SNES+Plex: use all cell values to interpolate to face

Previously the boundary residual/jacobian routines interpolated to face
quadrature points by taking the closure of those faces and using a
separ

SNES+Plex: use all cell values to interpolate to face

Previously the boundary residual/jacobian routines interpolated to face
quadrature points by taking the closure of those faces and using a
separate boundary discretization. This only worked if there were dofs on
faces and the discretization order of the cell and boundary were the
same.
Inverse element jacobians are now calculated from adjacent cells
to also have information on normal derivatives.

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SNES+Plex: allow auxiliary fields in boundary residual/jacobian calculations

SNES+Plex: move boundary jacobian calculation into seperate function

SNES+Plex: remove unnecessary (and wrong) loop in boundary residual/jacobian calculations

SNES+Plex: change DMGetField to PetscDSGetBdDiscretization in residual and jacobian calculation

SNES+Plex: get rid of dm->prob and change DMGetNumBoundary into PetscDSGetNumBoundary

SNES+Plex: remove duplicate lines

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

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Merge branch 'master' into psanan/pc-telescope-nearnullspace

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

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c

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

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

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Merge branch 'knepley/feature-plex-particle-example'

* knepley/feature-plex-particle-example: (103 commits)
PetscTypes: * Added newly types into fortran definition
DMSwarmMigrate: printf fix for

Merge branch 'knepley/feature-plex-particle-example'

* knepley/feature-plex-particle-example: (103 commits)
PetscTypes: * Added newly types into fortran definition
DMSwarmMigrate: printf fix for __float128
fix c++ comments for c89
fix scanf warnings using PetscInt_FMT
Sys+DM: Fixing 64-bit format strings
Swarm: Fixed 64-bit integer problems
Swarm: Fixed PetscFree() usage
Swarm: Correct format in scanf
Plex: Small cleanup
Plex: Fixes to draw for complex
Plex: Fixed type for GetNeighbors
Swarm: Cleanup of Dave's code - Guy has a kid and think he doesn't have to play by the rules anymore
SNES ex63: Stokes example with Particles
Swarm: Fixed prototypes
Swarm: Added missing PetscFunctionBegin
Swarm: Fixed DMGetLocalVecTor_Swarm()
Swarm: Added DMSwarmCreate/DestroyLocalVectorFromField()
Swarm: Added missing prototype
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
...

Conflicts:
src/dm/impls/plex/plexcreate.c
src/dm/interface/dm.c

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Merge branch 'tisaac/dmp4est-fix-overlap'

This branch makes a lot of fixes that fix PetscFV and DMP4est for
parallel. At the root of the issues were discrepencies related to the
overlapping cells t

Merge branch 'tisaac/dmp4est-fix-overlap'

This branch makes a lot of fixes that fix PetscFV and DMP4est for
parallel. At the root of the issues were discrepencies related to the
overlapping cells that are currently required for finite volume
calculations.

* tisaac/dmp4est-fix-overlap: (23 commits)
TS tutorial ex11: make p4est example parallel
TS tutorial ex11: globalize maxspeed before cfl computation
DMPlexTransferVecTree_Inject(): sum child to parent contributions
DMP4est: do not cause error if overlap > 1 in serial run
TS tutorial ex11: fix memory leaks
DMPlexTSComputeRHSFunctionFVM: ADD_VALUES from locF to F instead of INSERT_VALUES
DMPlexComputeResidual_Internal: global/local function mismatch
DMPlexShiftLabels_Internal: not-a-ghost is indicated by -1, not 0
DMPlexComputeResidual_Internal(): do not add contributions of ghost cells
DMPlexTree: do proper vector assembly
DMPlexReconstructGradients_Internal(): clarify ternary operator terms
DMPlexConstructGhostCells_Internal(): correct error message communicator
DMPforestGetTransferSF_Point: only compute covers for owned quads
TS tutorial ex11: only read gradients from local vectors
DMPlex: fix point migration / hybrid point interaction
DMPlex: fix PetscPartitionerPartition() to deal with overlap
DMPlexComputeInterpolatorTree: fix loop variables from recent change
DMP4est: search _both_ directions of tree for match
DMP4est: update regression tests for parallel
DMP4est: remove unused cell sf loop
...

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DMPlexComputeResidual_Internal: global/local function mismatch

DMPlexComputeResidual_Internal(): do not add contributions of ghost cells

Merge branch 'stefano_zampini/dmplex-matis-support-2'

Merge branch 'barry/housekeeping-2'

Merge branch 'tisaac/dm-boundary-in-ds'

Boundary conditions are better conceptually matched to the PetscDS,
which holds the equations, than to the DM. This makes it easier to
share the same problem

Merge branch 'tisaac/dm-boundary-in-ds'

Boundary conditions are better conceptually matched to the PetscDS,
which holds the equations, than to the DM. This makes it easier to
share the same problem between different meshes, such as in a hierarchy.

* tisaac/dm-boundary-in-ds:
PetscDS: fix examples affected by moving boundaries
builder.py: skip empty targets
DMPlex: don't copy coordinates to self
SNES ex69: fix recent PetscDS changes
DMSetDS(): reference, then destroy
PetscDS: fix _Basic creation and destruction
PETSC_DEPRECATED in source files doesn't play well with fortran interfaces
DM: switch to using PetscDS boundary in examples
PetscDS: add missing PetscDSCopyBoundary, fix copy loops
DM: set PetscDS from options in DMSetFromOptions()
DM: protect against changing prob when populating boundary
DM, PetscDS: remove redundant boundary representations
DM: transfer boundary methods to PetscDS
PetscDS: start creating parallel for DMBoundary

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Merge branch 'knepley/fix-dm-interpolation-parallel'

* knepley/fix-dm-interpolation-parallel:
Plex: Fix initialization of search array - New point location may return a subset of points

replace uses of PetscMalloc() with PetscNew() or PetscMalloc1() where appropriate

Plex: Fix initialization of search array
- New point location may return a subset of points

PetscDS: add missing PetscDSCopyBoundary, fix copy loops

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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Plex: Fixes for analyzer

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

DMPlex: construct the correct l2gmap for MatIS using the subdomainSection (for local indexing) and the globalSection

Update ComputeJacobian to set the closure in the local matrix