DM: Added a embedding dimension, different from the topological dimension
- This can now be set in DMSetCoordinateSection(), or it can be automatically determined

DM: Move dimension up into DM
- Both DA and Plex had this and I think it makes sense

DMPlex: Fix bug with intersecting submeshes
- The label for clamped vertices for a given submesh can get extraneous points from an adjacent submesh
- We filter these out before checking for cross-edg

DMPlex: Fix bug with intersecting submeshes
- The label for clamped vertices for a given submesh can get extraneous points from an adjacent submesh
- We filter these out before checking for cross-edges

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Merged upstream/master to feature-dmmoab

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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Merge branch 'knepley/fix-pylith-parallel'

* knepley/fix-pylith-parallel: (22 commits)
DMPlex: In refinement, merge hybrid and non-hybrid SF creation (should be done for everything) - If missing,

Merge branch 'knepley/fix-pylith-parallel'

* knepley/fix-pylith-parallel: (22 commits)
DMPlex: In refinement, merge hybrid and non-hybrid SF creation (should be done for everything) - If missing, define *Max as *End - Fixed bound on hybrid 2D simplicial hybrid cell refinement - Fixes bug in which wrong remote point number was calculated if local process had no hybrid cells, but remote process did so refiners were mismatched
DMPlex: Fix for hybrid refinement - Must correct offsets when neighbor process has no hybrid points
DMPlex: Fix hex hybrid refinement SF - Fixed offset - Fixed number of cell faces - Fixed missing edge offset - Fixed number of cells faces - FIxed missing edge offset
PetscSection: Must initialize remoteOffsets
DMPlex: Fixed cohesive cell creation for clamped boundaries - Explicitly tag cross-edges (edges with two clamped endpoints) with 2 in boundary label - Add cross-edge to vertices when looking for things that need split points replaced - Remove extra check for boundary vertices
DMPlex: Fixes for marking cohesive submesh - Do not mark points as split which are in the boundary label - Mark boundary points from label as unsplit
DMPlex: Changing meaning of boundary label in DMPlexLabelCohesiveComplete() - Now it marks vertices already present in the original label - We mark these as unsplit, and ignore their stars - Remove old code
DMPlex: Fixed stupid typo
DMPlex: Fixed refinement to respect embedded manifolds
DMPlex: Fixed types in DMPlexOrient()
DMPlex: Fixed initialization in DMPlexLabelCohesiveComplete()
DMPlex: Fixed logic in hybrid cell tagging and added missing declaration
DMPlex Fixed huge error with last change set - Default cellHeight is 0
DMPlex: Allow cellHeight argument for DMPlexMarkBoundaryFaces()
DMPlex: Added blabel argument to DMPlexLabelCohesiveComplete() - Lets user designate the boundary of a dividing surface - Added GetSurfaceSize_Static()
DMPlex: Fix for DMPlexOrient() - I was not symmetrizing the orientation graph on processes
DMPlex: Added DMPlexAddConeSize()
DMPlex: Fixed memory overwrite at depth 0 for viewing
PC+Doc: Fixed FieldSplit doc
Sys: Replace Malloc1() in multiple mallocs (fix size)
...

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DMPlex: Fixed cohesive cell creation for clamped boundaries
- Explicitly tag cross-edges (edges with two clamped endpoints) with 2 in boundary label
- Add cross-edge to vertices when looking for thin

DMPlex: Fixed cohesive cell creation for clamped boundaries
- Explicitly tag cross-edges (edges with two clamped endpoints) with 2 in boundary label
- Add cross-edge to vertices when looking for things that need split points replaced
- Remove extra check for boundary vertices

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DMPlex: Added DMPlexCopyBoundary()
- Copy boundary conditions after DMRefine() and DMPlexConstructGhostCells()

DMPlex: Fixes for marking cohesive submesh
- Do not mark points as split which are in the boundary label
- Mark boundary points from label as unsplit

DMPlex: Now numGhostCells is optional in DMPlexConstructGhostCells()

TS ex11+DMPlex: Treat ghost cells as hybrid cells

DMPlex: Changing meaning of boundary label in DMPlexLabelCohesiveComplete()
- Now it marks vertices already present in the original label
- We mark these as unsplit, and ignore their stars
- Remove o

DMPlex: Changing meaning of boundary label in DMPlexLabelCohesiveComplete()
- Now it marks vertices already present in the original label
- We mark these as unsplit, and ignore their stars
- Remove old code

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DMPlex: Fixed initialization in DMPlexLabelCohesiveComplete()

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

Merged petsc/petsc into master

DMPlex: Fixed logic in hybrid cell tagging and added missing declaration

DMPlex Fixed huge error with last change set
- Default cellHeight is 0

DMPlex: Allow cellHeight argument for DMPlexMarkBoundaryFaces()

DMPlex: Added blabel argument to DMPlexLabelCohesiveComplete()
- Lets user designate the boundary of a dividing surface
- Added GetSurfaceSize_Static()

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 'master' of bitbucket.org:petsc/petsc
Fuck if git tells me to git pull then I pull, if you want me to do something else than have git tell what to do