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 '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

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

Plex: Log performance for DMPlexMigrate and DMPlexDistributeOverlap

Merge branch 'master' into barry/experiment

Merge branch 'pr245/mapdes/dmcreateinjection-mat'

Merge branch 'tisaac/feature-gamg-extensible' into barry/experiment

Conflicts:
src/ksp/pc/impls/gamg/gamg.h

Merge branch 'knepley/feature-ts-fem+fvm-example'

* knepley/feature-ts-fem+fvm-example: (32 commits)
Plex: Fix printf
Plex: Use DMGetCoordinateDim() instead of a calculation
Plex: Added routin

Merge branch 'knepley/feature-ts-fem+fvm-example'

* knepley/feature-ts-fem+fvm-example: (32 commits)
Plex: Fix printf
Plex: Use DMGetCoordinateDim() instead of a calculation
Plex: Added routine to view geometry
TS ex18: Added new tests
TS ex18: Updated test output
TS ex18: Add support for functionals
TS ex18: Global field offsets depend on the point since we allow constraints
TS ex18: Move view to after LocalizeCoordinates()
Plex+HDF5: Fixed uninitialized variable
TS ex18: Advection tests working
Plex: Fixed integration with Toby's code that handles sub manifold interpolation - Needed to check for cEndInterior from adding ghost cells
TS ex18: Updated output
TS ex18: Trying out implicit and explicit TS - Added another test with implicit TS
TS ex18: Updated output
SNES ex62: Updated output for new Plex distribution
Plex: Fix leak - No need for extra BC copy
TS ex18: All examples now working - Added ability to use zero velocity - Fixed coordinate localization
TS ex18: Cast boundary values function
TS ex18: Fixes outflow boundary condition - Must index into vector of all field values
TS ex18: Added another advection test
...

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Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
Plex: Preserve periodicity

Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
Plex: Preserve periodicity when adding ghost cells
Plex: Fixed DMPlexGetGlobalFieldOffset_Private() in optimized mode
Plex+SNES: Offset should be into field components, not basis functions
Plex+SNES: Add guards for optional arrays
DS: Added PetscDSGetComponentOffset(), Added to petsc.h
Plex+TS: FVM RHS computation uses a global F
Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term
Plex: Added DMPlexPointGlobalFieldRead/Ref()
Plex+SNES: Fixed DMPlexGetFaceFields() - It returns field values, not coefficients - FE evaluation is now done
FV: In PetscFVIntegrateRHSFunction(), the arguments are field values, not coefficients
FE: Added EvaluateFaceFields() to FE fields at face centroids
Plex: Added DMPlexPointLocalFieldRead()
FE: Have a standard tabulation at face centroids
Plex: Copy BC for hierarchical refinement
FE: Allow P0 over 1D cells
Plex+FV: Fixed BC with gradient calculation
Plex ex1: Move overlap computation after SetFromOptions
Plex: DMPlexDistribute() no longer calls DMSetFromOptions() - Fixed examples
...

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Plex: Fix printf

Plex: Added routine to view geometry

Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Doe

Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Does SF stratification by depth, not by dimension - The old code numbered cells after vertices
Plex+SNES: Fixes for nonzero cStart
cannot call PetscObjectGetName() on a subset of the MPI processes
MatView() with some matrix formats and ASCII_MATLAB did not print correct matrix name
Plex: Preserve periodicity when adding ghost cells
Plex: Fixed DMPlexGetGlobalFieldOffset_Private() in optimized mode
Plex+SNES: Offset should be into field components, not basis functions
Plex+SNES: Add guards for optional arrays
DS: Added PetscDSGetComponentOffset(), Added to petsc.h
Plex+TS: FVM RHS computation uses a global F
Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term
Plex: Added DMPlexPointGlobalFieldRead/Ref()
Plex+SNES: Fixed DMPlexGetFaceFields() - It returns field values, not coefficients - FE evaluation is now done
FV: In PetscFVIntegrateRHSFunction(), the arguments are field values, not coefficients
FE: Added EvaluateFaceFields() to FE fields at face centroids
Plex: Added DMPlexPointLocalFieldRead()
FE: Have a standard tabulation at face centroids
Plex: Copy BC for hierarchical refinement
FE: Allow P0 over 1D cells
Plex+FV: Fixed BC with gradient calculation
...

Conflicts:
config/builder.py

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Plex: Fixes for default section creation
- Cannot assume the DM has numFields fields
- Must calculate the total dof per point since not all points are the same anymore

Plex: When creating default section, only FE should ignore hybrid cells

FE+FV: When mixing, FE should ignore hybrid (ghost) cells which FV uses for BC, and FV should evaluate on cells
- When creating default section, FE should not run over hybrid cells
- In DMPlexCompute

FE+FV: When mixing, FE should ignore hybrid (ghost) cells which FV uses for BC, and FV should evaluate on cells
- When creating default section, FE should not run over hybrid cells
- In DMPlexComputeResidual_Internal(), FE should not run over hybrid cells
- In EvaluateFieldJets(), FV does cellwise constant evaluation (should work in linear but demands per cell lookup which should be worked into the interface)
- In DMPlexProjectFunctionLabelLocal(), DMProejctFunctionLocal(), DMProjectFieldLocal(), DMPlexComputeL2Diff(), DMPlexComputeL2GradientDiff(), DMPlexComputeL2FieldDiff(), DMPlexComputeIntegralFEM(), DMPlexCompute InterpolatorFEM(), and DMPlexComputeInjectorFEM(), do not loop over hybrid cells
- Protect use of ghost label in DMPlexComputeGeometryFVM()

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Plex: Fix section creation for FVM

DMCreateInjection: return Mat rather than VecScatter

For (amongst others) FV discretisations, the natural injection may well
be cell averaging, which is not expressible as a VecScatter.

Merge branch 'shri/dmplex-add-mat-localtoglobalmapping'

Merge branch 'master' into barry/ksp-converged-reason-viewer

Conflicts:
src/sys/objects/options.c

Merge branch 'mlange/refactor-plex-distribute'

* mlange/refactor-plex-distribute: (31 commits)
Plex: MS compilers do not allow declarations in the middle of a block
DMLabel: Add DMLabelMakeAllVa

Merge branch 'mlange/refactor-plex-distribute'

* mlange/refactor-plex-distribute: (31 commits)
Plex: MS compilers do not allow declarations in the middle of a block
DMLabel: Add DMLabelMakeAllValid_Private
Plex ex12: Add fixed re-partitioning for load balance test
DMLabel: Validate/build point arrays per stratum
Plex: Remove obsolete partitioning routines
Plex: Fix deadlock in DMPlexCreatePointNumbering
Plex: Fix dynamic check for one-to-all pattern in DMPlexMigrate
Plex: Add missing header entries
Plex ex12: Enable L2-overlap test and switch to ascii_info_detail
Plex ex1: Fix overlap tests and switch to ascii_info_detail
Plex: Fix and clean up DMPlexCreatePointSF
Plex: Correctly restore closure in DMPlexPartitionLabelClosure
Plex: Let SegBuffer allocate partition graph to avoid memory corruption
Plex ex12: Enabling parallel re-partitioning test via scii_latex output
Plex: Enabling parallel re-partitioning via DMPlexDistribute
Plex ex12: Add new test for parallel re-partitioning
Plex: Add DMPlexCreatePointSF utility
Plex: Fix overlap point SF generation
Plex: Build complete overlap label and stratify resulting SF.
Plex: Create parallel partitions that ParMetis accepts
...

Conflicts:
config/builder.py
src/dm/impls/plex/examples/tests/output/ex1_13.out
src/dm/impls/plex/examples/tests/output/ex1_14.out
src/dm/impls/plex/plexlabel.c
src/dm/impls/plex/plexpartition.c

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Merge branch 'knepley/fix-plex-latex'

* knepley/fix-plex-latex:
Plex: Removed unused variable
Plex: Update LaTeX tests
Plex: Reorganized Latex output

DMPLEX: Set the LocalToGlobalMapping on the matrix created by DMPlex for MatSetValuesLocal() to work.

https://www.mail-archive.com/petsc-users@mcs.anl.gov/msg23619.html

Plex: Removed unused variable