Plex: Added DMPlexCreateFromFile()
- Dispatches to the right constructor based on extension

Plex: Remove superfluous argument from DMPlexDisitrbute()

Merge branch 'knepley/feature-plex-partitioner-shell' into mlange/feature-parallel-distribute

Partitioner+Plex: Added PetscPartitioner class
- Plex holds a PetscPartitioner
- Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition)
- Now partition routine

Partitioner+Plex: Added PetscPartitioner class
- Plex holds a PetscPartitioner
- Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition)
- Now partition routine takes a number of partitions instead of assuming commSize
- Added a shell partitioner intended to be used for regression testing

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Merge branch 'knepley/feature-plex-generator-args'

* knepley/feature-plex-generator-args:
Plex: Small fix
Plex: Fixed misspelling
Plex: Move generation to a separate source file, Can now speci

Merge branch 'knepley/feature-plex-generator-args'

* knepley/feature-plex-generator-args:
Plex: Small fix
Plex: Fixed misspelling
Plex: Move generation to a separate source file, Can now specify operator for mesh generators - Added DMPlexTriangleSetOptions() and DMPlexTetgenSetOptions()

Conflicts:
src/dm/impls/plex/makefile

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Merge branch 'tisaac/feature-fe-geom-dim' into tisaac/plex-flexible-projection

Use the new PetscFECellGeom

Conflicts:
include/petscdmplex.h
include/petscfe.h
src/dm/impls/plex/plexfem.c

Merge branch 'tisaac/thplex'

This merge brings in related work in the following areas:
- Added a local constraint matrix to DM (see DMSetDefaultConstraints())
- Added point-to-anchor-point constrain

Merge branch 'tisaac/thplex'

This merge brings in related work in the following areas:
- Added a local constraint matrix to DM (see DMSetDefaultConstraints())
- Added point-to-anchor-point constraints in DMPlex (see
DMPlexSetAnchors()), which build on the DM constraints
- Added hierarchically-constrained points to DMPlex (see
DMPlexSetReferenceTree(), DMPlexSetTree()), which builds on the anchor
constraints
- Tests for these constraints in src/dm/impls/plex/examples/ex3.c (try
runex3_* examples in that directory)
- Added quadrature order (see PetscQuadratureGet/SetOrder()) (work by
Matt Knepley)
- Added default return values for DMGetCoordinateDim() (defaults to
DMGetDimension())

Conflicts:
include/petscdmplex.h
src/dm/dt/interface/dt.c
src/dm/impls/plex/examples/tests/ex3.c
src/dm/impls/plex/makefile
src/dm/impls/plex/plexfem.c

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Plex: Move generation to a separate source file, Can now specify operator for mesh generators
- Added DMPlexTriangleSetOptions() and DMPlexTetgenSetOptions()

Plex: added DMPlexGet/SetMaxProjectionHeight()

The idea is to accomodate meshes (such as non-conforming meshes), where
a global basis function restricted to a cell may not correspond to a
single bas

Plex: added DMPlexGet/SetMaxProjectionHeight()

The idea is to accomodate meshes (such as non-conforming meshes), where
a global basis function restricted to a cell may not correspond to a
single basis function on the cell, but to a linear combination. The
most general case would be to do an L2 projection, but we would have to
find a way to invert control to use a KSPSolve(). This approach at
least expands the available set of local projection operations.

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Plex: remove the last vestiges of constraintSection/Mat

DM+Plex: change the collective status of default constraints, anchors, and reference tree

The default constraints, anchors, and reference tree are changed to have
PETSC_COMM_SELF communicators.

The

DM+Plex: change the collective status of default constraints, anchors, and reference tree

The default constraints, anchors, and reference tree are changed to have
PETSC_COMM_SELF communicators.

The reasoning is that we would like tree constraints to cause only
minimal changes to the solution workflow demonstrated in
snes/examples/tutorials/ex12.c. We would like to insert only the
following code:

/* ... (construct/choose a reference tree) */
DMPlexSetReferenceTree(dm,refTree);
/* ... (construct the tree structure) */
DMPlexSetTree(dm,...);

This means that the presence of some type of constraints may not be
detected until DMPlexMatSetClosure(), within a cell loop. If that
happens, the following call graph occurs:

DMPlexMatSetClosure(dm,...) calls
DMGetDefaultConstraints(dm,...) calls
*DMCreateDefaultConstraints_Plex(dm,...) calls
DMPlexGetAnchors(dm,...) calls
*DMPlexCreateAnchors_Tree(dm,...)
DMPlexComputeAnchorMatrix_Tree_FromReference(dm,...) calls
DMGetDefaultConstraints(refTree,...) calls
*DMCreateDefaultConstraints_Plex(refTree,...) calls
DMPlexGetAnchors(refTree,...) calls
*DMPlexCreateAnchors_Tree(refTree,...)

The objects created in this cascade have to be local.

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Plex: added createanchors method.

Now DMPlexGetAnchors() is like DMGetConstraints(): if a method exists to
create the constraints, it is called.

DM+Plex: added DMCreateDefaultConstraints_Plex().

Just reuse the existing code for creating a constraint matrix, but now
in service of the matrix that lives in DM instead of the matrix that
lives in

DM+Plex: added DMCreateDefaultConstraints_Plex().

Just reuse the existing code for creating a constraint matrix, but now
in service of the matrix that lives in DM instead of the matrix that
lives in DMPlex.

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DMPlexCreateFromDAG(): use embedding dimension

Plex: Fix calls to DMPlexGet/SetDimension()

DMPlex: added DMPlexReferenceTreeGetChildSymmetry()

DMPlex: add DMPlexReferenceTreeGetChildSymmetry()

DMPlex: fix DMPlexReferenceTreeGetChildSymmetry_Default()

DMPlex: change DMPlexGetTreeParent()

DMPlex: added DMPlexReferenceTreeGetChildSymmetry()

DMPlex: add DMPlexReferenceTreeGetChildSymmetry()

DMPlex: fix DMPlexReferenceTreeGetChildSymmetry_Default()

DMPlex: change DMPlexGetTreeParent() to remove magic constant

DMPlex: added DMPlexTreeGetChildren()

DMPlex: replace DMPlexGetTreeParent() loops with DMPlexGetTreeChildren()

Reorder

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DMPlex: added basic tree routines

DMPlex: change DMPlexGetTreeParent() to remove magic constant

DMPlex: added DMPlexTreeGetChildren()

DMPlex: added DMPlexGet/SetReferenceTree()

DMPlex: Take (right) constraints into account in preallocation

DMPlex: fix recent constraint additions

DMPlex: added constraints and constraint matrix

DMPlex: fix recent constraint additions

DMPlex: doc correction for DMPlexSetConstraintMatrix()

DMPlex: use PETSC_COMM_SELF for local error messages

DMPlex: added constraints and constraint matrix

DMPlex: fix recent constraint additions

DMPlex: doc correction for DMPlexSetConstraintMatrix()

DMPlex: use PETSC_COMM_SELF for local error messages

DMPlex: replace ISGetSize with ISGetLocalSize where appropriate for anchors

DMPlex: fix DMPlexGlobalToLocalHook_Plex_constraints

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DMPlex: Figure out first vertex in CreateFromDAG instead of assuming

DMPlex: use PETSC_COMM_SELF for local error message

DMPlex: added 3D HexBoxMesh

DMPlex: fix hex box creation

DMPlex: typo in plexcreate.c

DMPlex: make DMPlexCreateReferenceCell

Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex1

Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex11: Fixed calls to DMSetCoordinateSection()
DM: FIxed DMClone() to copy dimension
Plex+DA: Now cell geometry routine can take a PetscFE in order to evaluate at quadrature points - We evaluate isoparametrically at the quadrature points - Changed DMDAComputeCellGeometry() --> DMDAComputeCellGeometryFEM() - Changed DMPlexComputeCellGeometry() --> DMPlexComputeCellGeometryFEM() - Added DMPlexComputeCellGeometryAffineFEM()
DM: Added a embedding dimension, different from the topological dimension - This can now be set in DMSetCoordinateSection(), or it can be automatically determined
Plex: Fix output for ex4
DM: Added DMGetDimPoints() - This replicates DMPlex/DAGetDepthStratum(), but uses the dimension which people have said is more intuitive
DM: Move dimension up into DM - Both DA and Plex had this and I think it makes sense

Conflicts:
src/dm/impls/plex/plexcreate.c

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Merge branch 'knepley/fix-plex-coords-parallel'

* knepley/fix-plex-coords-parallel:
DMPlex: Incorrect periodicity information
KSP+SNES: Converged output now includes prefix
DMPlex ex4: Fixed t

Merge branch 'knepley/fix-plex-coords-parallel'

* knepley/fix-plex-coords-parallel:
DMPlex: Incorrect periodicity information
KSP+SNES: Converged output now includes prefix
DMPlex ex4: Fixed test output
Mat+Coloring: Greedy coloring fix - Use ocolors[] for off-diagonal piece
PetscSection: Added check for mismatch between SF and Section
DMPlex: DMPlexReplace_Static() fixes - Should share coordinateDM, not just the section, so we get correct SF - Pass on periodicity information
DMPlex: Refinement should create SF before coordinates, so coordinateDM gets correct SF - Also pass on periodicity information
DMPlex: Distribution should create SF before coordinates, so coordinateDM gets correct SF - Also pass on periodicity information

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