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

Merge branch 'knepley/fix-dm-coord-sf'

* knepley/fix-dm-coord-sf:
Plex: With new distribute code, we have to set the SF for the coordinate DM explicitly

Plex: Log performance for DMPlexMigrate and DMPlexDistributeOverlap

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

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

Plex: With new distribute code, we have to set the SF for the coordinate DM explicitly

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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Merge branch 'knepley/fix-plex-distribute-uninterpolated'

* knepley/fix-plex-distribute-uninterpolated:
Plex: Fix distribution of uninterpolated meshes - Does SF stratification by depth, not by di

Merge branch 'knepley/fix-plex-distribute-uninterpolated'

* knepley/fix-plex-distribute-uninterpolated:
Plex: Fix distribution of uninterpolated meshes - Does SF stratification by depth, not by dimension - The old code numbered cells after vertices

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Plex: Fix leak
- No need for extra BC copy

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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Merge branch 'knepley/fix-plex-distribute-uninterpolated' into knepley/feature-combined-tabulation

* knepley/fix-plex-distribute-uninterpolated:
Plex: Fix distribution of uninterpolated meshes - D

Merge branch 'knepley/fix-plex-distribute-uninterpolated' into knepley/feature-combined-tabulation

* knepley/fix-plex-distribute-uninterpolated:
Plex: Fix distribution of uninterpolated meshes - Does SF stratification by depth, not by dimension - The old code numbered cells after vertices
cannot call PetscObjectGetName() on a subset of the MPI processes
MatView() with some matrix formats and ASCII_MATLAB did not print correct matrix name

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Plex: Fix distribution of uninterpolated meshes
- Does SF stratification by depth, not by dimension
- The old code numbered cells after vertices

Plex: DMPlexDistribute() no longer calls DMSetFromOptions()
- Fixed examples

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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Plex: Fix dynamic check for one-to-all pattern in DMPlexMigrate

Check if the current point SF graph has been set (nroots > -1).

Plex: Fix and clean up DMPlexCreatePointSF

Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

Merge branch 'master' into mlange/refactor-plex-distribute

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_1.out
src/dm/impls/plex/examples/tests/output/ex12_2.out

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

Plex: Enabling parallel re-partitioning via DMPlexDistribute

This commit adds several fixes that allow DMPlexDistribute to be used on
an already distributed plex. It fixes the partition graph genera

Plex: Enabling parallel re-partitioning via DMPlexDistribute

This commit adds several fixes that allow DMPlexDistribute to be used on
an already distributed plex. It fixes the partition graph generation
and stratifies the migration SF used in DMPlexDistribute.

It also changes the point ordering again by always putting local points
first in DMPlexPartitionLabelInvert. This is done to deal with ParMetis
always returning the cell partitioning in local numbers.

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Plex: Add DMPlexCreatePointSF utility

This routine handles the initial point SF generation with ownership
voting, as well as the point remapping after overlap migration.

Note: Obsoletes DMPlexDistr

Plex: Add DMPlexCreatePointSF utility

This routine handles the initial point SF generation with ownership
voting, as well as the point remapping after overlap migration.

Note: Obsoletes DMPlexDistributeSF

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Plex: Fix overlap point SF generation

Plex: Build complete overlap label and stratify resulting SF.

Instead of building an SF of overlap contributions and merging it with
locally owned points, we now build a label of overlap and owned p

Plex: Build complete overlap label and stratify resulting SF.

Instead of building an SF of overlap contributions and merging it with
locally owned points, we now build a label of overlap and owned points
and stratify the resulting SF via a new utility function.

Note: This changes the point numbering of overlapping plexes, and thus
requires a test update for ex12.

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Plex: Derive original point numbering in DMPlexMigrate

We now don't need to carry around ISLToGs in DMPlexDistribute(Overlap).