Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Plex: Fixing up DMPlexComputeIntegralFEM()
- FVM does not break this function now
- Added Integral event
- Added Allreduce over procs

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

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

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'tisaac/simplify-register-all'

Removed the XXXRegisterAll() functions from the public interface. These should now only be handled by the package intialization functions.

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

Merge branch 'mlange/fix-plex-distribute-perf-logging'

* mlange/fix-plex-distribute-perf-logging:
Plex: Log performance for DMPlexMigrate and DMPlexDistributeOverlap

Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Plex: Log performance for DMPlexMigrate and DMPlexDistributeOverlap

Remove XXXRegisterAllCalled from public interface.

All XXXRegisterAll() methods are now idempotent, so a boolean indicating
whether they can be called or not is no longer necessary.

Merge branch 'master' into knepley/fix-plex-examples-refinement

* master: (62 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of

Merge branch 'master' into knepley/fix-plex-examples-refinement

* master: (62 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of infrastructure I think
Plex ex12: Fix output after label distribution fix
Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it
TS ex11: Since DMPlexDistribute() calls SetFromOptions(), do not call it again, and cleaned up tests
Plex+FV: If using FVM adjacency, do not create ghost cells for faces in the overlap, or set BC on them
Plex: If using FVM adjacency, we must include the closure in the overlap
Plex+Label: All processes with a valid label should participate in label distribution - Formerly it was just proc 0
Plex: Add check that parallel renumbering fully covers the cone points
Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap
Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()
Plex: Preallocation fixes for indegree > 1 - Again this should be rewritten
SNES ex62: Changes to output for fixes with quads
Plex+Label: Set default output flag to PETSC_TRUE
Plex ex1: Fixed LaTeX output
Plex ex12: Fixed overlap test
Plex: Fixed incorrect usage of PetscSFGatherBegin/End() in preallocation - This should be rewritten using new style
PetscSF: Incorrect check for computed degrees
Builder: Fix bad search and replace
Configure: Fix for Barry's change to organization - I do not know what happened here
Builder: Fix for Barry's change
...

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

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Merge branch 'mlange/feature-parallel-distribute'

* mlange/feature-parallel-distribute: (33 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would

Merge branch 'mlange/feature-parallel-distribute'

* mlange/feature-parallel-distribute: (33 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of infrastructure I think
Plex ex12: Fix output after label distribution fix
Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it
TS ex11: Since DMPlexDistribute() calls SetFromOptions(), do not call it again, and cleaned up tests
Plex+FV: If using FVM adjacency, do not create ghost cells for faces in the overlap, or set BC on them
Plex: If using FVM adjacency, we must include the closure in the overlap
Plex+Label: All processes with a valid label should participate in label distribution - Formerly it was just proc 0
Plex: Add check that parallel renumbering fully covers the cone points
Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap
Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()
Plex: Preallocation fixes for indegree > 1 - Again this should be rewritten
SNES ex62: Changes to output for fixes with quads
Plex ex1: Fixed LaTeX output
Plex ex12: Fixed overlap test
Plex: Fixed incorrect usage of PetscSFGatherBegin/End() in preallocation - This should be rewritten using new style
PetscSF: Incorrect check for computed degrees
Builder: Fix for Barry's change
PetscSF: Fixes for sparse leaves - When sf->mine exists, the leaves can be numbered non-sequentially. This causes allocation based upon sf->nleaves to underallocate. Replacing sf->nleaves with the maximum leaf number is sufficient in this case.
Plex: Fix leaks
Configure: How did this break?
...

Conflicts:
config/builder.py

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Merge branch 'knepley/feature-plex-partitioner-shell'

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Added DMPlexCreateFromFile() - Dispatches to

Merge branch 'knepley/feature-plex-partitioner-shell'

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Added DMPlexCreateFromFile() - Dispatches to the right constructor based on extension
Plex ex1: Added test partitioner
Plex: Added DMPlexGetPartitioner() and PetscPartitionerShellSetPartition()
PetscSection: Added PetscSectionCopy()
Plex ex1: Cleaned up mesh creation - Now use -dm_refine for uniform refinement
Plex: Remove superfluous argument from DMPlexDisitrbute()
Plex: Fixed Fortran stub
PetscFV: Lots of small naming fixes
Partitioner+Plex: Added PetscPartitioner class - Plex holds a PetscPartitioner - Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition) - Now partition routine takes a number of partitions instead of assuming commSize - Added a shell partitioner intended to be used for regression testing

Conflicts:
src/dm/impls/plex/examples/tests/ex1.c

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Plex: Add performance and debug logging

Merge branch 'knepley/feature-plex-partitioner-shell' into mlange/feature-parallel-distribute

Partitioner+Plex: Added PetscPartitioner class
- Plex holds a PetscPartitioner
- Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition)
- Now partition routine

Partitioner+Plex: Added PetscPartitioner class
- Plex holds a PetscPartitioner
- Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition)
- Now partition routine takes a number of partitions instead of assuming commSize
- Added a shell partitioner intended to be used for regression testing

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Merge branch 'knepley/feature-quad-fas'

* knepley/feature-quad-fas:
DMPlex: Proper preallocation for interpolators
DMPlex: Added events for interpolator and injector construction - Fixed event n

Merge branch 'knepley/feature-quad-fas'

* knepley/feature-quad-fas:
DMPlex: Proper preallocation for interpolators
DMPlex: Added events for interpolator and injector construction - Fixed event names
DM: Added sequence value for each number - Added DMOutputSequenceLoad() - Changed DMGet/SetOutputSequenceNumber() signature
Sys: Made a simple two-int hash - Someone should remove that other IJ crap
PetscDS: Renamed from PetscProblem
DMPlex: Fixed allocation
DMPlex: Support for injection from more complicated discretizations - Added DMPlexMatGetClosureIndicesRefined() - Added DMPlexComputeInjectorFEM() - Fixed check
PetscFE: Use in-cell test specific to cell shape
DMPlex: Added CellRefinerInCellTest_Internal()

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DMPlex: Added events for interpolator and injector construction
- Fixed event names

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

Merge branch 'knepley/feature-problem-class'

* knepley/feature-problem-class: (40 commits)
PetscDS: Renamed from PetscProblem
ftn-types: fix compilers errors with PetscSection [remove duplicate

Merge branch 'knepley/feature-problem-class'

* knepley/feature-problem-class: (40 commits)
PetscDS: Renamed from PetscProblem
ftn-types: fix compilers errors with PetscSection [remove duplicate code from petscvec*.h90]
PetscSection: Fix Fortran datatypes support
DMPlex: Added quads to cell refiner transform support
DMPlex ex3: Updated to Problem interface
DMDA: Fixed FE projection functions
PetscSection: Fixes for Fortran stubs
DMPlex+TS+Doc: Function docs
PetscSection: Fortran bindings
DMPlex+HDF5: Had revered handedness of transformed periodic coordinates
DMPlex+HDF5: Preserve aspect ratio with remapping of periodic coordinates
DMPlex: Added missing declarations
Sys+DMDT: Added PetscValidFunction()
DMPlex: Fix for DMPlexProjectField()
DMPlex+HDF5: Selectively output fields for viz - Fields with NULL name are ignored
PetscSection: Allow NULL names
DMPlex: Fixes for DMPlexProjectField()
PetscProblem: Added scalar integral (objective function) - Added PetscProblemGet/SetObjective() - Used in PetscFEIntegrate() - Reworked PetscProblemEnlarge_Static()
DM+DT: Adding Fortran bindings
PetscViewer: Added HDF_VIZ format to names
...

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Merge branch 'knepley/feature-problem-class' into knepley/feature-quad-fas

* knepley/feature-problem-class:
PetscDS: Renamed from PetscProblem
ftn-types: fix compilers errors with PetscSection [

Merge branch 'knepley/feature-problem-class' into knepley/feature-quad-fas

* knepley/feature-problem-class:
PetscDS: Renamed from PetscProblem
ftn-types: fix compilers errors with PetscSection [remove duplicate code from petscvec*.h90]

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Merge branch 'knepley/feature-problem-class' into knepley/fix-fe-gpu

* knepley/feature-problem-class:
PetscDS: Renamed from PetscProblem
ftn-types: fix compilers errors with PetscSection [remove

Merge branch 'knepley/feature-problem-class' into knepley/fix-fe-gpu

* knepley/feature-problem-class:
PetscDS: Renamed from PetscProblem
ftn-types: fix compilers errors with PetscSection [remove duplicate code from petscvec*.h90]
PetscSection: Fix Fortran datatypes support
DMPlex: Added quads to cell refiner transform support
DMPlex ex3: Updated to Problem interface
DMDA: Fixed FE projection functions

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PetscDS: Renamed from PetscProblem

Merge branch 'knepley/feature-problem-class' into knepley/feature-quad-fas

* knepley/feature-problem-class: (38 commits)
PetscSection: Fix Fortran datatypes support
DMPlex: Added quads to cell r

Merge branch 'knepley/feature-problem-class' into knepley/feature-quad-fas

* knepley/feature-problem-class: (38 commits)
PetscSection: Fix Fortran datatypes support
DMPlex: Added quads to cell refiner transform support
DMPlex ex3: Updated to Problem interface
DMDA: Fixed FE projection functions
PetscSection: Fixes for Fortran stubs
DMPlex+TS+Doc: Function docs
PetscSection: Fortran bindings
DMPlex+HDF5: Had revered handedness of transformed periodic coordinates
DMPlex+HDF5: Preserve aspect ratio with remapping of periodic coordinates
DMPlex: Added missing declarations
Sys+DMDT: Added PetscValidFunction()
DMPlex: Fix for DMPlexProjectField()
DMPlex+HDF5: Selectively output fields for viz - Fields with NULL name are ignored
PetscSection: Allow NULL names
DMPlex: Fixes for DMPlexProjectField()
PetscProblem: Added scalar integral (objective function) - Added PetscProblemGet/SetObjective() - Used in PetscFEIntegrate() - Reworked PetscProblemEnlarge_Static()
DM+DT: Adding Fortran bindings
PetscViewer: Added HDF_VIZ format to names
PetscFE+OpenCL: Make more respectable elasticity
PetscFE+OpenCL: Add flag for printing kernel
...

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