DMPlex: Fix support of edges in 2D uniform refinement

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynami

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynamic_library_preload that can be used to load/initialize all the
packages in advance, as used to be done when --with-dynamic-loading.

The PetscDLLibraryRegister_petscxxx functions have been kept, but are
not called unless -dynamic_library_preload is used. The petsc-dev
discussion, "Why --with-dynamic-loading?" did not reach consensus about
whether this was ever useful, so it may also be removable.

show more ...

PetscFE: Added auxiliary fields to PetscFEIntegrateJacobian()
- Hooked it up to DMPlexComputeJacobian()

DMPlex: ParMetis now working
- Ridiculous stub partition up front removed
- Metis does not return 0 on success, so fixed call

Merge remote-tracking branch 'origin/knepley/feature-plex-metis' into knepley/fix-plex-parmetis

* origin/knepley/feature-plex-metis:
DMPlex: remove unused variable
DMPlex: Put in METIS support

DMPlex: Changed DMPlexCreatePartition() to take the partitioner name

DMPlex: remove unused variable

DMPlex: Fix array length

DMPlex+PetscFE: Fix compile errors for complex
- LAPACK calls still broken

DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1)

Merge branch 'master' into knepley/feature-dt-fem

* master:
DMPlex: Fix 64-bit int problem in VTK
Mat: Fix for PetscSparseDenseMaxDot() for complex
Vec: Correct VecUniqueEntries() for 64-bit i

Merge branch 'master' into knepley/feature-dt-fem

* master:
DMPlex: Fix 64-bit int problem in VTK
Mat: Fix for PetscSparseDenseMaxDot() for complex
Vec: Correct VecUniqueEntries() for 64-bit indices
MatSeqAIJGetArrayF90: add man pages and fix typo in MatDense version
SF docs: add link to summary page and fix title
Doc: Fixed DM code in manual

show more ...

DMPlex: Fix 64-bit int problem in VTK

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c

show more ...

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
include/petscdmplex.h

show more ...

Merge branch 'knepley/plex-speed-tests' into knepley/feature-dt-fem

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need

Merge branch 'knepley/plex-speed-tests' into knepley/feature-dt-fem

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if array is passed in
DMPlex: Added special case for DMPlexVecSetClosure() - Could add more modes
DMPlex: Optimizations for DMPlexVecGetClosure() - Removed branch (seems to have little effect) - Removed calculation of size when array is provided (profiled for 20% effect)
DMPlex: Forgot one init for DMPlexVecGetClosure()
DMPlex: Must initialize argument to DMPlexVecGetClosure()
DMPlex ex9: Added ability to reuse array in VecGetClosure()
DMPlex: Allow DMPlexVecGetClosure() to take an input array
DMPlex: Fix bug in specialization of DMPlexVecGetClosure()
DMPlex: Bug fix for special case in DMPlexVecGetClosure()
DMPlex: Added optimization for depth 1 DMPlexVecGetClosure()
DMPlex ex9: Does not fail by default - Will turn back on failure once we calculate variance
SNES ex12: Cleaning up in preparation for speed testing
DMPlex: Added ex9 to test performance, put in depth 1 special case for TransitiveClosure

Conflicts:
config/builder.py
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/output/ex12_10.out
src/snes/examples/tutorials/output/ex12_11.out
src/snes/examples/tutorials/output/ex12_5.out
src/snes/examples/tutorials/output/ex12_6.out
src/snes/examples/tutorials/output/ex12_8.out
src/snes/examples/tutorials/output/ex12_9.out

show more ...

Merge branch 'knepley/plex-submesh-cohesive'

* knepley/plex-submesh-cohesive:
DMPlex: Fix hybrid bounds for interpolated mesh with cohesive cells
DMPlex: Fixes for cohesive label reconstruction

Merge branch 'knepley/plex-submesh-cohesive'

* knepley/plex-submesh-cohesive:
DMPlex: Fix hybrid bounds for interpolated mesh with cohesive cells
DMPlex: Fixes for cohesive label reconstruction - Do not put cohesive edges in labels - Do not reconstruct "depth" label
DMPlex: Now a label can be used to restrict the points for a cohesive submesh - Added label and value arguments to DMPlexCreateCohesiveSubmesh()

show more ...

Merge branch 'knepley/dm-view-partition'

* knepley/dm-view-partition:
SNES DMPlex examples: Can now just call VecView() for VTK viewer
DMPlex: If -dm_view_partition is given, a cell field with t

Merge branch 'knepley/dm-view-partition'

* knepley/dm-view-partition:
SNES DMPlex examples: Can now just call VecView() for VTK viewer
DMPlex: If -dm_view_partition is given, a cell field with the partition number is written in the ASCII VTK - Added DMPlexVTKWritePartition_ASCII

show more ...

Merge branch 'knepley/dm-view-partition' into knepley/feature-dt-fem

* knepley/dm-view-partition:
SNES DMPlex examples: Can now just call VecView() for VTK viewer
DMPlex: If -dm_view_partition i

Merge branch 'knepley/dm-view-partition' into knepley/feature-dt-fem

* knepley/dm-view-partition:
SNES DMPlex examples: Can now just call VecView() for VTK viewer
DMPlex: If -dm_view_partition is given, a cell field with the partition number is written in the ASCII VTK - Added DMPlexVTKWritePartition_ASCII

Conflicts:
src/snes/examples/tutorials/ex12.c

show more ...

Merge branch 'knepley/feature-dm-clone'

* knepley/feature-dm-clone:
DMPlex: Removed unused variables
DM: Dammit, forgot declaration
DM: Small fix to DMClone for DMPlex
DM: Added specializati

Merge branch 'knepley/feature-dm-clone'

* knepley/feature-dm-clone:
DMPlex: Removed unused variables
DM: Dammit, forgot declaration
DM: Small fix to DMClone for DMPlex
DM: Added specialization for DMCreateSubDM() with a PetscSection - Replace DMPlex implementation - Is used by DMDA when a section is defined
DM: Fix DMDA clone - Made it work for all dimensions (which makes DMCreateSubDM() work) - Removed DMSetUp() which should be called by caller
DM: Added DMClone() which makes a shallow copy - This is very useful for DM since it can have a lot of associated data and is used as a building block for different problems - This replaces DMPlexClone()

show more ...

Merge branch 'knepley/fix-3d-orientation'

* knepley/fix-3d-orientation:
DMPlex: Fix initialization for DMPlexVecGetClosure()
DMPlex: fix argument to DMPlexVecRestoreClosure
DMPlex: Fix orienta

Merge branch 'knepley/fix-3d-orientation'

* knepley/fix-3d-orientation:
DMPlex: Fix initialization for DMPlexVecGetClosure()
DMPlex: fix argument to DMPlexVecRestoreClosure
DMPlex: Fix orientation for VTU output
plex: remove unused variable
DMPlex: Fixed orientation conversion for VTK
DMPlex: Fixed field interpolation in tetrahedra and hexahedra for new orientation
DMPlex: Fixed face definition in tetrahedra and hexahedra for new orientation
DMPlex: Fixed point location in hexahedrons for new orientation
DMPlex: Added generic DMPlexInvertCell() to aid in changing orientation to the internal convention

show more ...

Merge branch 'knepley/fix-plex-geometry'

* knepley/fix-plex-geometry:
DMPlex: Now geometry tests can take an input mesh - Use Exodus format - Input all mesh data in options - Made builder runs for

Merge branch 'knepley/fix-plex-geometry'

* knepley/fix-plex-geometry:
DMPlex: Now geometry tests can take an input mesh - Use Exodus format - Input all mesh data in options - Made builder runs for 3 hexes
DMPlex: Test ex8 now runs interpolated tests separately - Added new builder runs
DMPlex: Added FVM geometry to interpolation test
DMPlex: FVM geometry was ignoring face orientation

show more ...

DMPlex: Fixed view

DMPlex+PetscFE: Looks like boundary integration is working
- DMComputeResidualFEM() checks for feBd, and does bd integral if present
- Normals are still not being calculated
- Added PetscFEIntegrateB

DMPlex+PetscFE: Looks like boundary integration is working
- DMComputeResidualFEM() checks for feBd, and does bd integral if present
- Normals are still not being calculated
- Added PetscFEIntegrateBdResidual() and a basic implementation
- Added normals to PetscCellGeometry
- Auxiliary fields not turned on in bd integrals

show more ...

DMPlex: Add plexrefine.c to makefile

DMPlex ex4: Had to turn off re-interpolation check for uniform refinement