Plex: rename Constraints as Anchors for clarity.

Now that there are DMGet/SetConstraints() functions, some clarity is
needed:

DMGet/SetConstraints() are any type of linear constraints that are
cons

Plex: rename Constraints as Anchors for clarity.

Now that there are DMGet/SetConstraints() functions, some clarity is
needed:

DMGet/SetConstraints() are any type of linear constraints that are
considered part of the global-to-local map.

DMPlexGet/SetAnchors() are linear constraints that make a point's dofs
linear dependent on the dofs of a set of anchor points.

DMPlexGet/SetTree() are anchor constraints that derive from a
hierarchically refined mesh.

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DMPlex: distribute the tree data

DMPlex: tighter bounds on work arrays

DMPlex: fix adjacency size when there are zero anchors

DMPlex: Take (right) constraints into account in preallocation

DMPlex: fix recent constraint additions

Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex1

Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex11: Fixed calls to DMSetCoordinateSection()
DM: FIxed DMClone() to copy dimension
Plex+DA: Now cell geometry routine can take a PetscFE in order to evaluate at quadrature points - We evaluate isoparametrically at the quadrature points - Changed DMDAComputeCellGeometry() --> DMDAComputeCellGeometryFEM() - Changed DMPlexComputeCellGeometry() --> DMPlexComputeCellGeometryFEM() - Added DMPlexComputeCellGeometryAffineFEM()
DM: Added a embedding dimension, different from the topological dimension - This can now be set in DMSetCoordinateSection(), or it can be automatically determined
Plex: Fix output for ex4
DM: Added DMGetDimPoints() - This replicates DMPlex/DAGetDepthStratum(), but uses the dimension which people have said is more intuitive
DM: Move dimension up into DM - Both DA and Plex had this and I think it makes sense

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

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

* knepley/fix-plex-coords-parallel:
DMPlex: Incorrect periodicity information
KSP+SNES: Converged output now includes prefix
DMPlex ex4: Fixed t

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

* knepley/fix-plex-coords-parallel:
DMPlex: Incorrect periodicity information
KSP+SNES: Converged output now includes prefix
DMPlex ex4: Fixed test output
Mat+Coloring: Greedy coloring fix - Use ocolors[] for off-diagonal piece
PetscSection: Added check for mismatch between SF and Section
DMPlex: DMPlexReplace_Static() fixes - Should share coordinateDM, not just the section, so we get correct SF - Pass on periodicity information
DMPlex: Refinement should create SF before coordinates, so coordinateDM gets correct SF - Also pass on periodicity information
DMPlex: Distribution should create SF before coordinates, so coordinateDM gets correct SF - Also pass on periodicity information

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

DMPlex: Distribution should create SF before coordinates, so coordinateDM gets correct SF
- Also pass on periodicity information

Merged upstream/master to feature-dmmoab

Merge remote-tracking branch 'upstream/master'

Merge branch 'jed/dmda-memusage'

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 '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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DMPlex: Distribution should copy over BC info

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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Merge branch 'knepley/feature-fe-derivatives'

* knepley/feature-fe-derivatives:
Doc+Plex: Small fix for distribution
PetscFE: Correct type for reference space derivatives
SNES ex62: Updated to

Merge branch 'knepley/feature-fe-derivatives'

* knepley/feature-fe-derivatives:
Doc+Plex: Small fix for distribution
PetscFE: Correct type for reference space derivatives
SNES ex62: Updated to new derivative mapping
SNES ex12: Updated to new derivative mapping
PetscFE: Changed mapping of derivatives - Now they are transformed only pointwise, instead of transforming the whole tabulation
SNES ex62: Works with new derivative mapping
SNES ex12: Works with new derivative mapping
PetscFE: Changed PetscFEIntegrateResidual_Basic() derivative mapping - Instead of mapping the basis derivatives, we only map the pointwise derivatives gradU and f_1 Suggested-by: Jed Brown <jedbrown@mcs.anl.gov>
PetscFE: Removed PetscGenerateFEMQuadrature*.py

Conflicts:
config/builder.py

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DMPlex: Preserve the block size of the coordinate vector after distribution

Doc+Plex: Small fix for distribution

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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