DMCreateDomainDecomposition: only copy ctx if it exists

Changed IS_COLORING_GHOSTED to IS_COLORING_LOCAL, added test case, fixed code to work properly

Time: 5 hours
Reported-by: Hong Zhang <hzhang@mcs.anl.gov>

Merge branch 'tisaac/dmplex-fix-nonaffine-geom' into tisaac/petscfe-matching-quadrature-order

* tisaac/dmplex-fix-nonaffine-geom:
fixing Toby's fix
DMPlexComputeGeometryFEM(): clarify what is ex

Merge branch 'tisaac/dmplex-fix-nonaffine-geom' into tisaac/petscfe-matching-quadrature-order

* tisaac/dmplex-fix-nonaffine-geom:
fixing Toby's fix
DMPlexComputeGeometryFEM(): clarify what is expected if fe != NULL and correct computations accordingly
added checks for AIJ in MIS and GAMG
Bib: Added refs
loop upper bound was one too high
force runex22_4 to produce same output in __float128 precision where it wants to do one more timestep
remove duplicate .bib item, fix typos in .bib items
Fortran wrapper for DMGetType (copy-pasted from src/mat/interface/ftn-custom/zmatregf.c).
Variants of example also need to handle atol convergence with quad precision in test
Add rtol and atol to output of TSView ASCII
Fortran wrapper for MatNullSpaceGetVecs
MATIS: fix compiling error from nightly builds
MATIS: set block size if it is greater than zero
MATIS: added MatTranspose_IS
Quadrature: Fix creation init
Plex: Fix output optimization - We obviously have no test for this logic

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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 'knepley/fix-plex-output'

* knepley/fix-plex-output:
Quadrature: Fix creation init
Plex: Fix output optimization - We obviously have no test for this logic

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

Merge branch 'knepley/fix-plex-output' into mark/snes-ex56

* knepley/fix-plex-output:
Quadrature: Fix creation init
Plex: Fix output optimization - We obviously have no test for this logic
All

Merge branch 'knepley/fix-plex-output' into mark/snes-ex56

* knepley/fix-plex-output:
Quadrature: Fix creation init
Plex: Fix output optimization - We obviously have no test for this logic
Allow the Richardson scale factor to be reset at each iteration
prevent a possible segfault when m is 0 (or less)
when configured --with-errorchecking=0, CHKERRV is missing
essl: fix PetscOptionsGetReal() usage
Fix code comment. Routine actually does not add arguments to database it just reads them in
Fix performance issue in MatAIJCUSPARSE after 34d6c7a
Plex ex6: fix PetscInt print codes
DMPlex: fix PetscPartitionerPartition() to deal with overlap

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Plex: Fix output optimization
- We obviously have no test for this logic

Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increa

Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increase patchlevel to 3.7.3
move runex3_3 to NOTSINGLE [ partial backport 9ed0bd76d5c329eb91401ebabfbd851446214e20 ]
DMPlex: local coordinate vector should be a sequential vector
DM: Name coordinate vectors in subdomain and restrict hooks
tests: disable a couple of TS examples from single precision tests
reduce TS ex12_2 output
fix PetscFormatRealArray() to cast PetscReal in print statement to double so works for __float128 precision
Vec: enable Fortran interfaces for VecGetLocalVectorRead and VecRestoreLocalVectorRead
Bib: Added refs
PCShell: man page fixes
update handling of latex in example code to use https
fix typo in isltog comment
test: Avoid conversion of object <-> function pointer type [-Wpedantic]
fortran: enable interface for VecGetLocalVector(), VecRestoreLocalVector()
update citation for cmz2016
PCBDDC: silent compilation warnings from nightlybuilds
...

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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Merge remote-tracking branch 'origin/maint'

Merged in dalcinl/fix-plex-coord-local (pull request #512)

DMPlex: Local coordinate vectors

DM: Name coordinate vectors in subdomain and restrict hooks

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/fix-plex-l2g'

* knepley/fix-plex-l2g:
SNES ex77: Use short monitor output
SNES ex69: Updated output
Plex test mesh: Fix for GMsh tet change
SNES ex12: Fixed output newl

Merge branch 'knepley/fix-plex-l2g'

* knepley/fix-plex-l2g:
SNES ex77: Use short monitor output
SNES ex69: Updated output
Plex test mesh: Fix for GMsh tet change
SNES ex12: Fixed output newlines
Plex: Separate ghost and constrained dofs in l2g

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Merge branch 'knepley/fix-dm-outputdm'

* knepley/fix-dm-outputdm:
Dammit
Plex: Remove DMPlexLoad() declaration
Plex: Fix package initializer in PlexPartitionCreate()
DM: Make check on DMGetO

Merge branch 'knepley/fix-dm-outputdm'

* knepley/fix-dm-outputdm:
Dammit
Plex: Remove DMPlexLoad() declaration
Plex: Fix package initializer in PlexPartitionCreate()
DM: Make check on DMGetOutputDM() collective

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Plex: Separate ghost and constrained dofs in l2g

DM: Make check on DMGetOutputDM() collective

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/dm-feature-adapt-label'

Adds an optional interface for adapting a DM by a specified label. Good
support in DMP4est; DMPlex will at least refine (I need to see if
Triangle/Tetge

Merge branch 'tisaac/dm-feature-adapt-label'

Adds an optional interface for adapting a DM by a specified label. Good
support in DMP4est; DMPlex will at least refine (I need to see if
Triangle/Tetgen support point-deletion coarsening); no DMDA
implementation, but I might put in one that at least detects uniform
coarsening/refinement.

* tisaac/dm-feature-adapt-label:
Plex tests ex20: add names to output meshes
DMPlex tests ex20: fix bad dev/null'd output in makefile test
DMPlex: gotta root out that c99 before it corrupts our kids
DMPlex test ex20: added triangle and ctetgen regression tests for DMLabelAdapt()
DMRefine_Plex_Label(): move DMPlexRestoreTransitiveClosure() after loop
DMPlex: added test ex20 for DMAdaptLabel()
DMPlex: put ifdef guards around static function only used when packages present.
DMFOREST: fix initialization
DMPlex: fix __FUNC__ of recent change
DMAdaptFlag: added DM_ADAPT_DETERMINE
DMPlex: added DMAdaptLabel implementation for DMPlex
DMAdaptLabel: change second argument to actual label
DM: added DMAdaptLabel() interface

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DMAdaptFlag: added DM_ADAPT_DETERMINE

- This way the default label value is DM_ADAPT_DETERMINE
- Removes some ambiguity about what DM_ADAPT_KEEP means

DMAdaptLabel: change second argument to actual label

Also move DM_FOREST_REFINE/COARSEN to DM_ADAPT_REFINE/COARSEN

DM: added DMAdaptLabel() interface

There is already DMForestAdapt, but DMPlex should also be able to adapt from a label of flags,
and DMDA can also at least be able to check to see if a label is uni

DM: added DMAdaptLabel() interface

There is already DMForestAdapt, but DMPlex should also be able to adapt from a label of flags,
and DMDA can also at least be able to check to see if a label is uniform coarsening/refinement
and dispatch to DMCoarsen()/DMRefine().

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

Merge branch 'barry/housekeeping-2'

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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