DMAdaptLabel: change second argument to actual label

Also move DM_FOREST_REFINE/COARSEN to DM_ADAPT_REFINE/COARSEN

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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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.

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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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 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 '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

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

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
...

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

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Merge branch 'tisaac/dmforest'

* tisaac/dmforest: (36 commits)
DMP4est: fix transfer of labels to parents
DMPlexCreateInterpolatorTree: fix handling of global dofs (can be < 0)
DMPlexComputeIn

Merge branch 'tisaac/dmforest'

* tisaac/dmforest: (36 commits)
DMP4est: fix transfer of labels to parents
DMPlexCreateInterpolatorTree: fix handling of global dofs (can be < 0)
DMPlexComputeInterpolatorTree(): fix workspace size
DM: warn when no injection implemented
DMPlexComputeInterpolatorTree(): use row layout to preallocate
DMP4est: all processes agree on root type
DMPlexComputeInterpolatorTree(): valgrind fixes
DMP4est: reset childID if anctecedent is not parent
DMP4est: send labels from children to parents and bcast
DMForest: added DMForestGetAdaptivityPurpose()
DMP4est: enable caching of results of DMPforestGetTransferSF()
Plex: fix empty partition errors
DMPforestGetTransferSF_Internal(): handle different type roots on different processes
DMP4est: broadcast labels when transfering for agreement
PetscSFBasic: fix usage of MPI_Reduce_local
DMPforestLabelsInitialize(): search through parents when finding a point in the closure
DMP4est: try to connect high strata points when transfering
DMP4est: can't use PetscSFCreateSectionSF. It compresses when we don't want to
DMP4est: expand transfer sfs by the CellSF
DMP4est: add DMForestCreateCellSF_p4est
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DMForest: added interface for mapping base coordinates to refined coordinates

Merged petsc/petsc into master

DMForest: added DMForestGetAdaptivityPurpose()

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelG

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
Plex ex12: Fixed variable initialization and some output
Plex ex11: Added error checking
Plex ex14: Now boundary label does not have cells
Plex ex1: Now boundary label does not have cells
Plex ex1: Fix for VTK format
added some debugging code, getting ready to branch
added some print statements, should be an -info...
smome cleaning up
restructured ex11 to allow for problem specific BCs
DMPlex: Update test ex12_5 with correct level-2 overlap
DMPlex: Use global processSF in DMPlexPartitionInvert
DMPlex: Add remote leaf contributions to roots in DMLabelPropagate
DMPlex: Add DMLabelGather to migrate label values from leafs to roots
DMPlex: Refactor DMLabelDistribute to separate point stratum distribution
DMPlex: Add propagation of remote point donations for multi-level overlap
DMPlex: Fix DMLabelDistribute for all-to-all migrations
Plex: make extern exactly match prototype: semantic match is not enough.
DMP4est: typo fix
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DMFOrest: added DMForestGetAdaptivitySF()

It makes most sense to compute transfer SFs when the new forest is being
setup, but we may not need them if we're doing some initiali a prior
refinement wit

DMFOrest: added DMForestGetAdaptivitySF()

It makes most sense to compute transfer SFs when the new forest is being
setup, but we may not need them if we're doing some initiali a prior
refinement with nothing to transfer.

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DMForest: added DMForestSetAdaptivityPurpose()

DMDestroy() can't do cycle checks with forest->adapt. I could try to
introduce a robust, extensible cycle check into DM, but that's a bigger
project.

DMForest: added DMForestSetAdaptivityPurpose()

DMDestroy() can't do cycle checks with forest->adapt. I could try to
introduce a robust, extensible cycle check into DM, but that's a bigger
project. This lets the user move forest->adapt to dm->coarseDM or
dm->fineDM, where it can be picked up in cycle detection.

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Merge branch 'tisaac/dmforest' into mlange/fix-plex-multi-level-overlap

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_5.out
src/dm/label/dmlabel.c