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 'knepley/feature-plex-projections'

* knepley/feature-plex-projections:
Plex: Expose projection routines

Plex: Since we are using an SF, ranks that are not found default to 0, not -1
- You need to check the index for the negative value

Plex: Added a new point location type to remove entries which are not found
- This was the default, but its not what DMSwarm wanted and its non-intuitive I agree

Plex: If point not found, return DMLOCATEPOINT_POINT_NOT_FOUND

Plex: Doc fix

Plex: Expose projection routines

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

DM: Added mode to DMLocatePoints() to change failure behavior
- Implement to NEAREST mode in Plex for 2D simplices
- Added DMPlexCLosestPoint_Internal()

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 'knepley/fix-plex-mf-prec'

* knepley/fix-plex-mf-prec: (26 commits)
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Plex: Updated examp

Merge branch 'knepley/fix-plex-mf-prec'

* knepley/fix-plex-mf-prec: (26 commits)
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Plex: Updated examples to new DMPlexCreateBoxMesh()
TS ex11: Fixed output for new ROSW
Plex: Forgot internal declaration
Plex: Fixed ComputeIntegral() to work with FVM - May still have a bug, not sure
Plex: Fixed ResconstructGradients_Internal() to take an FVM and to work in multifield problems - ApplyLimiter_Internal() now can limit an FV field within a multifield problem
PetscFV: Added -petscfv_compute_gradients
SNES ex12: Fixed output for NGS
PetscDS: Added GetFieldIndex() and GetFieldSize() - Fix to accept FV as well
Plex: Forgot to eliminate PetscRealPart() after type change
Plex: fix line geometry for localized
Plex: fix section access to last commit
DMPlex: fix rectanlge geometry for localized
DMConvert_p4est_plex: set projection height early, so it passes to coordinate dm
DMLocalizeCoordinates(): make more flexible and targeted
Plex: When forming Jacobian, just use identity for FV fields
Plex+FE: Added missing FV dual space
PetscFE: If all Jac pointwise functions are NULL, do not evaluate
DMP4est: change order of setting projection height and localizing coordinates
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DMPlex: cache FVM data

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

Plex: Fixed ComputeIntegral() to work with FVM
- May still have a bug, not sure

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

Merge branch 'tisaac/dmp4est-set-periodic-domain' into knepley/fix-plex-mf-prec

* tisaac/dmp4est-set-periodic-domain:
Plex: fix line geometry for localized
Plex: fix section access to last commi

Merge branch 'tisaac/dmp4est-set-periodic-domain' into knepley/fix-plex-mf-prec

* tisaac/dmp4est-set-periodic-domain:
Plex: fix line geometry for localized
Plex: fix section access to last commit
DMPlex: fix rectanlge geometry for localized
DMConvert_p4est_plex: set projection height early, so it passes to coordinate dm
DMLocalizeCoordinates(): make more flexible and targeted
DMP4est: change order of setting projection height and localizing coordinates
DMP4est: prefer [0,L) for periodic coordinates
Plex: more descriptive debugging

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Merge branch 'tisaac/dmplex-localize-targeted' into tisaac/dmp4est-set-periodic-domain

* tisaac/dmplex-localize-targeted:
Plex: fix line geometry for localized

Plex: fix line geometry for localized

Merge branch 'tisaac/dmplex-localize-targeted' into tisaac/dmp4est-set-periodic-domain

* tisaac/dmplex-localize-targeted:
Plex: fix section access to last commit

Plex: fix section access to last commit

Merge branch 'tisaac/dmplex-localize-targeted' into tisaac/dmp4est-set-periodic-domain

* tisaac/dmplex-localize-targeted:
DMPlex: fix rectanlge geometry for localized

DMPlex: fix rectanlge geometry for localized

Plex: Grid hashing only works in 2D

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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