into 'master'

DMPlexVecSetFieldClosure_Internal: skip user closure permutation

See merge request petsc/petsc!2498

DMPlexVecSetFieldClosure_Internal: plex-native rather than user closure permutation

If a user sets DMPlexSetClosurePermutationTensor(), but still uses
DMPlexInsertBoundaryValues (or anything involvi

DMPlexVecSetFieldClosure_Internal: plex-native rather than user closure permutation

If a user sets DMPlexSetClosurePermutationTensor(), but still uses
DMPlexInsertBoundaryValues (or anything involving a projection), this
function would mangle the results by assuming that the input data was
in user-specified permutation when in fact it was in plex-native.

Commit-type: bug-fix
Reported-by: Arash Mehraban <arash.mehraban@colorado.edu>
Reporteb-by: Jeremy Thompson <jeremy.thompson@colorado.edu>

show more ...

Merge branch 'haplav/fix-dmplexinterpolatepointsf-cannot-handle-face' into 'master'

fix dmplexinterpolatepointsf cannot handle face

See merge request petsc/petsc!2478

doc: add some more cross-references

add DMPlexGetPointHeight()

Merge branch 'knepley/feature-fem-pk' into 'master'

Knepley/feature fem pk

See merge request petsc/petsc!2464

DMPlex: Use coordinate dimension to check for field type

Merge branch 'barry/2019-12-01/nd-default-cholesky-icc-aij' into 'master'

Change the default behavior of PCCHOLESKY to use nested dissection...

See merge request petsc/petsc!2344

Update output files for new Cholesky ordering default

Reported-by: gitlab-ci

Merge branch 'knepley/feature-dm-cell-types' into 'master'

Knepley/feature dm cell types

See merge request petsc/petsc!2446

Doc: Text fixes

DM+Plex: Now classify cells by polytope type
- Defined the polytope type of a cell. added names and special shortcut
pointer like depth - Fixed DMLabelMakeValid() to optimize for contiguous
runs of

DM+Plex: Now classify cells by polytope type
- Defined the polytope type of a cell. added names and special shortcut
pointer like depth - Fixed DMLabelMakeValid() to optimize for contiguous
runs of points - Added cell polytope type label to DM - This needs
special processing, like depth - Added DMPlexGetPointDepth(),
DMPlexGetCellType(), DMPlexGetCellTypeLabel() - DMPlexComputeCellTypes()
infers the cell type for all points using dim/depth/coneSize/ghostCells
- DMPlexGetRawFace(Hybrid)_Internal() now takes the cell type. This
means we can unify the functions later. - Replaced switch(dim/coneSize)
constructs with cell type

show more ...

Merge branch 'master' into 'stefanozampini/sfwin-reuse-win'

# Conflicts:
# config/BuildSystem/config/packages/MPI.py