DMPlex: Added labels to HDF5 viewer/loader
- Only works in serial now

DMPlex+SNES ex12: Protect the HDF5 interface calls

PetscSection: Added an optional permutation for the chart
- Removed the unnecessary atlasLayout
- This permutation will allow people to segregate ghost unknowns at the end of their numbering,
and

PetscSection: Added an optional permutation for the chart
- Removed the unnecessary atlasLayout
- This permutation will allow people to segregate ghost unknowns at the end of their numbering,
and also to get around the stratification of point numbering in Plex

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DMPlex: Fix HDF5 groups for vector output
- Push the group only for global vectors, which allows coordinates to be put in another group

DMPlex: Added DM and Vec loading for Plex
- Added VecLoad_Plex() and VecLoad_Plex_Local()
- Added DMLoad_Plex()
- Only HDF5 works now

DMPlex: Now HDF5 viewer for vecs gets BC right in parallel
- Uses the output DM

DMPlex: Added DMPlexInsertBoundaryValues()
- Uses DMPlexGetBoundary() and DMPlexProjectFunction() to set boundary values
- Used in the viewers
- Some viewer cleanup

Fixing merge conflicts in dmregall.

DMPlex: Fixed local viewer projection

DMPlex: Fix boundary condition function handling for viewing

Merged petsc/petsc into master

DMPlex: Now for VTK and HDF5 we can put in the correct boundary values if they were registered using DMPlexAddBoundary()

DMPlex: Added an HDF5 viewer

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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Merge branch 'master' into knepley/fix-fem-multifield

* master:
tests: move ex151 out of complex tests to avoid compile errors on windows
DM: Fixed pointer comparison
Microsoft C++ compiler ne

Merge branch 'master' into knepley/fix-fem-multifield

* master:
tests: move ex151 out of complex tests to avoid compile errors on windows
DM: Fixed pointer comparison
Microsoft C++ compiler needs extra care with complex numbers and casting
DMPlex: C++ has fucking namespaces, use them assholes
Field has 3 components therefor need to initialize three components, Microsoft C compiler demands it
DMPlex ex3: Added interpolation test - Only works for 2D simplices - Shows the restriction only gets constants right - Other small cleanup
DMPlex ex3: Change to interpolated meshes by default
DMPlex: Fix interpolation of multicomponent fields
DM: Fix reference counting in DMSetField()
DMPlex: Fix interpolation scaling
DMPlex: Fix allocation in DMPlexMatSetClosureRefined()
DMDA: Fixed signature of DMDACreateSection()
When configuring with MPIUni remove any MPI includes in the $PETSC_DIR/PETSC_ARCH/include directory that may have been put there by earlier ./configure runs.

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Merge branch 'knepley/feature-interpolation-testing'

* knepley/feature-interpolation-testing:
DM: Fixed pointer comparison
DMPlex ex3: Added interpolation test - Only works for 2D simplices - Sh

Merge branch 'knepley/feature-interpolation-testing'

* knepley/feature-interpolation-testing:
DM: Fixed pointer comparison
DMPlex ex3: Added interpolation test - Only works for 2D simplices - Shows the restriction only gets constants right - Other small cleanup
DMPlex ex3: Change to interpolated meshes by default
DMPlex: Fix interpolation of multicomponent fields
DM: Fix reference counting in DMSetField()
DMPlex: Fix interpolation scaling
DMPlex: Fix allocation in DMPlexMatSetClosureRefined()
DMDA: Fixed signature of DMDACreateSection()

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DMPlex: Fix interpolation scaling

DMPlex: Fix allocation in DMPlexMatSetClosureRefined()

Merge branch 'knepley/feature-plex-fas'

* knepley/feature-plex-fas: (56 commits)
DMPlex: Removed unused variable
DMPlex: Fix for C++ build, small fix for PetscFE
DMPlex: Removed leak from Tria

Merge branch 'knepley/feature-plex-fas'

* knepley/feature-plex-fas: (56 commits)
DMPlex: Removed unused variable
DMPlex: Fix for C++ build, small fix for PetscFE
DMPlex: Removed leak from Triangle
SNES ex12: Two working unstructured FAS solves for the unregularized p-Laplacian
DMPlex: Cleaned up some memory issues
DMPlex: Implement injection - I don't think this should be required
DMPlex: DM interpolation requires the scaling vector for FAS
DMPlex: Can now create a map from coarse to fine vertices - This is currently necessary for FAS, which I think is wrong
DMPlex: Turn off Fortran stub
DMPlex: Fix DMPlexMatSetClosureRefined() - Reject duplicate fine points - Screen out point with dof = 0 - Fix the allocation for fine points
DMPlex: My brain did not work for several days - I have fixed the interpolation code - I think I can reuse that other code for something else
DMPlex: Fix setting Plex options on automatically refined meshed
SNES ex12/31/52/62/72: Use new SNESComputeJacobian() interface
DMPlex: Remove MatStructure from DMPlexComputeJacobianFEM() - Add missing declarations
Sys Logging: Fixes for log detail - Must preserve reduction count - Output objects and memory - Output stage summary
SNES ex12: Fixing things for multilevel - Need to set PetscFE on all coarse grids - Need application context for interpolator construction
SNES ex12: Use PetscFESetUp(), and fix quadrature ref handling
SNES ex52/62: Use PetscFESetUp(), and fix quadrature ref handling
DMPlex ex3: Uses automatic section creation, PetscFESetUp(), and fix quadrature ref handling
DMPlex: Fixing interpolator construction - Fixed definition of rectangular sizes - Use PetscFERefine() - Use special MatSet
...

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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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Merge branch 'master' into barry/google

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

* knepley/fix-plex-orient-parallel:
DMPlex: Added braindead simple parallel orientation solver - This gathers the graph to proc 0, solves, and scatt

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

* knepley/fix-plex-orient-parallel:
DMPlex: Added braindead simple parallel orientation solver - This gathers the graph to proc 0, solves, and scatters the answer - Need to store neighbor ranks and matches for each neighbor - This should be replaced with a parallel BFS
DMPlex: For 1D orientation, you have to use cone position rather than face orientation
DMPlex: Fixed some small mistakes - Initialize var - Declare at the top of the block - Added cone size call
DMPlex: Added parallel stage to DMPlexOrient() - The coarse solver is not implemented, so only works for p=2
PetscBT: Added PetscBTNegate()

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