DMPlexTree: do proper vector assembly

This is necessary once we assemble in parallel

DMPlexComputeInterpolatorTree: fix loop variables from recent change

DMP4est: fix some ghost cell bounds

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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DMPlex: fix parent/child interpolation with numFields > 0

There were several instances of off-by-one errors that had not been tested before but are tested now

DMPlexTree: some compilers want this var initialized

DMPlex/DMP4est: small fixes for next warnings and errors

DMPlexTree: do not skip out of child matrix loops early

Even in the matrix will have size zero rows, we still want to calculate the number of columns,
which is useful for keeping track of offsets of

DMPlexTree: do not skip out of child matrix loops early

Even in the matrix will have size zero rows, we still want to calculate the number of columns,
which is useful for keeping track of offsets of fields

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DMP4estTree: ignore negative values when getting/setting vector values for transfer

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

DMPlexTree: use local vector to interpolate in transfer

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

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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PlexTree: Fixed declaration for function which produce indices for assembly

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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Plex: Fixed declaration for function which produce indices for assembly

Plex: clarify precedence

DMP4est: cleanup for DMForestTransferVec()

DMP4est: fixes to DMPlexTranserVecTree_Inject()

DMP4est: fixes to DMPlexTranserVecTree_Interpolate()

DMPlex: correct usage of PetscSFCreateEmbeddedLeafSF()

Plex: first pass at tree transfer interpolator. FVM missing

Plex: finish first pass at injection component of transer

DMPlex: further refactoring in injection code