Merge remote-tracking branch 'upstream/master'

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 'knepley/feature-fv-class'

* knepley/feature-fv-class: (44 commits)
PetscFV: Another complex fix
DMPlex+TS: Fixing types
PetscFV: Straighten out complex types
TS ex11: Fix casts

Merge branch 'knepley/feature-fv-class'

* knepley/feature-fv-class: (44 commits)
PetscFV: Another complex fix
DMPlex+TS: Fixing types
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
PetscFV: Fix Fortran define
PetscFV: Complex fixes
SNES+DM: Added SNESMonitorFields() - Activated by -snes_monitor_fields
PetscFV: Add Fortran types
SNES ex62: Use new DMPlexAddBoundary() interface - Added declaration of DMPlexComputeL2FieldDiff() - Fixed cast
SNES ex12: Fixed Neumann boundary conditions, and moved to new DMPlexAddBoundary interface() - Now do not automatically mark boundary faces
PetscFV: Fixed Fortran bindings
PetscFV+Plex: Refactored to put reconstruction routines in PetscFV_LeastSquares - Added PetscFVComputeGradient() - Added PetscFVLeastSquaresSetMaxFaces() - Moved last squares fitting routines to PetscFV_LeastSquares, and all the work space
PetscLimiter: Add other implementations
TS ex11: Fixed parallel mesh creation - Distribute after physics - Add output for tests
DMPlex: Fixed bug when using refinement from options - Must copy over the point SF
DMPlex: Distribution should copy over BC info
TS ex11: Added refinement tests
TS ex11: Fix boundary conditions after refinement, set types from command line
DMPlex: Added DMPlexCopyBoundary() - Copy boundary conditions after DMRefine() and DMPlexConstructGhostCells()
TS ex11: Specify boundary label
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/plex.c
src/snes/examples/tutorials/ex62.c

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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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TS+DM: Added a Plex traversal for FV methods for RHS

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

Merged petsc/petsc into master

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

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this wa

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

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad)
outdated example that doesn't match coding style removed and buggy
petscversion.h: workaround ifort -cpp lack of referential transparency
configure: ignore AR, MAKEFLAGS [if set in env]
incorrect first entry in array being zeroed in example
sizeof.c: remove dependence on petsc [and fix syntax error]
nightlybuilds: use consistant PETSC_ARCH, machine names
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
change MPIVersion streams to use MPI_Wtime() to be portable to Windows do not use scalar square root on real number; it upsets Microsoft
cannot use I in PETSc code because in complex it sometimes represents imaginary number cannot pass PetscScalar * to VecNorm()
in dashboard don't warn about SSL and BOI deprecated
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
streams: translate code from 'bash' to 'sh' [fix freebsd]
barry is an idiot who doesn't have a clue as to what he is doing (and git's unfriendlyness doesn't help matters)
don't list examples under C that don't work with complex!
forgotten output file
removed valgrind warning about sending uninitialized data
nightly builds ignore unrecognized pragma and .c file as C++ code
...

Conflicts:
include/petsc-private/dmpleximpl.h

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Merge branch 'knepley/feature-plex-bc'

* knepley/feature-plex-bc:
DMPlex: Cells in the boundary marker should not be interpreted as constraints
DMPlex: Fix declaration
TS ex11: Replace ApplyBC

Merge branch 'knepley/feature-plex-bc'

* knepley/feature-plex-bc:
DMPlex: Cells in the boundary marker should not be interpreted as constraints
DMPlex: Fix declaration
TS ex11: Replace ApplyBC() with DMPlexInsertBoundaryValuesFVM()
DMPlex: Fixed DMPlexInsertBoundaryValuesFVM() - Remove redundant variable - Handle absence of id
TS ex11: Reorganization so that physics creation functions can take the DM - This required splitting the options block
DMPlex: DMPlexInsertBoundaryValues() --> DMPlexInsertBoundaryValuesFEM(), and added an FVM version - The FVM version depends on precalculated geometry which needs to be pulled into the library
TS ex11: Remove unused RHSFunction()
TS ex11: Remove Model from BC func - We do not want opaque objects outside of the context so we can pull this in the library
TS ex11: Now use TS infrastructure for local functions
DMPlex: Fix signature for IFunction - Note that the time is still not being passed down to the pointwise function
TS: Added local versions of assembly to DMTS - I was not sure whether everything was necessary
SNES ex62: Updated output
SNES ex12: Removed outdated BC handling - Removed unnecessary label completion - Updated output
DMPlex: Switched FEM assembly routines to use DMPlexInsertBoundaryValues()
DMPlex: Now DMPlexInsertBoundaryValue() only sets values for the given label - Added DMPlexProjectFunctionLabelLocal()
DMPlex: Now DMCreateSection() calls DMPlexLabelAddCells() - This is necessary for FEM boundary conditions, but we do not want it for FVM so we need some control divergence here soon
DMPlex: Added DMPlexLabelAddCells() - Needed this for FEM BC
DMPlex: Fix Gmsh test

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

* knepley/feature-plex-bc:
DMPlex: Cells in the boundary marker should not be interpreted as constraints
DMPlex: Fix dec

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

* knepley/feature-plex-bc:
DMPlex: Cells in the boundary marker should not be interpreted as constraints
DMPlex: Fix declaration
TS ex11: Replace ApplyBC() with DMPlexInsertBoundaryValuesFVM()
DMPlex: Fixed DMPlexInsertBoundaryValuesFVM() - Remove redundant variable - Handle absence of id
TS ex11: Reorganization so that physics creation functions can take the DM - This required splitting the options block
DMPlex: DMPlexInsertBoundaryValues() --> DMPlexInsertBoundaryValuesFEM(), and added an FVM version - The FVM version depends on precalculated geometry which needs to be pulled into the library
TS ex11: Remove unused RHSFunction()
TS ex11: Remove Model from BC func - We do not want opaque objects outside of the context so we can pull this in the library
TS ex11: Now use TS infrastructure for local functions
DMPlex: Fix signature for IFunction - Note that the time is still not being passed down to the pointwise function
TS: Added local versions of assembly to DMTS - I was not sure whether everything was necessary
SNES ex62: Updated output
SNES ex12: Removed outdated BC handling - Removed unnecessary label completion - Updated output
DMPlex: Switched FEM assembly routines to use DMPlexInsertBoundaryValues()
DMPlex: Now DMPlexInsertBoundaryValue() only sets values for the given label - Added DMPlexProjectFunctionLabelLocal()
DMPlex: Now DMCreateSection() calls DMPlexLabelAddCells() - This is necessary for FEM boundary conditions, but we do not want it for FVM so we need some control divergence here soon
DMPlex: Added DMPlexLabelAddCells() - Needed this for FEM BC
DMPlex: Fix Gmsh test

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TS: Added local versions of assembly to DMTS
- I was not sure whether everything was necessary

Merge branch 'master' into jed/ts-eimex

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

Conflicts:
src/ts/interface/tsregall.c

merge PetscSF implementation

Hg-commit: 98dccc99445b69cb7a66312149eb16fec359e294

removed trailing spaces from all files

Hg-commit: 1cfa55059afe46c5145e0e830cd797b97216abfb

commit after merge

Hg-commit: d0f613618ca66a5aeb1aac97d210d2cc29755d3d

reemove OBJSC and OBJSF from invididual makefiles and auto-define in conf/variables

Hg-commit: 2f01c17f3c19dc4b89aaf306cfd60a12312c270d

commit after merge

Hg-commit: 0213d38b3b86e395dfbe1b69eb2c6485120d2a06

Commit after merge.

Hg-commit: 21d705615136caf799e2c77a532f2c82c8fe058f

More complete TSDMDA docfix

Hg-commit: cdc107b316935eb893b84f7e9b9ff09ed959bcae

commit after merge

Hg-commit: 5d40997985620b0ab10e66197464bd8588e8f80b

TSDM: DM hooks for TS that look like SNESDM

Hg-commit: 9044db07be14c14c5b3cf55e6b55587892080a4d