DMPlex: Added code for 3D uniform refinement of hexes with tests
- Tests do not yet pass

DMPlex: Fixed bugs in 2D quad uniform refinement
- Wrong support for edge vertex
- Wrong SF addition for cells
- Added test cases

DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection
- Has not been tested with moment dofs
- Accommodates vector functions

DMPlex: Added support for INSERT_BC_VALUES in VecSetClosure()

Merge branch 'knepley/fix-plex-closure' into knepley/feature-dt-fem

* knepley/fix-plex-closure:
DMPlex: Fixed missing RestoreTransitiveClosure()

DMPlex: Fixed missing RestoreTransitiveClosure()

Merge branch 'knepley/fix-plex-closure' into knepley/feature-dt-fem

* knepley/fix-plex-closure:
DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array

DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array

Merge branch 'knepley/fix-plex-closure' into knepley/feature-dt-fem

* knepley/fix-plex-closure:
DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
DMPlex: Fix VecGetClosure() when the ar

Merge branch 'knepley/fix-plex-closure' into knepley/feature-dt-fem

* knepley/fix-plex-closure:
DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
DMPlex: Fix VecGetClosure() when the array is input

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DMPlex: Allow NULL array as input to DMPlexVecGetClosure()

DMPlex ex4: Added new tetrahedron refinement test

DMPlex: Fix VecGetClosure() when the array is input

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fort

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran interface
PetscSection: Added docs for Fortran binding for VecSetValuesSection()
Vec: Removed old F90 binding for PetscSection
bgq: fix deadlock on bgq due to inconsistant values returned by getpwuid(getuid()) on runs with 256nodes [or 4096 cores]. This fix removes the reliance on PetscGetHomeDirectory() returning 'same' value across nodes. [using the fact that PetscOptionsInsertFile() uses HOMEDIR from node-0 only]
DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1)
DMPlex: Fix 64-bit int problem in VTK
Mat: Fix for PetscSparseDenseMaxDot() for complex
Vec: Correct VecUniqueEntries() for 64-bit indices
MatSeqAIJGetArrayF90: add man pages and fix typo in MatDense version
SF docs: add link to summary page and fix title
Doc: Fixed DM code in manual
metis/parmetis: update to metis-5.1.0/parmetis-4.0.3 Also update the test output as the partitioning appears to have changed.
DMPlex: remove unused variables
blaslapack: update f,f2c tarballs to 3.4.2 version
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
...

Conflicts:
include/petscdmplex.h

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Merge branch 'master' into knepley/feature-dt-fem

* master: (51 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran inte

Merge branch 'master' into knepley/feature-dt-fem

* master: (51 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran interface
PetscSection: Added docs for Fortran binding for VecSetValuesSection()
Vec: Removed old F90 binding for PetscSection
bgq: fix deadlock on bgq due to inconsistant values returned by getpwuid(getuid()) on runs with 256nodes [or 4096 cores]. This fix removes the reliance on PetscGetHomeDirectory() returning 'same' value across nodes. [using the fact that PetscOptionsInsertFile() uses HOMEDIR from node-0 only]
DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1)
metis/parmetis: update to metis-5.1.0/parmetis-4.0.3 Also update the test output as the partitioning appears to have changed.
DMPlex: remove unused variables
blaslapack: update f,f2c tarballs to 3.4.2 version
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
DMPlex: Added flip argument to DMPlexLabelCohesiveComplete() to reverse submesh normal - Fixed ex5 test
DMPlex ex5: Fixed existing tests and added two cohesive cell test - Fixed tests for new cohesive cell orientation
DMPlex: Propagate orientation information to the submesh properly
DMPlex: Orientation of cohesive cell should come from face to which it is attached
DMPlex: Added subdm argument to DMPlexLabelCohesiveComplete() - Use the subdm for orientation information so we replace vertices all on the same side
DMPlex: Fix DMPlexOrient() for submeshes - Need to also reverse cone orientation of cells attached to fault faces when we flip them
...

Conflicts:
config/builder.py
include/petsc-private/dmpleximpl.h
include/petscdm.h
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexfem.c
src/dm/interface/dlregisdmdm.c
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/output/ex12_10.out
src/snes/examples/tutorials/output/ex12_11.out
src/snes/examples/tutorials/output/ex12_5.out
src/snes/examples/tutorials/output/ex12_6.out
src/snes/examples/tutorials/output/ex12_7.out
src/snes/examples/tutorials/output/ex12_8.out
src/snes/examples/tutorials/output/ex12_9.out

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Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
DMPlex: Fixed bug with mesh orientation - flipped marker must be a boolean for ^ operation - Final check needs a mismatch as well

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
DMPlex: Fixed bug with mesh orientation - flipped marker must be a boolean for ^ operation - Final check needs a mismatch as well
DMInterpolation: Fixed declarations
DMPlex: Added declaration

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Merge branch 'knepley/fix-plex-matclosure'

* knepley/fix-plex-matclosure:
DMPlex: Update calls to DMPlexMatSetClosure() to eliminate default arguments
DMPlex: Do not allow default sections in DM

Merge branch 'knepley/fix-plex-matclosure'

* knepley/fix-plex-matclosure:
DMPlex: Update calls to DMPlexMatSetClosure() to eliminate default arguments
DMPlex: Do not allow default sections in DMPlexMatSetClosure() - This makes the call collective

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Merge branch 'knepley/fix-plex-matrix-sbaij'

* knepley/fix-plex-matrix-sbaij:
DMPlex: Move Mat option set after preallocation - SEGV on SBAIJ if we do not do this

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

* knepley/fix-plex-submesh-orient:
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put i

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

* knepley/fix-plex-submesh-orient:
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
DMPlex: Added flip argument to DMPlexLabelCohesiveComplete() to reverse submesh normal - Fixed ex5 test
DMPlex ex5: Fixed existing tests and added two cohesive cell test - Fixed tests for new cohesive cell orientation
DMPlex: Propagate orientation information to the submesh properly
DMPlex: Orientation of cohesive cell should come from face to which it is attached
DMPlex: Added subdm argument to DMPlexLabelCohesiveComplete() - Use the subdm for orientation information so we replace vertices all on the same side
DMPlex: Fix DMPlexOrient() for submeshes - Need to also reverse cone orientation of cells attached to fault faces when we flip them
DMPlex: Propagate orientations in cohesive cell creation - Also fix hybrid bounds

Conflicts:
src/dm/impls/plex/plexsubmesh.c

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Merge branch 'knepley/plex-depth-label'

* knepley/plex-depth-label:
DMPlex: remove unused variables
DMPlex: Use BFS to calculate depth rather than crazy recursive scheme
DMPlex: Now use DMPlex

Merge branch 'knepley/plex-depth-label'

* knepley/plex-depth-label:
DMPlex: remove unused variables
DMPlex: Use BFS to calculate depth rather than crazy recursive scheme
DMPlex: Now use DMPlexGetDepthLabel() to interrogate point depths
DMPlex: Optimize depth retrieval by storing a pointer to the label - This is a little unsafe since someone could go in and create a new "depth" label out from under you

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Merge branch 'knepley/plex-profile-distribution'

* knepley/plex-profile-distribution:
DMPlex: Added new events for distribution

Merge branch 'knepley/fix-plex-parallel'

* knepley/fix-plex-parallel:
DMPlex: Fixed creation of global sections - The size of neg[] must be all of nroots instead of pEnd-pStart
DMPlex: Fixed coh

Merge branch 'knepley/fix-plex-parallel'

* knepley/fix-plex-parallel:
DMPlex: Fixed creation of global sections - The size of neg[] must be all of nroots instead of pEnd-pStart
DMPlex: Fixed cohesive submesh SF - I misclassified points which were not owned in the original mesh, but are owned in the submesh
DMPlex: Fixed bug with cohesive submesh SF - Needed to put in owned subpoints since they do not come from leaves OR from the original mesh
DMPlex: Fix out of bounds access for empty mesh
DMPlex: Fixed creation of PetscSF in DMPlexCreateCohesiveSubmesh_Uninterpolated() - Could not assume that original owner of subvertex owned it in submesh because it might have no subcells - Needed to redetermine ownership of subpoints
Plex VTK: Handle missing submesh pieces in parallel
DMPlex: Initializeremote locations when calculating SF for submesh
DMPlex: FIxed hang in DMPlexCreateCohesiveSubmesh()
DMPlex: Added PetscSF creation to DMPlexCreateCohesiveSubmesh_Uninterpolated() - Added DMPlexFilterPoint_Internal() - Still need this for the interpolated variant
DMPlex: Remove dead code
DMPlex: Removed aggressive checks for cohesive cells - How should we handle extraction in parallel?
PetscSection: PetscSectionCreateSubmeshSection() now can take an empty IS
DMPlex: Allow submesh creation with empty mesh and empty label
DMPlex: Allow DMPlexOrient() of empty mesh

Conflicts:
src/dm/impls/plex/plexsubmesh.c

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Merge branch 'knepley/plex-speed-tests'

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if arr

Merge branch 'knepley/plex-speed-tests'

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if array is passed in
DMPlex: Added special case for DMPlexVecSetClosure() - Could add more modes
DMPlex: Optimizations for DMPlexVecGetClosure() - Removed branch (seems to have little effect) - Removed calculation of size when array is provided (profiled for 20% effect)
DMPlex: Forgot one init for DMPlexVecGetClosure()
DMPlex: Must initialize argument to DMPlexVecGetClosure()
DMPlex ex9: Added ability to reuse array in VecGetClosure()
DMPlex: Allow DMPlexVecGetClosure() to take an input array
DMPlex: Fix bug in specialization of DMPlexVecGetClosure()
DMPlex: Bug fix for special case in DMPlexVecGetClosure()
DMPlex: Added optimization for depth 1 DMPlexVecGetClosure()
DMPlex ex9: Does not fail by default - Will turn back on failure once we calculate variance
SNES ex12: Cleaning up in preparation for speed testing
DMPlex: Added ex9 to test performance, put in depth 1 special case for TransitiveClosure

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c
src/snes/examples/tutorials/output/ex12_5.out

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DMPlex: Test output fixes

DMPlex ex4: Now passes all tests, added 2D simplex test
- Only check symmetry for non-hybrid meshes right now (need to fix support of cohesive edges)
- Took out hacky code for hybrid distribution
- A

DMPlex ex4: Now passes all tests, added 2D simplex test
- Only check symmetry for non-hybrid meshes right now (need to fix support of cohesive edges)
- Took out hacky code for hybrid distribution
- Added new test output

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DMPlex: Fix creation of SF in 3D uniform refinement