DMPlex/DMP4est: small fixes for next warnings and errors

DMForest: fix recently added DMForestAdaptLabel()

Was not using the given string

DMForest: add DMForestAdaptLabel() wrapper

This implements a common refinement pattern

DMForest: added DMForestGetAdapaptivitySuccess()

A refinement loop might want to exit when there has been no change made. This is how that information is provided.

DMBoundary: avoid caching the associated label

I would like to be able to add a boundary before the topology is
fixed/determined in DMForest. This means, however, that if a boundary
is declared wit

DMBoundary: avoid caching the associated label

I would like to be able to add a boundary before the topology is
fixed/determined in DMForest. This means, however, that if a boundary
is declared with a name that isn't in the existing labels, that
DMIsBoundaryPoint() can be really bad: searching for a label for every
point. A better solution needs to be implemented.

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DMPlex: uses BCs, FV gradient reconstruction in DMPlexTransferVecTree()

The reason these can be in the tranfer function but not in the tranfer
matrix constructors (interpolate or inject) is that the

DMPlex: uses BCs, FV gradient reconstruction in DMPlexTransferVecTree()

The reason these can be in the tranfer function but not in the tranfer
matrix constructors (interpolate or inject) is that these are nonlinear
(either affine from boundary conditions or whatever from gradient
limiting)

WIP: reconstruct gradients when interpolating

Plex: introduce gradient reconstruction into DMPlexTransferVecTree

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DMForest: make it possible to clear stale dms when adapting

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

Merge branch 'master' into barral/feature-dmplex-adapt

Merge branch 'jose/maint/tabs-print-class' into maint

Merge branch 'knepley/fix-plex-namespace'

* knepley/fix-plex-namespace: (24 commits)
PlexTree: Fixed declaration for function which produce indices for assembly
Plex: Forgot to zero out Jacobian

Merge branch 'knepley/fix-plex-namespace'

* knepley/fix-plex-namespace: (24 commits)
PlexTree: Fixed declaration for function which produce indices for assembly
Plex: Forgot to zero out Jacobian
Plex: Changed every *_Internal() function to PETSC_INTERN - Except the residual and Jacobian computation which should not be internal
Plex: Fixed declaration for function which produce indices for assembly
Plex: clarify precedence
DMForest tests ex2: typo fixes
DMP4est: cleanup for DMForestTransferVec()
DMP4est: fixes to DMPlexTranserVecTree_Inject()
DMP4est: fixes to DMPlexTranserVecTree_Interpolate()
DMPlex: correct usage of PetscSFCreateEmbeddedLeafSF()
DMP4est: address extra vertices in transfers
DMP4est: address missing vertices in transfers
DMP4est: fix array initialization
DMP4est: fix interface to nonuniform refinement
DMP4est: interface to nonuniform refinement
DMForest test ex2: leave data until end for debugging
DMForest: added test for DMForestTransferVec()
Plex: first pass at tree transfer interpolator. FVM missing
Plex: finish first pass at injection component of transer
DMPlex: further refactoring in injection code
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Merge branch 'master' into barral/feature-dmplex-adapt

Merge remote-tracking branch 'origin/tisaac/ts-ex11-amr' into knepley/fix-plex-namespace

* origin/tisaac/ts-ex11-amr:
Plex: clarify precedence
DMForest tests ex2: typo fixes
DMP4est: cleanup f

Merge remote-tracking branch 'origin/tisaac/ts-ex11-amr' into knepley/fix-plex-namespace

* origin/tisaac/ts-ex11-amr:
Plex: clarify precedence
DMForest tests ex2: typo fixes
DMP4est: cleanup for DMForestTransferVec()
DMP4est: fixes to DMPlexTranserVecTree_Inject()
DMP4est: fixes to DMPlexTranserVecTree_Interpolate()
DMPlex: correct usage of PetscSFCreateEmbeddedLeafSF()
DMP4est: address extra vertices in transfers
DMP4est: address missing vertices in transfers
DMP4est: fix array initialization
DMP4est: fix interface to nonuniform refinement
DMP4est: interface to nonuniform refinement
DMForest test ex2: leave data until end for debugging
DMForest: added test for DMForestTransferVec()
Plex: first pass at tree transfer interpolator. FVM missing
Plex: finish first pass at injection component of transer
DMPlex: further refactoring in injection code
DMPlex: refactor injector code for reuse
DMForestTransferVec_p4est(): shift work to plex
DMForest: start stub of DMForestTransferVec()
TS ex11: proposed control flow for initial refinement

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

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()

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

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()
Update the xSDKTrilinos test message to use interactive session and ctest
gcc6: fix comple warnings with -Wmisleading-indentation
fix compile warning
bugfix for MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable()
minor formatting cleanup of gamg.c
add ml example to tutorials page for xsdk
bugfix of MatDuplicate for mpiaij matrix product Reported-by: Miorelli, Federico <Federico.Miorelli@cgg.com>
The deprecated -log_summary_exclude was still being used when it should have been -log_exclude
cpardiso: requires mkl_blacs so check for that. Also common code to detect MKL for both pardiso and cpardiso
cpardiso: fix segv and memory leaks
resume MatGetSubMatrix_SeqSBAIJ() because it cannot share routine with BAIJ due to cast
fix bad relative links
replace MatSeqBAIJSetPreallocation_SeqBAIJ with MatSeqBAIJSetPreallocation to skip this call when input mat is sbaij type
fix a variety of set but not used variables in examples detected by clang static analyzer
removed declared but not used variable
ANL Report formatting requires listing authors by affiliation
DMP4est: uncrustify
DMP4est: remove memset()
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DMForest: start stub of DMForestTransferVec()

Merge branch 'tisaac/dmforest-uncrustify'

* tisaac/dmforest-uncrustify:
DMP4est: uncrustify
DMP4est: remove memset()
DMForest: uncrustify

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

DMForest: uncrustify

Merge branch 'tisaac/dmp4est-feature-mapped-coordinates'

* tisaac/dmp4est-feature-mapped-coordinates:
DMForest: fix mapped coordinates prototype
DMP4est: fix bounds in DMPforestMapCoordinates()

Merge branch 'tisaac/dmp4est-feature-mapped-coordinates'

* tisaac/dmp4est-feature-mapped-coordinates:
DMForest: fix mapped coordinates prototype
DMP4est: fix bounds in DMPforestMapCoordinates()
DMForest: added base DM and a point in base DM to the coordinate map callback
DMP4est: fix DMPforestMapCoordinates()
DMForest: accidentally set wrong map
DMP4est: use NULL geometry unless specified
DMP4est: use correct coordinate frame in mapping
"DMP4est: fix use of p4est_geometry
DMP4est: pass along geometry function to p4est if supplied
DMForest: added interface for mapping base coordinates to refined coordinates
DMP4est: added DMPforestMapCoordinates()
WIP: DMPforestMapCoordinates()

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doc fixes

DMForest: fix mapped coordinates prototype

DMForest: added base DM and a point in base DM to the coordinate map callback

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

DMForest: accidentally set wrong map

Merge branch 'tisaac/dmp4est-feature-injection'

* tisaac/dmp4est-feature-injection: (27 commits)
DMP4est: linear solve regression tests
DMP4est: regression tests for exact interpolation/injectio

Merge branch 'tisaac/dmp4est-feature-injection'

* tisaac/dmp4est-feature-injection: (27 commits)
DMP4est: linear solve regression tests
DMP4est: regression tests for exact interpolation/injection
PetscDualSpace: create height subspaces at setup.
DMClone(): get agreement on cloning coordinates
DMP4est: bump number of procs in regression test
DMP4est: fix memory leaks
DMP4est: added diagnostic views
DMP4est: adding regression tests
SNES tutorials ex12: added RUN_EXACT, solve from exact solution
DMPlex: memory clean up in Injector/InterpolatorTree routines
DMP4est: use DMCoarsen_Forest
DMPlexComputerInterpolatorTree(): restore another work array
DMPlexAnchorsModifyMat(): restore work arrays
DMPlexComputeInjectorTree(): fix local / off-process bounds
DMPlexComputeInjectorTree(): more fixes
DMPlexComputeInjectorTree(): fix coarse/fine char mixup
DMPlexComputeInjectorTree() compiles
WIP: DMPlexComputeInjectorTree()
Plex tests ex3: added regression tests for injectors
DMPlex tests ex3: fix viewing, creating injectors
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