Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
Plex: Fix serial orientation
TetGen: Syntax fix
Plex: Fix MPI type for orientation
Plex: Small orientation fix
Plex ex13:

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
Plex: Fix serial orientation
TetGen: Syntax fix
Plex: Fix MPI type for orientation
Plex: Small orientation fix
Plex ex13: Orientation now working for flipped connected components
Plex: Reworked orientation to respect connected components on each process
Plex ex13: Check in initial output
Plex: Now mark initial cell as seen - Changes the outcome slightly
Plex: Added DMPlexCheckFace_Internal() - This checks a face in the mesh for orientation consistency
Plex: Fix orientation diagnostics
Plex: Added declaration for DMPlexReverseCell()
Plex ex13: Tests orientation - Only 2D triangle tests now - Last test shows problem for disconnected domains
Plex: Small example fixes
PetscBT: Do not overwrite a viewer passed to PetscBTView()
Plex: Remove unneeded headers
Plex: Added a file for orientation calculations - Moved DMPlexOrient()

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

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Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

PetscBT: Do not overwrite a viewer passed to PetscBTView()

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]
gfortran: remove 132 char limit from f90 free-form
SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc
DMPlex-Gmsh: Use trueNumCells when building the coordinate section
Sys: Got guard logic reversed
Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*()
PetscFV: I hate fucking complex
removed ltog scatter from DMDA since functionality can be obtained with gtol scatter and less memory
fix test of DMLocalToGlobalBegin/End and add actual test cases
improve object memory logging for DA, ISLocalToGlobal and ISBLOCK
lower high water mark of constructing parallel scatter by allocating only as much room in svalues as needed
owner in VecScatter construction is the rank, therefor can use PetscMPIInt to hold it do not PetscInt
another reuse of allocated array in 2d/3d DMDA create
improved high water mark of DMDASetups by implementing and using PETSC_USE_POINTER for ISCreateBlock()
PetscFV: Another complex fix
DMPlex+TS: Fixing types
ISIdentity() was wrong for block IS! Indices are NOT scaled by bs
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
...

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Merge branch 'master' into barry/saws-options

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

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

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

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

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Fixing merge conflicts in dmregall.

Merged petsc/petsc into master

Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'master' into prbrune/matcoloring-greedy

Merge branch 'master' into barry/google

Merge branch 'knepley/fix-plex-orient-parallel'

* knepley/fix-plex-orient-parallel:
DMPlex: Added braindead simple parallel orientation solver - This gathers the graph to proc 0, solves, and scatt

Merge branch 'knepley/fix-plex-orient-parallel'

* knepley/fix-plex-orient-parallel:
DMPlex: Added braindead simple parallel orientation solver - This gathers the graph to proc 0, solves, and scatters the answer - Need to store neighbor ranks and matches for each neighbor - This should be replaced with a parallel BFS
DMPlex: For 1D orientation, you have to use cone position rather than face orientation
DMPlex: Fixed some small mistakes - Initialize var - Declare at the top of the block - Added cone size call
DMPlex: Added parallel stage to DMPlexOrient() - The coarse solver is not implemented, so only works for p=2
PetscBT: Added PetscBTNegate()

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PetscBT: Added PetscBTNegate()

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

Merged petsc/petsc into rmills/petsc master.

Merged in dalcinl/petscbt-lookupclear (pull request #26)

PetscBT: Add PetscBTLookupClear()

PetscBT: Add PetscBTLookupClear()

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

avoid PETSC_VIEWERSTDOUT_ in source
missing examples in test compiles in makefile

Hg-commit: beacb2a8cc0058d9376612df7a28ccb293f604f3

Remove petscviewer.h from petscsys.h

Much of sys is independent of viewer. Viewer is used in so many other
places that it is now included by petscvec.h.

Hg-commit: 1d745f01618aa51d3043fb1f87b0546f6

Remove petscviewer.h from petscsys.h

Much of sys is independent of viewer. Viewer is used in so many other
places that it is now included by petscvec.h.

Hg-commit: 1d745f01618aa51d3043fb1f87b0546f60e6e730

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Clean up a couple header dependencies

Hg-commit: 11d62dee14b4cd8f0885a0f296b51b3346d7e18a

merge PetscSF implementation

Hg-commit: 98dccc99445b69cb7a66312149eb16fec359e294