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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Plex+Label: Added output flag for labels
- Meant storing labels in a struct inside Plex
- Added DMPlexGetLabelByNum()
- Added DMPlexGet/SetLabelOutput()
- Got rid of most of the mucking with the inte

Plex+Label: Added output flag for labels
- Meant storing labels in a struct inside Plex
- Added DMPlexGetLabelByNum()
- Added DMPlexGet/SetLabelOutput()
- Got rid of most of the mucking with the internal label storage

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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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Plex: Added methods to support distributed overlap calculation
- Added DMPlexCreateTwoSidedProcessSF()
- Added DMPlexDistributeOwnership()
- Added DMPlexCreateOverlap()

PetscSF: The declaration of PetscSFNode should be in the types header

Plex: move DMPlexProjectionFunction() back to libdm

When I first implemented hanging constraints, I moved
DMPlexProjectFunction() to libksp because I used a global solve to
determine the values of d

Plex: move DMPlexProjectionFunction() back to libdm

When I first implemented hanging constraints, I moved
DMPlexProjectFunction() to libksp because I used a global solve to
determine the values of dofs on an anchor point that is not in the
closure of any cell. This was a hack, as those values do not require a
global solve, but can be determined with functionals evaluated on the
anchor point: -dm_plex_max_projection_height > 0 allows functionals to
be evaluated on these anchor points, so the global solve is no longer
necessary.

To see the effect, you can modify the scripts to run ex3 in
src/dm/impls/plex/examples/tests: set -dm_plex_max_projection_height 0
in the runex3_nonconforming_{simplex,tensor}_{2,3} examples, and
projecting a function fails.

I did not move DMPlexProjectField() back into libdm because it evaluates
field jets, not just field values, and doing this on non-cells isn't
straightforward.

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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: Fixed misspelling

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove unused var
Plex+SNES+TS: Complete reorganization of residual evaluation - Now both FE and FV examples use the same method, but there are a bunch of switches which should be eliminated - There is a confusion about IFunction and RHS, but I think they can both be in one function - Added DMPlexSNESGetGeometryFVM() and DMPlexSNESGetGradientFVM() - Added DMPlexGet/RestoreCellFields() and DMPlexGet/RestoreFaceFields() and DMPlexGet/RestoreFaceGeometry() - I think that FV geometry caching needs to be redone - Added DMPlexReconstructGradients_Internal() - Added DMPlexComputeBdResidual_Internal() which does not work for FV - Replaced DMPlexComputeResidualFEM_Internal() with DMPlexComputeResidual_Internal()
Plex: Added DMPlexInsertBoundaryValues() - Unified FE and FV boundary values
Plex: DMPlexProjectFunctionLableLocal() gets discretizations from the DM now
Plex: Added DMPlexComputeGradientFVM()
PetscDS: Fix up some functions to work for both FV and FE
PetscFV: Change PetscFVIntegrateRHSFunction() to get info from PetscDS
TS ex11: There is only one field in our current paradigm - We would need to split Riemann solvers for multiple fields right now
Plex+TS: Remove use of computeGradients in favor of check for dmGrad
TS ex11: Updated interface calls
Plex+TS: Change DMPlexTSGetGradientDM() to automatically construct the gradient info, DMPlexTSSetRHSFunctionLocal() can now be replaced by the DMTS version - Remove unnecessary declarations
Plex+SNES: Add missing declaration
Plex+FE: Removed all use of PetscCellGeometry, Changed FE integration to use PetscFECellGeom
DMSNES+Plex: Added DMPlexSNESGetGeometryFEM() to cache geometry
PetscDualSpace: Remove use of PetscCellGeometry in PetscDualSpaceApply() - Fixed up calls to it for projection into spaces
DMDA: Remove use of PetscCellGeometry in DMDAProjectFunctionLocal()
Plex: Added DMPlexComputeGeometryFEM() and PetscFECellGeom structure
...

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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 DMPlexInsertBoundaryValues()
- Unified FE and FV boundary values

Plex: Added DMPlexComputeGradientFVM()

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: 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: 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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Move DMPlexProject*() functions to src/ksp to remove ksp dependency in dm

DMPlex: added DMPlexTreeRefineCell()

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 DMPlexGetTree()

DMPlex: added DMPlexSetTree()

DMPlex: added basic tree routines

DMPlex: change DMPlexGetTreeParent() to remove magic constant

DMPlex: added DMPlexTreeGetChildren()

DMPlex: added DMPlexCreateDefaultReferenceTree()

DMPlex: added DMPlexGet/SetReferenceTree()

DMPlex: Take (right) constraints into account in preallocation

DMPlex: fix recent constraint additions