Plex: Added DMPlexInsertBoundaryValues()
- Unified FE and FV boundary values

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: complete rename of constraints to anchors, make matrix construction automatic.

Now all the user has to do is set the reference tree, set the tree, and
the constraint matrix is automatically co

Plex: complete rename of constraints to anchors, make matrix construction automatic.

Now all the user has to do is set the reference tree, set the tree, and
the constraint matrix is automatically constructed in the call to
DMGetDefaultConstraints()

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Plex: added createanchors method.

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

Plex: rename Constraints as Anchors for clarity.

Now that there are DMGet/SetConstraints() functions, some clarity is
needed:

DMGet/SetConstraints() are any type of linear constraints that are
cons

Plex: rename Constraints as Anchors for clarity.

Now that there are DMGet/SetConstraints() functions, some clarity is
needed:

DMGet/SetConstraints() are any type of linear constraints that are
considered part of the global-to-local map.

DMPlexGet/SetAnchors() are linear constraints that make a point's dofs
linear dependent on the dofs of a set of anchor points.

DMPlexGet/SetTree() are anchor constraints that derive from a
hierarchically refined mesh.

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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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Fixed compiler warning

Added DMGlobalToLocalSolve()

DMPlex: added basic tree routines

DMPlex: change DMPlexGetTreeParent() to remove magic constant

DMPlex: added DMPlexTreeGetChildren()

DMPlex: added DMPlexGet/SetReferenceTree()

DMPlex: added DMPlexProjectConstraints_Internal()

DMPlex: use constraint matrix in DMPlexMatSetClosure()

DMPlex: tighter bounds on work arrays

DMPlex: fix adjacency size when there are zero anchors

DMPlex: added DMPlexCreateConstraintMatrix()

DMPlex: fix constraint matrix construction

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: make vtk viewing an option in DMView_Plex()

Plex+TS ex11: Now default section computation can handle an FVM discretization

Plex+Doc: Removed useless comment

Plex: Fix DMCreateDefaultSection_Plex() to handle FV discretizations
- I will check CLASSID until a superclass for FE/FV becomes clear

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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DM: Added a embedding dimension, different from the topological dimension
- This can now be set in DMSetCoordinateSection(), or it can be automatically determined

DM: Move dimension up into DM
- Both DA and Plex had this and I think it makes sense

Merge branch 'stefano_zampini/pcbddc-maint' into stefano_zampini/pcbddc_deluxe

Merge remote-tracking branch 'origin/irving/doc-cleanup'

Conflicts:
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexgeometry.c
src/snes/examples/tutorials/ex62.c