DM, PetscDS: remove redundant boundary representations

The DMBoundary is now just a container for the DSBoundary

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize t

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize the amount of code that is specialized to the
different DMs, and in the future more work can be done to improve this
interface.

* tisaac/ts-ex11-amr: (62 commits)
DMP4est: type fix
Plex: Fixes for analyzer
DMP4est: update snes ex12 regressions
DMPlex: fix parent/child interpolation with numFields > 0
DMP4est: also compute anyChange for uniformly refined/coarsened meshes
TS ex11: fix command line for AMR without computed gradients
TS ex11: remove gradient reconstruction from adaptivity requirements
DMPlexTree: some compilers want this var initialized
Plex: Changed Get/RestoreFaceFields() and Get/RestoreFaceGeometry() to return the number of active faces - This fixes a long-standing bad access in FV, although the values were never actually used.
DMPlexTS: removed unused variables
DMPlex/DMP4est: small fixes for next warnings and errors
SNES ex36 and ex52: These do not work anymore
DMPforestGetTransferSF_Point(): try to match parents
PetscViewerHDF5: destroy old file data if setting new filename
DMPlex + FV: remove leaky references in projection functions
Plex: Fixed incredibly stupid bug in Jacobian computation
PetscViewer HDF5: added get name method
DMPlexTree: do not skip out of child matrix loops early
PetscFV: correct field offsets when limiting gradients
DMP4estTree: ignore negative values when getting/setting vector values for transfer
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Merge branch 'dmay/feature-dm-swarm' into knepley/feature-plex-particle-example

* dmay/feature-dm-swarm: (69 commits)
DMSwarm: * Check for size compatabaility between vectors created for DMSwarm f

Merge branch 'dmay/feature-dm-swarm' into knepley/feature-plex-particle-example

* dmay/feature-dm-swarm: (69 commits)
DMSwarm: * Check for size compatabaility between vectors created for DMSwarm fields * Bug fix for the field register function
DMSwarm DataBucket: * Added guards to ensure that internal arrays are never re-sized if any raw pointers are being currently being accessed
DMSwarm: * Added missing part of macro
DMSwarm: * Added documentation
DMSwarm example: * Added example with DMShell and user point location
DMSwarm Migrate: * Updated to use DMLOCATEPOINT_POINT_NOT_FOUND flag
DM definition: * Added special flag for marking points as being not found within an element during a call to DMLocatePoints
DMSwarm migrate: * Fixed bug with point removal
DMSwarm: * Removed print from data exchanger
DMSwarm: * Use common field names * Re-organized init/finalize fields with DMCreate/DMSetUp * Added methods, flags, checks when using DMSwarmType PIC
SwarmMigrate: * Use common field names
PetscDMSwarm: * Added common names * Corrected extern to PETSC_EXTERN * Added names for migrate
DMSwarm implementation: * Remove unused member
DM implementation: * Added new method locatepointssubdomin
DataBucket: * Print block size
DMSwarm example: * Removed comment
DMSwarm example: * Updated function names
DMSwarm test: * Added new test for variable block sizes
DMSwarm: * Fixed typo in vector name
DMSwarm: * Finishing support for block size != 1
...

Conflicts:
include/petsc/private/dmimpl.h

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Merge branch 'knepley/feature-dm-point-location-failure'

* knepley/feature-dm-point-location-failure:
Plex: Fixed declaration and complex conversion
DM: Added mode to DMLocatePoints() to change

Merge branch 'knepley/feature-dm-point-location-failure'

* knepley/feature-dm-point-location-failure:
Plex: Fixed declaration and complex conversion
DM: Added mode to DMLocatePoints() to change failure behavior - Implement to NEAREST mode in Plex for 2D simplices - Added DMPlexCLosestPoint_Internal()

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Plex: Fixed declaration and complex conversion

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary c

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary commitid] - and dirname in tarball
Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES
CUDA: Added external declaration for cuBLAS handle.
docs: fix reference to KSP_Create in parent commit
Add information on PETSC_EXTERN and PETSC_INTERN to developers manual
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Configure: Fix check for spaces in PETSC_DIR
Plex: Updated examples to new DMPlexCreateBoxMesh()
sick of failure due to incorrect master branch
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Examples that require Fortran to compile but were listed in tests that did not require Fortran
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
...

Conflicts:
src/dm/impls/plex/makefile
src/snes/utils/dmplexsnes.c

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Merge branch 'pr478/knepley/feature-dmplex-adapt/master'

* pr478/knepley/feature-dmplex-adapt/master: (34 commits)
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GM

Merge branch 'pr478/knepley/feature-dmplex-adapt/master'

* pr478/knepley/feature-dmplex-adapt/master: (34 commits)
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
Plex: Fixes for c89
Plex: Fixes for complex
SNES ex12: Updated output for coarsening
Plex ex3: Updated output for coarsening
Plex ex19: Now working with refactored Adapt()
Plex: Refactored DMPlexAdapt() - Added DMPlexRemesh_Internal() - Use Remesh inside DMCoarsen_Plex() - Use Join() to set label on faces
Plex ex19: Simplified parallel construction of metric
Plex ex19: General cleanup
Plex: DMPlexCreateBoxMesh() now takes the number of faces
Add output files for tests
Fix previous memory fix
Fix memory problems
...

Conflicts:
config/BuildSystem/config/packages/petsc4py.py
config/builder.py

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Merge branch 'knepley/feature-parallel-mesh-load'

* knepley/feature-parallel-mesh-load:
Plex ex18: Small fixes - Use DMBOUNDARY_NONE correctly, document partition edges
Plex ex18: Added simplex

Merge branch 'knepley/feature-parallel-mesh-load'

* knepley/feature-parallel-mesh-load:
Plex ex18: Small fixes - Use DMBOUNDARY_NONE correctly, document partition edges
Plex ex18: Added simplex 3D tests
fix compile warnings
Plex: Removed unused variable
DMLabel: Fixed DMLabelGather() - The leaves are not compact, but rather follow the local numbering, so we need to allocate nroots space
Plex: Fix for parallel interpolation
Plex-ex18: Enabling 2D simplex tests with interpolation
Plex: Create pointSF for edge/facet points after interpolation
Plex-ex18: Add another test for 2D simplices on 3 ranks
Plex: Fix hash usage in DMPlexBuildFromCellList_Parallel_Private
Plex ex18: Added test for parallel mesh loads - Interpolation test is broken
Plex: Fixed static declaration of some functions
Plex: Added DMPlexCreateFromCellListParallel() - This directly creates a parallel mesh from pieces

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Plex: Store a flag indicating whether the boundary should change during remeshing
- Set using -dm_plex_remesh_bd
- Changed Remesh_Internal() signature

Plex: Fixes for c89

Plex: DMPlexCreateBoxMesh() now takes the number of faces

Plex: added labels on all processes

Plex: Removed unused variable

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c

Plex: Fix hash usage in DMPlexBuildFromCellList_Parallel_Private

Plex: Fixed static declaration of some functions

Plex: Added DMPlexCreateFromCellListParallel()
- This directly creates a parallel mesh from pieces

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'tisaac/dm-locate-points-sf'

* tisaac/dm-locate-points-sf:
Plex: missed in IS
DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

Merged collection routines from dmay/swarm-boundingbox-collect

Merge branch 'dmay/swarm-boundingbox-collect' into dmay/swarm-next

DM:
* Add method for getneighbors
* Added new DM API
* Added getneighbor support for PLEX and DMDA

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping cells, it's clearer which
in which process/cell the point is located.
- A natural next step after DMLocatePoints() is to send each point to
its cell for some local computation. With a PetscSF this is easy with
PetscSFGatherBegin()/PetscSFGatherEnd().

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
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Conflicts:
src/dm/impls/plex/plexfem.c

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Merge branch 'knepley/fix-plex-point-location'

* knepley/fix-plex-point-location:
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logg

Merge branch 'knepley/fix-plex-point-location'

* knepley/fix-plex-point-location:
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static

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