Merge branch 'barry/add-matfdcoloring-ghosted-example'

Merge branch 'pr520/psanan/psanan/vtk-viewer-leak-fix/master' into maint

Merge branch 'pr520/psanan/psanan/vtk-viewer-leak-fix/master'

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 'maint'

PetscViewerVTK: Move DM reference increment into the VTK viewer and out of the DM implementation, as suggested by Jed Brown

Some Fortran stubs that returned strings could produce garbage

Some Fortran stubs that returned strings did not properly use FIXRETURNCHAR() to blank out the end of the Fortran string. Thus the Fort

Some Fortran stubs that returned strings could produce garbage

Some Fortran stubs that returned strings did not properly use FIXRETURNCHAR() to blank out the end of the Fortran string. Thus the Fortran string would contain "garbage".

Time: .2 hours
Reported-by: Mark Filipiak <m.filipiak@epcc.ed.ac.uk>

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Implemented Barry's comment (no need for work variables on optional arguments).

Added a couple of custom fortran subs to handle optional arguments correctly in 2D and 3D

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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fix c++ comments for c89

removed a variety of #include <xxximpl.h> from source code that was not needed

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
...

Conflicts:
include/petsc/private/dmimpl.h

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Merge branch 'maint'

Document not to call AODestroy() on DMDAGetAO() object

Reported-by: Paul Urbanczyk <gomer@stanford.edu>

sys: Petsc64bitInt -> PetscInt64 [and be consistant with MPIU_INT64]
PetscIntMult64bit() -> PetscInt64Mult()
PetscBagRegister64bitInt() -> PetscBagRegisterInt64()

removed a bunch of unneeded inclusions of xxximpl.h which exposed private data where it did not have to be exposed

also made more systematic the inclusion of the base xxximpl.h in the derived yyyimp

removed a bunch of unneeded inclusions of xxximpl.h which exposed private data where it did not have to be exposed

also made more systematic the inclusion of the base xxximpl.h in the derived yyyimpl.h
so the inclusion is done in the include file rather than in each source code that includes it

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Merge branch 'barry/fix-source-clang'

gcc6: fix comple warnings with -Wmisleading-indentation