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 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 ex13: Tests orientation
- Only 2D triangle tests now
- Last test shows problem for disconnected domains

Plex: Small example fixes

Plex: Remove unneeded headers

Plex: Added a file for orientation calculations
- Moved DMPlexOrient()

Plex ex9: Updated to new logging interface

Plex-Gmsh: Improve error handling

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

Plex-Gmsh: Fixes for 64-bit integer mode

Since Gmsh files always use 32-bit integers, use PETSC_ENUM to
enforce 32-bit integer reads.

Plex-Gmsh: Fix and test parallel Gmsh reads

For parallel binary reads we read data on all ranks, but we build
the plex on rank 0. Also, we inspect the header only on rank 0.

Plex-Gmsh: Add new Gmsh tests based on 2D square

Plex-Gmsh: Add DMPlexCreateGmshFromFile, which determines file type

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

Plex-Gmsh: Enabling binary mesh file reads in DMPlexCreateGmsh

Adds a utility function DMPlexGmshRead that wraps
PetscViewerRead. This adds byte swaps for binary Gmsh files in
little endian format a

Plex-Gmsh: Enabling binary mesh file reads in DMPlexCreateGmsh

Adds a utility function DMPlexGmshRead that wraps
PetscViewerRead. This adds byte swaps for binary Gmsh files in
little endian format and emulates fgets when asked for a
PETSC_STRING.

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Plex-Gmsh: Read gmsh elements into memory for repeated file traversal.

Plex-Gmsh: Fix cell and dimension counting

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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Merged in mlange/fix-plex-distributed-refine (pull request #220)

Plex: Test and fix parallel refinement

Plex ex12: Enabling parallel re-partitioning test via scii_latex output

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 ex12: Add new test for parallel re-partitioning

The prescribed two-rank partition is effectively coloured, so parmetis
can do it's thing.

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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