Partitioner+Plex: Added PetscPartitioner class
- Plex holds a PetscPartitioner
- Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition)
- Now partition routine

Partitioner+Plex: Added PetscPartitioner class
- Plex holds a PetscPartitioner
- Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition)
- Now partition routine takes a number of partitions instead of assuming commSize
- Added a shell partitioner intended to be used for regression testing

show more ...

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 'tisaac/thplex'

This merge brings in related work in the following areas:
- Added a local constraint matrix to DM (see DMSetDefaultConstraints())
- Added point-to-anchor-point constrain

Merge branch 'tisaac/thplex'

This merge brings in related work in the following areas:
- Added a local constraint matrix to DM (see DMSetDefaultConstraints())
- Added point-to-anchor-point constraints in DMPlex (see
DMPlexSetAnchors()), which build on the DM constraints
- Added hierarchically-constrained points to DMPlex (see
DMPlexSetReferenceTree(), DMPlexSetTree()), which builds on the anchor
constraints
- Tests for these constraints in src/dm/impls/plex/examples/ex3.c (try
runex3_* examples in that directory)
- Added quadrature order (see PetscQuadratureGet/SetOrder()) (work by
Matt Knepley)
- Added default return values for DMGetCoordinateDim() (defaults to
DMGetDimension())

Conflicts:
include/petscdmplex.h
src/dm/dt/interface/dt.c
src/dm/impls/plex/examples/tests/ex3.c
src/dm/impls/plex/makefile
src/dm/impls/plex/plexfem.c

show more ...

DMPlex: take tree into account when creating partitions

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

show more ...

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

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
...

show more ...

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

show more ...

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

Merged petsc/petsc into master

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

show more ...

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

show more ...

Fixing merge conflicts in dmregall.

Merged petsc/petsc into master

DMPlex: Fix DMPlexGetAdjacency_Internal() to allocate if necessary

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

DMPlex: Reorganized the handling of point adjacency
- Replaced centerDim with useCone, useClosure, Added DMPlexGet/SetAdjacencyUseCone/Closure()
- Now partitioning and preallocation use the same adja

DMPlex: Reorganized the handling of point adjacency
- Replaced centerDim with useCone, useClosure, Added DMPlexGet/SetAdjacencyUseCone/Closure()
- Now partitioning and preallocation use the same adjacency routines
- Added DMPlexGetAdjacency() and the internal version which does not allocate
- Moved distribution and partitioning code into separate files
-

show more ...