Merge branch 'tisaac/feature-fe-geom-dim' into tisaac/plex-flexible-projection

Use the new PetscFECellGeom

Conflicts:
include/petscdmplex.h
include/petscfe.h
src/dm/impls/plex/plexfem.c

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/ex49-bs

Merge branch 'barry/docs-matblocksize'

MatGetVecs() and KSPGetVecs() replaced with MatCreateVecs() and KSPCreateVecs()
since they are creators not getters

ISLocalToGlobalMapping: added ISGlobalToLocalMappingApplyIS

Merged upstream/master to feature-dmmoab

Merge remote-tracking branch 'upstream/master'

Merge branch 'jed/dmda-memusage'

fixed ISLocalToGlobalMappingGetInfo() to handle block and non-block cases

added ISGlobalToLocalMappingApplyBlock() and fixed the ISGlobalToLocalMappingApply() to work for points
added simple test for these

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 'jed/dmda-memusage'

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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removed blocked versions of ISLocalToGlobalMapping in Vec and Mat
the single ISLocalToGlobalMapping supports ISLocalToGlobalMappingApply and ISLocalToGlobalMappingApplyBlock
still some fixes need for

removed blocked versions of ISLocalToGlobalMapping in Vec and Mat
the single ISLocalToGlobalMapping supports ISLocalToGlobalMappingApply and ISLocalToGlobalMappingApplyBlock
still some fixes need for these extensive changes

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added bs argument to ISLocalToGlobalMappingCreate(), not yet used for bs > 1

Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

Merge branch 'knepley/feature-plex-hdf5-parallel-load'

* knepley/feature-plex-hdf5-parallel-load:
HDF5: Fixed Xdmf script
Plex+HDF5: Do not use vectors for periodic visualization
Plex+HDF5: Ig

Merge branch 'knepley/feature-plex-hdf5-parallel-load'

* knepley/feature-plex-hdf5-parallel-load:
HDF5: Fixed Xdmf script
Plex+HDF5: Do not use vectors for periodic visualization
Plex+HDF5: Ignore negative sequence numbers
DMPlex: Now Plex output is parallel - We now write visualization specific topology in /viz/topology - We output a point reordering, coneSizes, cones, and orientations - Now longer need to interpolate on load
DMPlex: Use the presence of faceGeometry in the DM to signal we are using FVM - This will become a PetscFVM object soon
DMPlex: Preserve the block size of the coordinate vector after distribution
Plex+HDF5: Moved all HDF5 to a separate file, and mapped 2D periodic mesh to the cylinder - Now visualization specific things are in /viz
HDF5: Made petsc_gen_xdmf.py executable
Viewer+Options: Added Fortran interface for PetscObjectViewFromOptions()
IS: Stupid mistake. Damn you compiler
DMPlex: Now parallel HDF5 label output does not fail - However, it is also now clear that we will have to write the full interpolation connectivity in order for these to be meaningful
DMPlex: Added DMPlexCreatePointNumbering() - Made DMPlexCreateNumbering_Private() more flexible
IS: Added ISSortRemoveDups()
DMPlex: Added DMPlexInvertCell_Internal() - Stupid type matching
HDF5: Added petsc_gen_xdmf.py which processes PETSc HDF5 output and produces an Xdmf file
DMPlex: Force a serial load in DMLoad_HDF5(), after which we call DMPlexDistribute() - Eventually we would load into a naive partition
IS+HDF5: Corrected code for new block size interface where it is never negative
Viewer+HDF5: Added PetscViewerHDF5ReadSizes() - This allows me to check the size of a Vec or IS to be loaded

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IS: Added ISSortRemoveDups()

Merge branch 'knepley/feature-plex-hdf5'

* knepley/feature-plex-hdf5: (63 commits)
DMPlex ex2: Added an example that checks a mesh
DMPlex: #ifdef support functions for HDF5
TS: Fix output sequ

Merge branch 'knepley/feature-plex-hdf5'

* knepley/feature-plex-hdf5: (63 commits)
DMPlex ex2: Added an example that checks a mesh
DMPlex: #ifdef support functions for HDF5
TS: Fix output sequence
DMPlex: Check for HDF5 attributes before writing them
DMPlex: Label with timestep number since we do not have times
Viewer+HDF5: Added PetscViewerHDF5HasAttribute()
TS: Set output sequence for timesteps
DMPlex: Handle output sequences - Added static to some functions
DM: Add idea of an output sequence - Added DMGet/SetOutputSequenceNumber() - Added doc for outputDM
REVERT TS: Timestep gets set into DMTS
DMPlex: Fix up HDF5 segregation
DMPlex: Replace MAXPATHLEN with PETSC_MAX_PATH_LEN
DMPlex: Fix HDF5 timestep handling
DMPlex: Set correct block size on HDF5 field vectors
TS: Timestep gets set into DMTS
DMTS: Added timestep
DMPlex: Fix output of fields - Corrected name - Fixed vector type
DMPlex: Return errors from HDF5 function
DMPlex+Viewer: Now output separate fields for viz - Added the PETSC_VIEWER_HDF5_VIZ format for creating viz fields - Added field type determination
Sys+HDF5: Added PetscDataType string and HDF5 support for it
...

Conflicts:
config/BuildSystem/config/packages/__init__.py
src/ts/interface/ts.c

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Merge branch 'knepley/feature-plex-hdf5' into knepley/feature-plex-bc

* knepley/feature-plex-hdf5: (61 commits)
TS: Fix output sequence
DMPlex: Check for HDF5 attributes before writing them
DM

Merge branch 'knepley/feature-plex-hdf5' into knepley/feature-plex-bc

* knepley/feature-plex-hdf5: (61 commits)
TS: Fix output sequence
DMPlex: Check for HDF5 attributes before writing them
DMPlex: Label with timestep number since we do not have times
Viewer+HDF5: Added PetscViewerHDF5HasAttribute()
TS: Set output sequence for timesteps
DMPlex: Handle output sequences - Added static to some functions
DM: Add idea of an output sequence - Added DMGet/SetOutputSequenceNumber() - Added doc for outputDM
REVERT TS: Timestep gets set into DMTS
DMPlex: Fix up HDF5 segregation
DMPlex: Replace MAXPATHLEN with PETSC_MAX_PATH_LEN
DMPlex: Fix HDF5 timestep handling
DMPlex: Set correct block size on HDF5 field vectors
TS: Timestep gets set into DMTS
DMTS: Added timestep
DMPlex: Fix output of fields - Corrected name - Fixed vector type
DMPlex: Return errors from HDF5 function
DMPlex+Viewer: Now output separate fields for viz - Added the PETSC_VIEWER_HDF5_VIZ format for creating viz fields - Added field type determination
Sys+HDF5: Added PetscDataType string and HDF5 support for it
IS: Fix compiler warning
IS: Forgot to protect HDF5
...

Conflicts:
config/BuildSystem/config/packages/__init__.py
src/ts/interface/ts.c

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Merge branch 'knepley/feature-section-reorder'

* knepley/feature-section-reorder:
DMPlex: Fixed F90 binding for DMPlexCreateSection()
DMPlex exf90: Forgot Fortran change
DMPlex: Added permutat

Merge branch 'knepley/feature-section-reorder'

* knepley/feature-section-reorder:
DMPlex: Fixed F90 binding for DMPlexCreateSection()
DMPlex exf90: Forgot Fortran change
DMPlex: Added permutation argument to DMPlexCreateSection() - Need it because it calls PetscSectionSetUp()
PetscSection: Added an optional permutation for the chart - Removed the unnecessary atlasLayout - This permutation will allow people to segregate ghost unknowns at the end of their numbering, and also to get around the stratification of point numbering in Plex

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Merge branch 'knepley/feature-section-reorder' into knepley/feature-plex-bc

* knepley/feature-section-reorder:
DMPlex: Fixed F90 binding for DMPlexCreateSection()
DMPlex exf90: Forgot Fortran ch

Merge branch 'knepley/feature-section-reorder' into knepley/feature-plex-bc

* knepley/feature-section-reorder:
DMPlex: Fixed F90 binding for DMPlexCreateSection()
DMPlex exf90: Forgot Fortran change
DMPlex: Added permutation argument to DMPlexCreateSection() - Need it because it calls PetscSectionSetUp()
PetscSection: Added an optional permutation for the chart - Removed the unnecessary atlasLayout - This permutation will allow people to segregate ghost unknowns at the end of their numbering, and also to get around the stratification of point numbering in Plex

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IS: Added ISLoad() and an HDF5 implementation
- I know this only works for general now