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

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Ste

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

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Stefano
fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
MatSchurComplement: Must initialize KSP package
bib: fix inbook citation
Bib: Updated some refs
SNES: fix copy/paste in man page
fortran: fix KSPCONVERGEDDEFAULT and SNESCONVERGEDSKIP in fortran includes
Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used
PCGAMG: remove distracting comment
KSP ex49: restrict near-null space for elasticity example with sym BC
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
Fix accidental creation of the matrices in SNESNCG used for linear analogue LS.
PCGAMG: add man page for PCGAMGType
fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()
rm //
Sys: new_ir changed from PetscInt to PetscObjectState - so fix mallocs to use the new type
SNES: Fixed package init in SNESLineSearchCreate()
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex5.c
src/dm/impls/plex/plex.c
src/dm/interface/dm.c

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DMPlex: Added DMPlexCheckSymmetry() and DMPlexCheckSkeleton()
- These are diagnostic functions

Merge branch 'knepley/feature-closure-cache'

* knepley/feature-closure-cache:
DMPlex: Added declaration of DMPlexCreateClosureIndex()
SNES ex62: Use closure index
DMPlex: Use closure index if

Merge branch 'knepley/feature-closure-cache'

* knepley/feature-closure-cache:
DMPlex: Added declaration of DMPlexCreateClosureIndex()
SNES ex62: Use closure index
DMPlex: Use closure index if available for DMPlexVecGetClosure()
DMPlex: Added DMPlexCreateClosureIndex() - Uses a PetscSection+IS and stashes in the original Section
PetscSection: Added an index for optimization of closure queries - Added PetscSectionGet/SetClosureIndex() - The index is keyed to the DM which built it (use PetscObject) - Only use a single key for now since a lot of checking would be slow

Conflicts:
src/snes/examples/tutorials/ex62.c

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Merge branch 'knepley/feature-plex-generic-distribute'

* knepley/feature-plex-generic-distribute:
mpiuni: add in MPI_Type_f2c()
DMPlex: add missing declarations DMPlexDistribute{Field,Data}
bf

Merge branch 'knepley/feature-plex-generic-distribute'

* knepley/feature-plex-generic-distribute:
mpiuni: add in MPI_Type_f2c()
DMPlex: add missing declarations DMPlexDistribute{Field,Data}
bfort: update to using MPI_Type_f2c() [for plexf.c]
DMPlex: Added DMPlexDistributeData() to distribute arbitrary data types
DMPlex: Change DMPlexDistribute() to give back the PetscSF - This can be used to distribute sections and fields

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DMPlex: Added missing declarations

Merge branch 'knepley/feature-plex-generic-distribute' into knepley/feature-plex-reordering

The DMPlexDistribute interface changed to return a PetscSF.

* knepley/feature-plex-generic-distribute:

Merge branch 'knepley/feature-plex-generic-distribute' into knepley/feature-plex-reordering

The DMPlexDistribute interface changed to return a PetscSF.

* knepley/feature-plex-generic-distribute:
mpiuni: add in MPI_Type_f2c()
DMPlex: add missing declarations DMPlexDistribute{Field,Data}
bfort: update to using MPI_Type_f2c() [for plexf.c]
DMPlex: Added DMPlexDistributeData() to distribute arbitrary data types
DMPlex: Change DMPlexDistribute() to give back the PetscSF - This can be used to distribute sections and fields

Conflicts:
include/petscdmplex.h

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DMPlex: Added DMPlexCreateDoublet()

DMPlex: Added DMPlexCopyLabels()

Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreat

Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreate.c
src/dm/impls/mesh/section.c
src/snes/examples/tutorials/ex10.c
src/snes/examples/tutorials/ex12.c
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/ex62.c
src/snes/utils/mesh/dmmeshsnes.c

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Merge branch 'knepley/feature-plex-generic-distribute' into shri/projects-dmcircuit

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

DMPlex: add missing declarations DMPlexDistribute{Field,Data}

Fixes failing Fortran build.

Merge remote-tracking branch 'remotes/origin/knepley/feature-plex-generic-distribute' into shri/projects-dmcircuit

DMPlex: Change DMPlexDistribute() to give back the PetscSF
- This can be used to distribute sections and fields

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

* master: (124 commits)
SNES ex12: Fix buggy checkin
add missing output file src/snes/examples/tutorials/output/ex14_3.out
fixed bunch

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

* master: (124 commits)
SNES ex12: Fix buggy checkin
add missing output file src/snes/examples/tutorials/output/ex14_3.out
fixed bunch of bibtex items that should ahve used abbreviations only
PetscDualSpace: Pointer check barfs for function pointer
Sys: Add ability to turn off CUBLAS initialization - This continually SEGVs on my Air
SNES ex62: Updated test output - Matrix now prints attached nullspace indicator - 3D tests are wierdly different, they need to be verified by hand
SNES ex12: Updated test output - Mostly for completed labels
SNES ex12/62: Changed to new DMPlexProjectFunction() interface - Took DM out of main struct
SNES ex12/62: Complete boundary label - Puts in edges in 3D - Perhaps should be moved to the creation routine
PetscDualSpace: Fixed orientation of reference tetrahedron - Now this does not match FIAT
PetscDualSpace: Fixed numDof for P0
PetscDualSpace: Added PetscDualSpaceApply() for the action of a functional - Declared PetscDualSpaceGetFunctional()
DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection - Has not been tested with moment dofs - Accommodates vector functions
DMPlex: Added support for INSERT_BC_VALUES in VecSetClosure()
DMPlex: Fixed missing RestoreTransitiveClosure()
DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array
DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
DMPlex: Fix VecGetClosure() when the array is input
PetscFE: OpenCL is hardcoded for P0 coefficients right now
SNES ex12: Added test cases for variable coefficient Laplace - The P1 tests reproduce the analytic linear coefficient
...

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

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Merge branch 'knepley/feature-dt-fem'

* knepley/feature-dt-fem: (122 commits)
SNES ex12: Fix buggy checkin
PetscDualSpace: Pointer check barfs for function pointer
Sys: Add ability to turn off

Merge branch 'knepley/feature-dt-fem'

* knepley/feature-dt-fem: (122 commits)
SNES ex12: Fix buggy checkin
PetscDualSpace: Pointer check barfs for function pointer
Sys: Add ability to turn off CUBLAS initialization - This continually SEGVs on my Air
SNES ex62: Updated test output - Matrix now prints attached nullspace indicator - 3D tests are wierdly different, they need to be verified by hand
SNES ex12: Updated test output - Mostly for completed labels
SNES ex12/62: Changed to new DMPlexProjectFunction() interface - Took DM out of main struct
SNES ex12/62: Complete boundary label - Puts in edges in 3D - Perhaps should be moved to the creation routine
PetscDualSpace: Fixed orientation of reference tetrahedron - Now this does not match FIAT
PetscDualSpace: Fixed numDof for P0
PetscDualSpace: Added PetscDualSpaceApply() for the action of a functional - Declared PetscDualSpaceGetFunctional()
DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection - Has not been tested with moment dofs - Accommodates vector functions
DMPlex: Added support for INSERT_BC_VALUES in VecSetClosure()
DMPlex: Fixed missing RestoreTransitiveClosure()
DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array
DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
DMPlex: Fix VecGetClosure() when the array is input
PetscFE: OpenCL is hardcoded for P0 coefficients right now
SNES ex12: Added test cases for variable coefficient Laplace - The P1 tests reproduce the analytic linear coefficient
PetscFE: Added auxiliary fields to PetscFEIntegrateJacobian() - Hooked it up to DMPlexComputeJacobian()
SNES ex12: Removed code generation
...

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DMPlex: Added declaration of DMPlexCreateClosureIndex()

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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

* knepley/feature-dt-fem: (123 commits)
SNES ex12: Fix buggy checkin
Builder: strip test output before comparing
PetscDua

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

* knepley/feature-dt-fem: (123 commits)
SNES ex12: Fix buggy checkin
Builder: strip test output before comparing
PetscDualSpace: Pointer check barfs for function pointer
Sys: Add ability to turn off CUBLAS initialization - This continually SEGVs on my Air
SNES ex62: Updated test output - Matrix now prints attached nullspace indicator - 3D tests are wierdly different, they need to be verified by hand
SNES ex12: Updated test output - Mostly for completed labels
SNES ex12/62: Changed to new DMPlexProjectFunction() interface - Took DM out of main struct
SNES ex12/62: Complete boundary label - Puts in edges in 3D - Perhaps should be moved to the creation routine
PetscDualSpace: Fixed orientation of reference tetrahedron - Now this does not match FIAT
PetscDualSpace: Fixed numDof for P0
PetscDualSpace: Added PetscDualSpaceApply() for the action of a functional - Declared PetscDualSpaceGetFunctional()
DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection - Has not been tested with moment dofs - Accommodates vector functions
DMPlex: Added support for INSERT_BC_VALUES in VecSetClosure()
DMPlex: Fixed missing RestoreTransitiveClosure()
DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array
DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
DMPlex: Fix VecGetClosure() when the array is input
PetscFE: OpenCL is hardcoded for P0 coefficients right now
SNES ex12: Added test cases for variable coefficient Laplace - The P1 tests reproduce the analytic linear coefficient
PetscFE: Added auxiliary fields to PetscFEIntegrateJacobian() - Hooked it up to DMPlexComputeJacobian()
...

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Merge branch 'knepley/fix-test-output-parsing' into knepley/feature-dt-fem

* knepley/fix-test-output-parsing:
Builder: strip test output before comparing
DMPlex: ParMetis now working - Ridiculou

Merge branch 'knepley/fix-test-output-parsing' into knepley/feature-dt-fem

* knepley/fix-test-output-parsing:
Builder: strip test output before comparing
DMPlex: ParMetis now working - Ridiculous stub partition up front removed - Metis does not return 0 on success, so fixed call
DMPlex: Changed DMPlexCreatePartition() to take the partitioner name
DMPlex: remove unused variable
DMPlex: Put in METIS support

Conflicts:
config/builder.py

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Merge branch 'knepley/fix-test-output-parsing' into knepley/feature-plex-refine-3d

* knepley/fix-test-output-parsing:
Builder: strip test output before comparing
DMPlex: ParMetis now working - R

Merge branch 'knepley/fix-test-output-parsing' into knepley/feature-plex-refine-3d

* knepley/fix-test-output-parsing:
Builder: strip test output before comparing
DMPlex: ParMetis now working - Ridiculous stub partition up front removed - Metis does not return 0 on success, so fixed call
DMPlex: Changed DMPlexCreatePartition() to take the partitioner name
DMPlex: remove unused variable
DMPlex: Put in METIS support

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Merge branch 'knepley/fix-plex-parmetis'

* knepley/fix-plex-parmetis:
DMPlex: ParMetis now working - Ridiculous stub partition up front removed - Metis does not return 0 on success, so fixed call

Merge branch 'knepley/fix-plex-parmetis'

* knepley/fix-plex-parmetis:
DMPlex: ParMetis now working - Ridiculous stub partition up front removed - Metis does not return 0 on success, so fixed call
DMPlex: Changed DMPlexCreatePartition() to take the partitioner name
DMPlex: remove unused variable
DMPlex: Put in METIS support

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Merge branch 'knepley/fix-cublas-init' into knepley/feature-dt-fem

* knepley/fix-cublas-init:
Sys: Allow CUBLAS init to be turned off - This causes SEGV on my Air all the time
DMPlex: Removed de

Merge branch 'knepley/fix-cublas-init' into knepley/feature-dt-fem

* knepley/fix-cublas-init:
Sys: Allow CUBLAS init to be turned off - This causes SEGV on my Air all the time
DMPlex: Removed dead declaration (thanks Lisandro)
added citation for superlu99

Conflicts:
src/sys/objects/pinit.c

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