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

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

Knepley/feature dm cell types

See merge request petsc/petsc!2446

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

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Merge branch 'knepley/feature-project-different-spaces' into 'master'

Knepley/feature project different spaces

See merge request petsc/petsc!2153

Plex: Now for projection allow 3 DMs: input, output, and auxiliary
- We get the input DM from the input Vec
- Now we can have more general relations between input/output/auxiliary meshes in projectio

Plex: Now for projection allow 3 DMs: input, output, and auxiliary
- We get the input DM from the input Vec
- Now we can have more general relations between input/output/auxiliary meshes in projection and integration
- Added DMEnclosureType
- Added DMGetEnclosureRelation() and DMGetEnclosurePoint()
- Removed DMPlexGetSubpoint() and DMPlexGetAuxiliaryPoint()
- In projection, convert output mesh points to input mesh points
- Coordinates must be reordered after depth label is constructed
- DMPlexLabelAddFaceCells() only adds cells adjacent to faces
- Put in extra debugging for missing point enclosures
- In boundary projection, calculate face data for geometry
- p4est: use known point maps instead of projection to interp from base to coarse

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Merge remote-tracking branch 'origin/haplav/feature-dmplexisinterpolated'

Add DMPlexIsInterpolated and DMPlexIsInterpolatedCollective.

See merge request petsc/petsc!2146

Merge branch 'knepley/fix-fv-ghost-cells' into 'master'

Knepley/fix fv ghost cells

See merge request petsc/petsc!2132

Plex: When constructing ghost cells, must preserve the hybrid cell information

- Need to distribute ghost cell info along with hybrid info

- Change the output format for ghost cells - Update TS ex18

Plex: Use new API to handle hybrid and FV ghost cells

DMPlex: Improved error checking through DMPlexIsInterpolated.

* Check interpolatedness in DMPlexMarkBoundaryFaces, DMPlexMarkBoundaryFaces, DMPlexCreateSubmesh
* Interpolate and Uninterpolate set th

DMPlex: Improved error checking through DMPlexIsInterpolated.

* Check interpolatedness in DMPlexMarkBoundaryFaces, DMPlexMarkBoundaryFaces, DMPlexCreateSubmesh
* Interpolate and Uninterpolate set the flags as well.
* Moved PetscValidHeaderSpecific from DMPlexMarkBoundaryFaces_Internal to DMPlexMarkBoundaryFaces.

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Merged in stefano_zampini/dmplex-speedup (pull request #1665)

Last speedups to the PLEX code with large number of MPI processes

Approved-by: Matthew Knepley <knepley@gmail.com>

DMPLEX: fix improper usage of STDOUT_WORLD

Merge branch 'master' of bitbucket.org:petsc/petsc

Merged in knepley/feature-move-adj-to-dm (pull request #1424)

Knepley/feature move adj to dm

Merge branch 'knepley/fix-plex-aux-integrate' [PR #1422]

* knepley/fix-plex-aux-integrate:
Plex: Added DMPlexGetAuxiliaryPoint(), and used it in integration

DM: Eliminate DMPlexGet/SetAdjacencyUseCone/Closure() in favor of DMGet/SetBasicAdjacency()

Plex: Added DMPlexGetAuxiliaryPoint(), and used it in integration
- It was already being used in projection

Merge branch 'master' into wence/feature-patch-all-at-once

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'knepley/feature-multiple-ds' [PR #1309]

Merge branch 'master' into knepley/feature-snes-patch