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
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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 '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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DMLabel: added DMLabelSetStratumIS()

Merge branch 'dmay/feature-dm-swarm' into knepley/feature-plex-particle-example

* dmay/feature-dm-swarm: (69 commits)
DMSwarm: * Check for size compatabaility between vectors created for DMSwarm f

Merge branch 'dmay/feature-dm-swarm' into knepley/feature-plex-particle-example

* dmay/feature-dm-swarm: (69 commits)
DMSwarm: * Check for size compatabaility between vectors created for DMSwarm fields * Bug fix for the field register function
DMSwarm DataBucket: * Added guards to ensure that internal arrays are never re-sized if any raw pointers are being currently being accessed
DMSwarm: * Added missing part of macro
DMSwarm: * Added documentation
DMSwarm example: * Added example with DMShell and user point location
DMSwarm Migrate: * Updated to use DMLOCATEPOINT_POINT_NOT_FOUND flag
DM definition: * Added special flag for marking points as being not found within an element during a call to DMLocatePoints
DMSwarm migrate: * Fixed bug with point removal
DMSwarm: * Removed print from data exchanger
DMSwarm: * Use common field names * Re-organized init/finalize fields with DMCreate/DMSetUp * Added methods, flags, checks when using DMSwarmType PIC
SwarmMigrate: * Use common field names
PetscDMSwarm: * Added common names * Corrected extern to PETSC_EXTERN * Added names for migrate
DMSwarm implementation: * Remove unused member
DM implementation: * Added new method locatepointssubdomin
DataBucket: * Print block size
DMSwarm example: * Removed comment
DMSwarm example: * Updated function names
DMSwarm test: * Added new test for variable block sizes
DMSwarm: * Fixed typo in vector name
DMSwarm: * Finishing support for block size != 1
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Conflicts:
include/petsc/private/dmimpl.h

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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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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 stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'tisaac/dm-locate-points-sf'

* tisaac/dm-locate-points-sf:
Plex: missed in IS
DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make regression test that fails
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
Communicator passed to VecCreateSeq should be PETSC_COMM_SELF
PCMG man page: fix typo in options name
Bib: Added refs
DMLabel: Removed unused variable
Metis tries to use backtrace which requires -lexecinfo on some systems such as freebsd Remove -lexecinfo from freebsd configure files since it is only needed by metis
add alternative output that occurs on some systems due to use of random number generator in partitioner
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
need to show diffs of ex22 if it fails
Support two different output for test example, since due to roundoff this example can produce slightly different convergence history
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Merge branch 'master' of https://bitbucket.org/petsc/petsc

DM definition:
* Added special flag for marking points as being not found within an element during a call to DMLocatePoints

Merged collection routines from dmay/swarm-boundingbox-collect

Merge branch 'dmay/swarm-boundingbox-collect' into dmay/swarm-next

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'knepley/fix-dmlabel-declaration'

* knepley/fix-dmlabel-declaration:
DMLabel: Moved declaration since dmlabel.h does not include dm.h

DM API:
* Added prototype for DMGetNeighbors

DMLabel: Moved declaration since dmlabel.h does not include dm.h

DMSwarm:
* Added place holder for DMSwarm implementation

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping cells, it's clearer which
in which process/cell the point is located.
- A natural next step after DMLocatePoints() is to send each point to
its cell for some local computation. With a PetscSF this is easy with
PetscSFGatherBegin()/PetscSFGatherEnd().

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

Merge branch 'barry/add-dmshellcreaterestriction'