Plex: Forgot to zero out Jacobian

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 ...

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'knepley/fix-plex-blocksize'

* knepley/fix-plex-blocksize:
Plex ex12: Mark p4est requirements
Plex: Fix line geometry - There was a bad dependency
Plex: Fix FVM geometry - There w

Merge branch 'knepley/fix-plex-blocksize'

* knepley/fix-plex-blocksize:
Plex ex12: Mark p4est requirements
Plex: Fix line geometry - There was a bad dependency
Plex: Fix FVM geometry - There was a bad dependency
Plex: Fixed possibly bad access
PetscFE: Fixed missing initializations
PetscFE: PetscDualSpaceGetNumDof() can no longer return NULL - Had to implement it for Simple dual space
DM: Protect possibly NULL input
Plex: Fixed parallel block size for DM matrix
DM: Fixed block size for LocalToGlobal mapping with PetscSection

Conflicts:
config/builder.py

show more ...

Plex: Fix line geometry
- There was a bad dependency

Plex: Fix FVM geometry
- There was a bad dependency

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'tisaac/dm-locate-points-sf'

* tisaac/dm-locate-points-sf:
Plex: missed in IS
DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

Merge branch 'sanderarens/fix-plex-neumann-bc'

* sanderarens/fix-plex-neumann-bc:
SNES ex77: Test now passing - Fixed memory leak - Use parser for numeric output
SNES ex77: Added test from Sande

Merge branch 'sanderarens/fix-plex-neumann-bc'

* sanderarens/fix-plex-neumann-bc:
SNES ex77: Test now passing - Fixed memory leak - Use parser for numeric output
SNES ex77: Added test from Sander - Does not work yet
SNES ex77: add small penalty term to Lagrangian density. This speeds up the linear solver convergence a lot and also allows for larger pressure loadings.
SNES ex62: Fixed output for proper block sizes
DM: pass down block size to subIS when creating a subDM.
SNES ex77: delete some unused variables.
SNES ex77: call DMPlexLabelComplete for correct Dirichlet bc's.
SNES+Plex: Add checks for valid IS after calls to DMLabelGetStratumIS.
SNES ex77: check if IS from DMGetStratumIS is a valid pointer as it can be NULL if used in parallel.
SNES: Add ex77: nonlinear elasticity with pressure loading
Plex: R should be a proper rotation from \hat z to n
SNES+Plex: Allow for multiple label values per boundary condition in BdResidual/BdJacobian
SNES+Plex: Fix the dimensions in BdResidual/BdJacobian

show more ...

Plex: R should be a proper rotation from \hat z to n

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping cells, it's clearer which
in which process/cell the point is located.
- A natural next step after DMLocatePoints() is to send each point to
its cell for some local computation. With a PetscSF this is easy with
PetscSFGatherBegin()/PetscSFGatherEnd().

show more ...

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

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
...

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

show more ...

Merge branch 'knepley/fix-plex-point-location'

* knepley/fix-plex-point-location:
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logg

Merge branch 'knepley/fix-plex-point-location'

* knepley/fix-plex-point-location:
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static

show more ...

Plex: Add info for grid hashing

Merged petsc/petsc into master

const fixes for win32 warnings - related to 081a2d76edd0f29fad78624936ea4a95a96da0e2

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelG

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
Plex ex12: Fixed variable initialization and some output
Plex ex11: Added error checking
Plex ex14: Now boundary label does not have cells
Plex ex1: Now boundary label does not have cells
Plex ex1: Fix for VTK format
added some debugging code, getting ready to branch
added some print statements, should be an -info...
smome cleaning up
restructured ex11 to allow for problem specific BCs
DMPlex: Update test ex12_5 with correct level-2 overlap
DMPlex: Use global processSF in DMPlexPartitionInvert
DMPlex: Add remote leaf contributions to roots in DMLabelPropagate
DMPlex: Add DMLabelGather to migrate label values from leafs to roots
DMPlex: Refactor DMLabelDistribute to separate point stratum distribution
DMPlex: Add propagation of remote point donations for multi-level overlap
DMPlex: Fix DMLabelDistribute for all-to-all migrations
Plex: make extern exactly match prototype: semantic match is not enough.
DMP4est: typo fix
...

show more ...

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/imp

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

show more ...

Merge branch 'tisaac/dmforest' into mlange/fix-plex-multi-level-overlap

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_5.out
src/dm/label/dmlabel.c

Merge branch 'master' into barry/add-pcfieldsplit-logevent

DM: Promote DMPlexLocalizeCoordinates --> DMLocalize coordinates
- There is one small problem here in that the iteration still needs Plex-like things. This will be rewritten to use a projection rathe

DM: Promote DMPlexLocalizeCoordinates --> DMLocalize coordinates
- There is one small problem here in that the iteration still needs Plex-like things. This will be rewritten to use a projection rather than Plex, but right now we need it for the magma presentation.

show more ...

Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

Merge remote-tracking branch 'origin/tisaac/dm-label-promote'

* origin/tisaac/dm-label-promote:
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all

Merge remote-tracking branch 'origin/tisaac/dm-label-promote'

* origin/tisaac/dm-label-promote:
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all DMs
builder: update regression tests
builder: update some missing package requirements
DM: set coordinate vector name
ts tutorials ex11_sa: make it compile

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

show more ...

Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master