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

DMPlex: Set block size correctly on coordinate vectors

DMPlex: Now DMPlexInterpolate() allows the new mesh to be inserted into an existing DM
- If the input is non-NULL, no new DM is created
- This allows it to functions within the DMLoad() paradigm

Fixing merge conflicts in dmregall.

Merged petsc/petsc into master

Merge branch 'mlange05/feature-plex-multi-faced-cube'

* mlange05/feature-plex-multi-faced-cube:
DMPlex: Fixing c89 incompatibility.
DMPlex: Adding multi-face support in DMPlexCreateCubeBoundary

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

DMPlex: Fixing c89 incompatibility.

DMPlex: Adding multi-face support in DMPlexCreateCubeBoundary

Cone orientation and the local cone numbering follow the previous
(1x1x1 unit cube) implementation.

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 '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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DMPlex: Fix setting Plex options on automatically refined meshed

Merging master with feature-dmmoab. Only conflict was with SOURCECXX specification under impls/moab/makefile.

Merged petsc/petsc into master

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

DM: If the local section is not present, it will be created automatically from PetscFE structures and boundary conditions
- Added createdefaultsection() to DM

DMPlex: Added DMBoundary struct
- This will replace the stuff in TS ex11

DMPlex: Adding support for interpolation between regularly refined meshes
- Added DMPlexComputeInterpolatorFEM()
- Added PetscFERefine()
- Added PetscFEIntegrateInterpolator_Basic()
- Not working now

DMPlex: Adding support for interpolation between regularly refined meshes
- Added DMPlexComputeInterpolatorFEM()
- Added PetscFERefine()
- Added PetscFEIntegrateInterpolator_Basic()
- Not working now since coarse meshes do not have Sections attached

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Merge branch 'master' into barry/ts-rhsjacobian-only

Merge branch 'shri/update-SuiteSparse' into shri/external-package-KLU

Conflicts:
conf/test
config/examples/arch-linux-pkgs-dbg-ftn-interfaces.py
config/examples/arch-linux-pkgs-opt.py

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

Conflicts:
src/dm/examples/tests/ex42.c
src/dm/examples/tutorials/ex65dm.c
src/ksp/ksp/examples/tutorials/ex42.c
src/snes/examples/tutorials/cahn-hi

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

Conflicts:
src/dm/examples/tests/ex42.c
src/dm/examples/tutorials/ex65dm.c
src/ksp/ksp/examples/tutorials/ex42.c
src/snes/examples/tutorials/cahn-hilliard-schemes/ex1.c
src/snes/examples/tutorials/ex54.c
src/snes/examples/tutorials/ex55.c
src/snes/examples/tutorials/ex60.c
src/snes/examples/tutorials/ex61.c
src/snes/examples/tutorials/ex63.c
src/snes/examples/tutorials/ex633d_db.c
src/snes/examples/tutorials/ex64.c
src/snes/examples/tutorials/ex65.c
src/snes/examples/tutorials/ex653d.c
src/ts/examples/tutorials/ex23.c

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DMPlex: Added DMRefineHierarchy() and DMCoarsen() support
- DMRefineHierarchy() sets coarseMesh, so DMRefine() does not cause the initial mesh to keep on living
- DMCoarsen() returns coarseMesh
- The

DMPlex: Added DMRefineHierarchy() and DMCoarsen() support
- DMRefineHierarchy() sets coarseMesh, so DMRefine() does not cause the initial mesh to keep on living
- DMCoarsen() returns coarseMesh
- These are handled by DMSetFromOptions(), which I had to move

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Merge branch 'knepley/feature-periodic-mesh'

* knepley/feature-periodic-mesh:
Matt moved DMDA_BOUNDARY.. to DM_BOUNDARY... but did not fix ex2f.F includes
DM Fortran examples: fix petscdm.h -> f

Merge branch 'knepley/feature-periodic-mesh'

* knepley/feature-periodic-mesh:
Matt moved DMDA_BOUNDARY.. to DM_BOUNDARY... but did not fix ex2f.F includes
DM Fortran examples: fix petscdm.h -> finclude/petscdm.h
DMPlex: Fixed markers on periodic boundary
DM examples: include petscdm.h in examples that use DM_BOUNDARY_*
DMBoundary: fix line length for Fortran
DMPlex: Now DMPlexCreateHexBox() can have a Mobius topology using DM_BOUNDARY_TWIST
DM: Moved DMDABoundaryTypes to DMBoundaryTypes - Changed the enum values as well - Changed docs and updated Changes - Updated examples
DMPlex: DMPlexCreateHexBoxMesh() now allows periodicity - Changed declaration and uses - DMPlexCreateSquareMesh() now allows periodicity - Works with refinement

Conflicts:
src/dm/impls/plex/plexcreate.c
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

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