Plex: Fix compiler warning

DMPlex: added DMPlexComputeAnchorAdjacencies()

DMPlex: fixes to DMPlexComputeAnchorAdjacencies()

DMPlex: fix DMPlexComputeAnchorAdjacencies()

DMPlex: replace ISGetSize with ISGetLocalSize where ap

DMPlex: added DMPlexComputeAnchorAdjacencies()

DMPlex: fixes to DMPlexComputeAnchorAdjacencies()

DMPlex: fix DMPlexComputeAnchorAdjacencies()

DMPlex: replace ISGetSize with ISGetLocalSize where appropriate for anchors

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DMPlex: Take (right) constraints into account in preallocation

DMPlex: fix recent constraint additions

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

Merged upstream/master to feature-dmmoab

Merge remote-tracking branch 'upstream/master'

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]
gfortran: remove 132 char limit from f90 free-form
SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc
DMPlex-Gmsh: Use trueNumCells when building the coordinate section
Sys: Got guard logic reversed
Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*()
PetscFV: I hate fucking complex
removed ltog scatter from DMDA since functionality can be obtained with gtol scatter and less memory
fix test of DMLocalToGlobalBegin/End and add actual test cases
improve object memory logging for DA, ISLocalToGlobal and ISBLOCK
lower high water mark of constructing parallel scatter by allocating only as much room in svalues as needed
owner in VecScatter construction is the rank, therefor can use PetscMPIInt to hold it do not PetscInt
another reuse of allocated array in 2d/3d DMDA create
improved high water mark of DMDASetups by implementing and using PETSC_USE_POINTER for ISCreateBlock()
PetscFV: Another complex fix
DMPlex+TS: Fixing types
ISIdentity() was wrong for block IS! Indices are NOT scaled by bs
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
...

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Merge branch 'master' into barry/saws-options

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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Merge branch 'knepley/feature-fe-dg-space'

* knepley/feature-fe-dg-space: (38 commits)
DMPlex: Added coordinate field info for generated mesh
DMPlex: Update to new DMPlexGetBoundary() interface

Merge branch 'knepley/feature-fe-dg-space'

* knepley/feature-fe-dg-space: (38 commits)
DMPlex: Added coordinate field info for generated mesh
DMPlex: Update to new DMPlexGetBoundary() interface
PetscFE: Fix complex casting
DMPlex: Fixup type mismatch in PetscFEIntegrate()
DMPlex ex62: Fixed test output
SNES ex62: Added test output
SNES ex62: Added tests for Q2-Q1 and Q2-P1disc - Added -show_error - Removed spurious refinement of quads - Fixed cast - CreatePressureNullspace() now uses DMPlexProjectFunction() - Replace SetupElement() with PetscFECreateDefault()
DMPlex ex3: Added tests for P1disc
SNES ex12: Updated to new PetscFECreateDefault()
PetscFE: Fixes for discontinuous elements
PetscSpace: Fixed polynomial space view
PetscFE: Changed PetscFECreateDefault() - Now continuity and reference cell shape are set from the command line
PetscFE: Added domain integration - Added PetscFEIntegrate(), only implemented for Basic - Added DMPlexComputeIntegralFEM() and DMPlexComputeL2FieldDiff() - This should replace the L2Diff functions
Mat+Doc: Fixed MatNullSpaceRemove()
SNES ex62: Updated to new PetscFECreateDefault()
SNES ex12: Updated to new PetscFECreateDefault() - 3D simplex moves the P_0 point from the centroid
DMPlex ex3: Updated for corrected cell dof
PetscFE: I think I finally fixed the cell dof
DMPlex ex3: Added test case for P1disc on a quad
DMPlex ex3: Added P1 discontinuous test - Something looks wrong with interpolation
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Merge branch 'knepley/feature-optcontrol-mg' into knepley/feature-fe-dg-space

* knepley/feature-optcontrol-mg:
TAO ex1: documentation
TAO ex1: Now we have a full optimal control problem - The da

Merge branch 'knepley/feature-optcontrol-mg' into knepley/feature-fe-dg-space

* knepley/feature-optcontrol-mg:
TAO ex1: documentation
TAO ex1: Now we have a full optimal control problem - The data for the state is perfect (Q is I) - The regularization is perfect (L is I and a_ref is the exact control)
TAO ex1: Constructed saddle point problem, but control is given exactly
PetscFE: Fix array initialization bug
TAO ex1: Starting an IPM example
DMPlex: When creating a section, we should only complete a label once
DMPlex: Now DMPlexProjectFieldLocal() correctly masks out fields with no function
DMPlex: Added DMPlexVecSetFieldClosure_Internal() - Allows fields to be masked
SNES ex62: Updates for printing changes
DMPlex: Fixes preallocation checks
SNES ex12: Updates for printing changes

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DMPlex: Fixes preallocation checks

Fixing merge conflicts in dmregall.

Merged petsc/petsc into master

Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'master' into prbrune/matcoloring-greedy

DMPlex: Reorganized the handling of point adjacency
- Replaced centerDim with useCone, useClosure, Added DMPlexGet/SetAdjacencyUseCone/Closure()
- Now partitioning and preallocation use the same adja

DMPlex: Reorganized the handling of point adjacency
- Replaced centerDim with useCone, useClosure, Added DMPlexGet/SetAdjacencyUseCone/Closure()
- Now partitioning and preallocation use the same adjacency routines
- Added DMPlexGetAdjacency() and the internal version which does not allocate
- Moved distribution and partitioning code into separate files
-

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DMPlex: Fix preallocation with cell variables
- I had an incorrect loop optimization

Merge branch 'knepley/fix-plex-submesh-edge'

* knepley/fix-plex-submesh-edge:
DMPlex: Removed unused variable in refinement
DMPlex: Also mark hybrid cells with unsplit vertices
DMPlex: Docs fo

Merge branch 'knepley/fix-plex-submesh-edge'

* knepley/fix-plex-submesh-edge:
DMPlex: Removed unused variable in refinement
DMPlex: Also mark hybrid cells with unsplit vertices
DMPlex: Docs for preallocation
DMPlex: Fix for parallel refinement - PetscSF needs the leaves in sorted local order for it to get SFGather correct
DMPlex: Label hybrid cells with unsplit edges during submesh creation - I don't like this completely since we have to use -(cell number) to avoid aliasing vertices in the original mesh
DMPlex: Fixed submesh boundary in 3D - Correct support for unsplit edges - Correct support for hybrid faces from unsplit edges - Added checks
DMPlex: Now DMPlexCheclSymmetry() also checks multiple cone/support entries
DMPlex: Fix unsplit vertex support in submeshes - Assumed only a single split edge, which is true in 2D
DMPlex: Fixing marking of unsplit vertices - Check for presence in label was wrong (has to be exactly -1) - Check for incidence was wrong (was also getting unsplit marker)

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DMPlex: Docs for preallocation

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
include/makefile

Merge branch 'master' into knepley/feature-mat-zerorowscols-baij