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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Merge branch 'barry/dmvecmattypes'

The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.

* barry/dmvecm

Merge branch 'barry/dmvecmattypes'

The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.

* barry/dmvecmattypes:
DMPlex ExodusII: fix dm->vectype pointer syntax
removed use of VecSetFromOptions() all over the placed, instead use MatGetVecs() or use dm->vectype to determine type added DMGetVecType() and DMGetMatTYpe()
removed MatType argument from DMCreateMatrix() and DMCreateColoring() since information is obtained from DM

Conflicts:
src/dm/impls/da/fdda.c
src/dm/impls/plex/plex.c

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Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-d

Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-dynamic-loading-option:
Sys: PetscContainerCreate must call PetscSysInitializePackage
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

Conflicts:
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/docs/website/documentation/changes/dev.html

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DMPlex: fix my mistake using NULL in place of (int) 0

doc: restore functions in PETSc zero their arguments

This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use

doc: restore functions in PETSc zero their arguments

This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use of arrays after restoration is invalid.

Suggested-by: Wolfgang Bangerth <bangerth@math.tamu.edu>

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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 'master' into barry/wirth-fusion-materials

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

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

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

Merge branch 'knepley/fix-label-partition'

* knepley/fix-label-partition:
DMPlex: Replaced algorithm for label distribution with one that does not suck - Need more tests

Merge branch 'knepley/fix-hybrid-distribution'

* knepley/fix-hybrid-distribution:
DMPlex: Better fix for distribution of hybrid bounds - Bounds are now computed from the reordering at distribution

Merge branch 'knepley/fix-hybrid-distribution'

* knepley/fix-hybrid-distribution:
DMPlex: Better fix for distribution of hybrid bounds - Bounds are now computed from the reordering at distribution time - Still incomplete since we need to compute the interpolated bounds after interpolation
DMPlex: Temporary fix for handling hybrid meshes in parallel - Try to compute the hybrid structure - Should really send it out with Distribute()

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

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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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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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DMPlex: Replaced algorithm for label distribution with one that does not suck
- Need more tests

removed use of VecSetFromOptions() all over the placed, instead use MatGetVecs() or use dm->vectype to determine type
added DMGetVecType() and DMGetMatTYpe()

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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DMPlex: Use closure index if available for DMPlexVecGetClosure()

DMPlex: Added DMPlexCreateClosureIndex()
- Uses a PetscSection+IS and stashes in the original Section

removed MatType argument from DMCreateMatrix() and DMCreateColoring() since information is obtained from DM