DMPlex: fix parent/child interpolation with numFields > 0

There were several instances of off-by-one errors that had not been tested before but are tested now

DMPlex: construct the correct l2gmap for MatIS using the subdomainSection (for local indexing) and the globalSection

Update ComputeJacobian to set the closure in the local matrix

Plex: Added PetscDraw support

DMPLEX: filling the matrix during preallocation will generate MAT_NEW_NONZERO_ALLOCATION_ERR (on the local matrices) with MATIS

In order to be set up properly, MATIS needs to know the l2gmap before any preallocation

The communicator for the l2gmap provided by the DM should be the same of the DM

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary c

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary commitid] - and dirname in tarball
Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES
CUDA: Added external declaration for cuBLAS handle.
docs: fix reference to KSP_Create in parent commit
Add information on PETSC_EXTERN and PETSC_INTERN to developers manual
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Configure: Fix check for spaces in PETSC_DIR
Plex: Updated examples to new DMPlexCreateBoxMesh()
sick of failure due to incorrect master branch
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Examples that require Fortran to compile but were listed in tests that did not require Fortran
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
...

Conflicts:
src/dm/impls/plex/makefile
src/snes/utils/dmplexsnes.c

show more ...

Merge branch 'knepley/fix-plex-mf-prec'

* knepley/fix-plex-mf-prec: (26 commits)
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Plex: Updated examp

Merge branch 'knepley/fix-plex-mf-prec'

* knepley/fix-plex-mf-prec: (26 commits)
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Plex: Updated examples to new DMPlexCreateBoxMesh()
TS ex11: Fixed output for new ROSW
Plex: Forgot internal declaration
Plex: Fixed ComputeIntegral() to work with FVM - May still have a bug, not sure
Plex: Fixed ResconstructGradients_Internal() to take an FVM and to work in multifield problems - ApplyLimiter_Internal() now can limit an FV field within a multifield problem
PetscFV: Added -petscfv_compute_gradients
SNES ex12: Fixed output for NGS
PetscDS: Added GetFieldIndex() and GetFieldSize() - Fix to accept FV as well
Plex: Forgot to eliminate PetscRealPart() after type change
Plex: fix line geometry for localized
Plex: fix section access to last commit
DMPlex: fix rectanlge geometry for localized
DMConvert_p4est_plex: set projection height early, so it passes to coordinate dm
DMLocalizeCoordinates(): make more flexible and targeted
Plex: When forming Jacobian, just use identity for FV fields
Plex+FE: Added missing FV dual space
PetscFE: If all Jac pointwise functions are NULL, do not evaluate
DMP4est: change order of setting projection height and localizing coordinates
...

show more ...

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

Merge branch 'master' into barral/feature-dmplex-adapt

Merge branch 'tisaac/dmp4est-set-periodic-domain' into knepley/fix-plex-mf-prec

* tisaac/dmp4est-set-periodic-domain:
Plex: fix line geometry for localized
Plex: fix section access to last commi

Merge branch 'tisaac/dmp4est-set-periodic-domain' into knepley/fix-plex-mf-prec

* tisaac/dmp4est-set-periodic-domain:
Plex: fix line geometry for localized
Plex: fix section access to last commit
DMPlex: fix rectanlge geometry for localized
DMConvert_p4est_plex: set projection height early, so it passes to coordinate dm
DMLocalizeCoordinates(): make more flexible and targeted
DMP4est: change order of setting projection height and localizing coordinates
DMP4est: prefer [0,L) for periodic coordinates
Plex: more descriptive debugging

show more ...

Merge branch 'master' into knepley/fix-plex-mf-prec

* master:
GAMG: Fix nearnullspace check
Plex: Must check block size in parallel from DMGetLocalToGlobalMapping() - Small format cleanup
Mov

Merge branch 'master' into knepley/fix-plex-mf-prec

* master:
GAMG: Fix nearnullspace check
Plex: Must check block size in parallel from DMGetLocalToGlobalMapping() - Small format cleanup
Move spinlocks definitions to pinit.c, where they don't depend on PETSC_HAVE_FORTRAN
Allow empty data
Update output files after change in PetscObjectPrintClassNamePrefixType
Deactivate tabs when printing several things in the same line

show more ...

Merge branch 'tisaac/dmplex-localize-targeted' into tisaac/dmp4est-set-periodic-domain

* tisaac/dmplex-localize-targeted:
DMLocalizeCoordinates(): make more flexible and targeted
GAMG: Fix nearn

Merge branch 'tisaac/dmplex-localize-targeted' into tisaac/dmp4est-set-periodic-domain

* tisaac/dmplex-localize-targeted:
DMLocalizeCoordinates(): make more flexible and targeted
GAMG: Fix nearnullspace check
Move spinlocks definitions to pinit.c, where they don't depend on PETSC_HAVE_FORTRAN
Allow empty data
Update output files after change in PetscObjectPrintClassNamePrefixType
Deactivate tabs when printing several things in the same line

show more ...

DMLocalizeCoordinates(): make more flexible and targeted

More flexible because methods that do calculations on facets might need
to localize them as well. This information can be passed to the
coor

DMLocalizeCoordinates(): make more flexible and targeted

More flexible because methods that do calculations on facets might need
to localize them as well. This information can be passed to the
coordinate DM with DMPlexSetMaxProjectionHeight().

More targeted by only localizing cells/points that are needed. If I'm
localizing cells _and_ facets, then that's a lot of indiscriminate
localizing, when I only need it for a lower dimensional manifold.

show more ...

Merge branch 'knepley/fix-plex-mat-bs'

* knepley/fix-plex-mat-bs:
Plex: Must check block size in parallel from DMGetLocalToGlobalMapping() - Small format cleanup

Plex: Must check block size in parallel from DMGetLocalToGlobalMapping()
- Small format cleanup

Plex: Do not use existing Mat block size when it is 1

Merge branch 'knepley/fix-plex-namespace'

* knepley/fix-plex-namespace: (24 commits)
PlexTree: Fixed declaration for function which produce indices for assembly
Plex: Forgot to zero out Jacobian

Merge branch 'knepley/fix-plex-namespace'

* knepley/fix-plex-namespace: (24 commits)
PlexTree: Fixed declaration for function which produce indices for assembly
Plex: Forgot to zero out Jacobian
Plex: Changed every *_Internal() function to PETSC_INTERN - Except the residual and Jacobian computation which should not be internal
Plex: Fixed declaration for function which produce indices for assembly
Plex: clarify precedence
DMForest tests ex2: typo fixes
DMP4est: cleanup for DMForestTransferVec()
DMP4est: fixes to DMPlexTranserVecTree_Inject()
DMP4est: fixes to DMPlexTranserVecTree_Interpolate()
DMPlex: correct usage of PetscSFCreateEmbeddedLeafSF()
DMP4est: address extra vertices in transfers
DMP4est: address missing vertices in transfers
DMP4est: fix array initialization
DMP4est: fix interface to nonuniform refinement
DMP4est: interface to nonuniform refinement
DMForest test ex2: leave data until end for debugging
DMForest: added test for DMForestTransferVec()
Plex: first pass at tree transfer interpolator. FVM missing
Plex: finish first pass at injection component of transer
DMPlex: further refactoring in injection code
...

show more ...

Merge branch 'knepley/fix-plex-bs'

* knepley/fix-plex-bs:
Plex: deal correctly with off-process dof when calculating block size
Plex: Fix default partition weighting
Plex: Fix support for ADD_

Merge branch 'knepley/fix-plex-bs'

* knepley/fix-plex-bs:
Plex: deal correctly with off-process dof when calculating block size
Plex: Fix default partition weighting
Plex: Fix support for ADD_BC_VALUES
Plex: Allow incoming blocksize in DMCreateMatrix()
Plex: Fix for blocksize in preallocation
Plex: Fix blocksizes determination in ltog mapping
Plex: Set block size regardless of whether the Mat has block storage

show more ...

Plex: deal correctly with off-process dof when calculating block size

Plex: Fixed declaration for function which produce indices for assembly

Merge branch 'knepley/fix-plex-bs' into knepley/fix-plex-namespace

* knepley/fix-plex-bs:
Plex: Fix default partition weighting
Plex: Fix support for ADD_BC_VALUES
Plex: Allow incoming blocksi

Merge branch 'knepley/fix-plex-bs' into knepley/fix-plex-namespace

* knepley/fix-plex-bs:
Plex: Fix default partition weighting
Plex: Fix support for ADD_BC_VALUES
Plex: Allow incoming blocksize in DMCreateMatrix()
Plex: Fix for blocksize in preallocation
Plex: Fix blocksizes determination in ltog mapping
Plex: Set block size regardless of whether the Mat has block storage

show more ...

Plex: Fix support for ADD_BC_VALUES

Plex: Allow incoming blocksize in DMCreateMatrix()

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()
Update the xSDKTrilinos test message to use interactive session and ctest
gcc6: fix comple warnings with -Wmisleading-indentation
fix compile warning
bugfix for MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable()
minor formatting cleanup of gamg.c
add ml example to tutorials page for xsdk
bugfix of MatDuplicate for mpiaij matrix product Reported-by: Miorelli, Federico <Federico.Miorelli@cgg.com>
The deprecated -log_summary_exclude was still being used when it should have been -log_exclude
cpardiso: requires mkl_blacs so check for that. Also common code to detect MKL for both pardiso and cpardiso
cpardiso: fix segv and memory leaks
resume MatGetSubMatrix_SeqSBAIJ() because it cannot share routine with BAIJ due to cast
fix bad relative links
replace MatSeqBAIJSetPreallocation_SeqBAIJ with MatSeqBAIJSetPreallocation to skip this call when input mat is sbaij type
fix a variety of set but not used variables in examples detected by clang static analyzer
removed declared but not used variable
ANL Report formatting requires listing authors by affiliation
DMP4est: uncrustify
DMP4est: remove memset()
...

show more ...

Plex: Set block size regardless of whether the Mat has block storage