Merge branch 'knepley/feature-partitioner-simple'

* knepley/feature-partitioner-simple:
Plex: Removed unused variable
Partitioner: Added tests for simple partitioner
Plex: Added a simple parti

Merge branch 'knepley/feature-partitioner-simple'

* knepley/feature-partitioner-simple:
Plex: Removed unused variable
Partitioner: Added tests for simple partitioner
Plex: Added a simple partitioner

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

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

Plex: Added a simple partitioner

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

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

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

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/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: Added DMPlexPointGlobalFieldRead/Ref()

Plex: Added DMPlexPointLocalFieldRead()

Plex: Added DMPlexPointLocalFieldRef

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 'icl/lawrence/dmplex-1d-refinement'

* icl/lawrence/dmplex-1d-refinement:
PetscFE: Use enum for cell refiner
Plex Refinment: Fixed error check
Plex Refinment: Fixed coordinate crea

Merge branch 'icl/lawrence/dmplex-1d-refinement'

* icl/lawrence/dmplex-1d-refinement:
PetscFE: Use enum for cell refiner
Plex Refinment: Fixed error check
Plex Refinment: Fixed coordinate creation
Plex Refinment: Replaced ints with enums
DMPlex: support uniform refinement of intervals
DMPlex: make CellRefiner an enum rather than PetscInt

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Remove XXXRegisterAll() from public interface

This means we are relying on packages to be well behaved, to set
themselves up properly. Passes testexamples in my builds (haven't tried
complex).

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.

DMPlex: make CellRefiner an enum rather than PetscInt

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
Plex: Fix serial orientation
TetGen: Syntax fix
Plex: Fix MPI type for orientation
Plex: Small orientation fix
Plex ex13:

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
Plex: Fix serial orientation
TetGen: Syntax fix
Plex: Fix MPI type for orientation
Plex: Small orientation fix
Plex ex13: Orientation now working for flipped connected components
Plex: Reworked orientation to respect connected components on each process
Plex ex13: Check in initial output
Plex: Now mark initial cell as seen - Changes the outcome slightly
Plex: Added DMPlexCheckFace_Internal() - This checks a face in the mesh for orientation consistency
Plex: Fix orientation diagnostics
Plex: Added declaration for DMPlexReverseCell()
Plex ex13: Tests orientation - Only 2D triangle tests now - Last test shows problem for disconnected domains
Plex: Small example fixes
PetscBT: Do not overwrite a viewer passed to PetscBTView()
Plex: Remove unneeded headers
Plex: Added a file for orientation calculations - Moved DMPlexOrient()

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

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Plex: Add missing header entries

Merge branch 'mlange/plex-gmsh-binary'

* mlange/plex-gmsh-binary:
Viewer: Fix 64-bit integer parse
Plex-Gmsh: Improve error handling
Viewer: Use %lld to parse 64-bit integers
Plex-Gmsh: Fixe

Merge branch 'mlange/plex-gmsh-binary'

* mlange/plex-gmsh-binary:
Viewer: Fix 64-bit integer parse
Plex-Gmsh: Improve error handling
Viewer: Use %lld to parse 64-bit integers
Plex-Gmsh: Fixes for 64-bit integer mode
Plex-Gmsh: Fix and test parallel Gmsh reads
Plex-Gmsh: Add new Gmsh tests based on 2D square
Plex-Gmsh: Add DMPlexCreateGmshFromFile, which determines file type
Plex-Gmsh: Enabling binary mesh file reads in DMPlexCreateGmsh
Viewer: Add PetscViewerRead()
Plex-Gmsh: Adding PetscViewerASCIIRead()
Plex-Gmsh: Read gmsh elements into memory for repeated file traversal.
Plex-Gmsh: Fix cell and dimension counting

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

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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

Plex: Added declaration for DMPlexReverseCell()

Plex-Gmsh: Add DMPlexCreateGmshFromFile, which determines file type

The file type is determined by reading the first two lines of the header.

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

Merge remote-tracking branch 'origin/tisaac/plex-flexible-projection'

* origin/tisaac/plex-flexible-projection:
PetscDualSpace: Fixed function signature
Plex: update libraries for ex3
Plex: mo

Merge remote-tracking branch 'origin/tisaac/plex-flexible-projection'

* origin/tisaac/plex-flexible-projection:
PetscDualSpace: Fixed function signature
Plex: update libraries for ex3
Plex: move DMPlexProjectionFunction() back to libdm
Plex: use -dm_plex_max_projection_height in non-conforming examples
Plex: fixed a typo in DMPlexProjectFunctionLocal()
Plex: added DMPlexComputeProjection3Dto1D_Internal()
Plex: fixes to recent merge
PetscFE: added dim, dimEmbed to PetscFECellGeom
Plex: skip empty loops for empty dual spaces
DualSpace: 0-order Lagrange spaces do not have dual spaces for height > 0.
Plex: protect against field projection with height > 0.
Plex: start implementing projection with height > 0.
PetscDualSpace: added PetscDualSpaceGetHeightSubspace()
Plex: added DMPlexGet/SetMaxProjectionHeight()

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

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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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