DMPlexReconstructGradients_Internal(): clarify ternary operator terms

DMPlexConstructGhostCells_Internal(): correct error message communicator

DMPlex: fix point migration / hybrid point interaction

First, when we stratify, we have to put the hybrid points at the end.
Then, we have to identify hybrid points in the migrated dm in a way that

DMPlex: fix point migration / hybrid point interaction

First, when we stratify, we have to put the hybrid points at the end.
Then, we have to identify hybrid points in the migrated dm in a way that doesn't assume
we're coming from a serial dm.

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DMPlex: fix PetscPartitionerPartition() to deal with overlap

It returned an IS that gave indices that had sf leaves filtered out, but the result is
used in DMPlexDistribute() as though the leaves ar

DMPlex: fix PetscPartitionerPartition() to deal with overlap

It returned an IS that gave indices that had sf leaves filtered out, but the result is
used in DMPlexDistribute() as though the leaves are present.

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DMPlexComputeInterpolatorTree: fix loop variables from recent change

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

DMP4est: fix some ghost cell bounds

Merge branch 'tisaac/dm-label-use-is'

* tisaac/dm-label-use-is:
IS: fix ISLocate(): ex7 passes
IS: added test for ISLocate()
IS: added ISLocate implementations for block and stride
ISGeneral

Merge branch 'tisaac/dm-label-use-is'

* tisaac/dm-label-use-is:
IS: fix ISLocate(): ex7 passes
IS: added test for ISLocate()
IS: added ISLocate implementations for block and stride
ISGeneral: add locate implementation
DMLabel: use ISLocate()
IS: added ISLocate() interface and default implementation
change regression logs for increased number of index sets
DMLabel: added DMLabelSetStratumIS()
DMLabel: switch internal storage from array to IS

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

* tisaac/dm-boundary-in-ds:
DMPlex: skip bcs whose labels are present

DMPlex: skip bcs whose labels are present

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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Plex: set block size on local coordinates when creating mesh from gmsh file

Plex: invert read tetrahedra and hexahedra from gmsh file

Plex+Doc: Added page for DMPlexInsertBoundaryValues()

change regression logs for increased number of index sets

DMLabel: added DMLabelSetStratumIS()

DMLabel: switch internal storage from array to IS

This is intended to allow for more efficient storage of common label types, such as the depth label,
where each stratum is contiguous. In the long

DMLabel: switch internal storage from array to IS

This is intended to allow for more efficient storage of common label types, such as the depth label,
where each stratum is contiguous. In the long view, I think this will be useful when making DA and
Plex use the same interface. For a DA, it might be convenient to specify a subset (for, e.g.,
boundary conditions), using an ISStride or some kind of tbd ISSlice.

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Merge branch 'knepley/fix-plex-order'

* knepley/fix-plex-order:
Plex: Fixed bad assumption of sorted Label values

Merge branch 'knepley/feature-plex-closure-reorder'

* knepley/feature-plex-closure-reorder:
IS+Plex: Changed interface to closure permutation to take an IS
IS+Plex: Changed interface to closure

Merge branch 'knepley/feature-plex-closure-reorder'

* knepley/feature-plex-closure-reorder:
IS+Plex: Changed interface to closure permutation to take an IS
IS+Plex: Changed interface to closure permutation to take an IS
Plex ex9: Can now test closure reordering - Also fixed some small bugs
Plex ex6: Example that shows how to set and retrieve values with the spectral element ordering
Plex: Allow closure permutation in PlexVecGet/SetClosure() - This supports spectral element ordering - This does not seem to introduce any performance degradation
Plex: Added DMPlexCreateSpectralClosurePermutation()
PetscSection: Added support for closure permutation - This supports entry in the spectral element ordering

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Plex: Small cleanup

Builder+Doc: Fix interpolation option and improve error message

Plex: Fixes to draw for complex

Plex: Fixed type for GetNeighbors

Merge branch 'tisaac/plex-fix-copy-coordinates' into tisaac/dm-boundary-in-ds

Fixes some regression tests so that I can verify the changes of this branch

* tisaac/plex-fix-copy-coordinates:
DMPle

Merge branch 'tisaac/plex-fix-copy-coordinates' into tisaac/dm-boundary-in-ds

Fixes some regression tests so that I can verify the changes of this branch

* tisaac/plex-fix-copy-coordinates:
DMPlex: don't copy coordinates to self
add X monitoring of residual norm and true residual norm to example since not currently tested
TSAdaptSetType() had no manual page
remove a couple of seemingly strange unneeded PetscReturnFunction(ierr)
manual page for PetscLogObjectMemory()
missing manual page for TaoConvergedReason
tree: workarround bug 'cannot handle multipe #requirespackage listing'.
add no-change test for KSPCR and KSPLCD
configure: improve -fPIC test for ubuntu 16.10
sys: print scanf/PetscInt with --with-clanguage=C++ --with-64-bit-indices=1 --with-scalar-type=complex --with-mpi=0
Fix PCTFS and add test code for symmetric and non-symmetric version
fix a bug due to Lisandro Dalcin's commit d61f013 TS: Run forward cost integral after event handling if step not rolled back
name space Event* and Class* utility functions with Petsc

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DMPlex: don't copy coordinates to self