DMPlex: make vtk viewing an option in DMView_Plex()

DMPlex: early exits from empty partitions in plexfem.c

This avoids trying to get the closure of cell 0 in an empty process,
which was causing errors.

Conflict was DMPlexGetDimension()/DMGetDimensio

DMPlex: early exits from empty partitions in plexfem.c

This avoids trying to get the closure of cell 0 in an empty process,
which was causing errors.

Conflict was DMPlexGetDimension()/DMGetDimension()

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

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

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Plex+FE: Removed all use of PetscCellGeometry, Changed FE integration to use PetscFECellGeom

PetscDualSpace: Remove use of PetscCellGeometry in PetscDualSpaceApply()
- Fixed up calls to it for projection into spaces

Plex: Added DMPlexComputeGeometryFEM() and PetscFECellGeom structure

Plex ex3: Fix use of I
- This change was lost in the cleanup

Plex+SNES+TS: Moved residual computation to solver utilities

Plex: Moved BC stuff to plexbc.c

Plex+TS: Now the minimum cell radius is held by the Plex
- Its a geometric thing that is stashed

Plex: Added FEM geometry into example

Plex: Fortran bindings for geometry fixed

PetscDS: Added a DMPlex example

Plex+TS ex11: Now default section computation can handle an FVM discretization

Plex+FE+FV: Fixed projection and L2 diff for FV
- Make a fake, simple PetscDualSpace for FV when projecting
- Added PetscFE/FVInterpolate_Static() for synthesis of field from coefficients

Plex+Doc: Removed useless comment

Plex: Fix DMCreateDefaultSection_Plex() to handle FV discretizations
- I will check CLASSID until a superclass for FE/FV becomes clear

Merge remote-tracking branch 'origin/knepley/fix-plex-submesh-intersection'

* origin/knepley/fix-plex-submesh-intersection:
DMPlex: Fix bug with intersecting submeshes - The label for clamped vert

Merge remote-tracking branch 'origin/knepley/fix-plex-submesh-intersection'

* origin/knepley/fix-plex-submesh-intersection:
DMPlex: Fix bug with intersecting submeshes - The label for clamped vertices for a given submesh can get extraneous points from an adjacent submesh - We filter these out before checking for cross-edges

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Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex1

Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex11: Fixed calls to DMSetCoordinateSection()
DM: FIxed DMClone() to copy dimension
Plex+DA: Now cell geometry routine can take a PetscFE in order to evaluate at quadrature points - We evaluate isoparametrically at the quadrature points - Changed DMDAComputeCellGeometry() --> DMDAComputeCellGeometryFEM() - Changed DMPlexComputeCellGeometry() --> DMPlexComputeCellGeometryFEM() - Added DMPlexComputeCellGeometryAffineFEM()
DM: Added a embedding dimension, different from the topological dimension - This can now be set in DMSetCoordinateSection(), or it can be automatically determined
Plex: Fix output for ex4
DM: Added DMGetDimPoints() - This replicates DMPlex/DAGetDepthStratum(), but uses the dimension which people have said is more intuitive
DM: Move dimension up into DM - Both DA and Plex had this and I think it makes sense

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

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Merge branch 'jed/fix-checkpointer-char'

* jed/fix-checkpointer-char:
Sys: PetscCheckPointer PETSC_CHAR checks char*, not char**
Sys: PetscCheckPointer for PETSC_CHAR checks char*, not char**

Sys: PetscCheckPointer PETSC_CHAR checks char*, not char**

Plex: Allow zero-size partition in refinement

Plex: Fixed simplicial refinement SF
- Was just a typo
- Added SF check

Merged in jychang48/petsc/jychang48/added-case-15-1point-vertex-to-dmplexcre-1406667503114 (pull request #182)

Added case 15: 1-point vertex to DMPlexCreateGmsh_ReadElement()

Plex: Fix for isoparametric geometry

Merge branch 'knepley/fix-plex-coords-parallel'

* knepley/fix-plex-coords-parallel:
DMPlex: Incorrect periodicity information
KSP+SNES: Converged output now includes prefix
DMPlex ex4: Fixed t

Merge branch 'knepley/fix-plex-coords-parallel'

* knepley/fix-plex-coords-parallel:
DMPlex: Incorrect periodicity information
KSP+SNES: Converged output now includes prefix
DMPlex ex4: Fixed test output
Mat+Coloring: Greedy coloring fix - Use ocolors[] for off-diagonal piece
PetscSection: Added check for mismatch between SF and Section
DMPlex: DMPlexReplace_Static() fixes - Should share coordinateDM, not just the section, so we get correct SF - Pass on periodicity information
DMPlex: Refinement should create SF before coordinates, so coordinateDM gets correct SF - Also pass on periodicity information
DMPlex: Distribution should create SF before coordinates, so coordinateDM gets correct SF - Also pass on periodicity information

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