DMPlex: Fixed refinement of hybrid hex cells
- Copied code from the tet case

DMPlex+SNES ex12: Protect the HDF5 interface calls

Plex-Gmsh: Add boundary IDs to facets

Boundary IDs are marked with the "Face Sets" label, as used in ExodusII,
to maintain a single convention.

Plex-Gmsh: Move element identification into a utility function

Plex-Gmsh: Derive the true number of vertices and facets

The Gmsh format disguises facets as elements, so we have to
run through all "element" entries to get the correct number
of cells and decide t

Plex-Gmsh: Derive the true number of vertices and facets

The Gmsh format disguises facets as elements, so we have to
run through all "element" entries to get the correct number
of cells and decide the topological dimension of the mesh.

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PetscSection: Added an optional permutation for the chart
- Removed the unnecessary atlasLayout
- This permutation will allow people to segregate ghost unknowns at the end of their numbering,
and

PetscSection: Added an optional permutation for the chart
- Removed the unnecessary atlasLayout
- This permutation will allow people to segregate ghost unknowns at the end of their numbering,
and also to get around the stratification of point numbering in Plex

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DMLabel: Name stratum IS

DMPlex: Fix HDF5 groups for vector output
- Push the group only for global vectors, which allows coordinates to be put in another group

DMPlex: Added DM and Vec loading for Plex
- Added VecLoad_Plex() and VecLoad_Plex_Local()
- Added DMLoad_Plex()
- Only HDF5 works now

DMPlex: Set block size correctly on coordinate vectors

DMPlex: Now DMPlexInterpolate() allows the new mesh to be inserted into an existing DM
- If the input is non-NULL, no new DM is created
- This allows it to functions within the DMLoad() paradigm

DMPlex: Now HDF5 viewer for vecs gets BC right in parallel
- Uses the output DM

DMPlex: Added DMPlexInsertBoundaryValues()
- Uses DMPlexGetBoundary() and DMPlexProjectFunction() to set boundary values
- Used in the viewers
- Some viewer cleanup

DMPlex: Fixed local viewer projection

DMPlex+PetscFE: Adding support for TS
- Added DMPlexCompiteIFunctionFEM()
- Added PetscFEIntegrateIFunction() and Bd version
- Added IFunction to FEM struct

DMPlex: Added Fortran example for geometry

DMPlex: Fix boundary condition function handling for viewing

Merge branch 'mlange/feature-plex-mesh-from-file'

* mlange/feature-plex-mesh-from-file:
DMPlex: Switching more tests to the new ExodusII wrappers
DMPlex: Switching tests to use the new ExodusII/

Merge branch 'mlange/feature-plex-mesh-from-file'

* mlange/feature-plex-mesh-from-file:
DMPlex: Switching more tests to the new ExodusII wrappers
DMPlex: Switching tests to use the new ExodusII/CGNS file wrappers
DMPlex: Add DMPlexCreateCGNSFromFile() wrapper
DMPlex: Add DMPlexCreateExodusFromFile() wrapper

Conflicts:
config/BuildSystem/config/packages/__init__.py

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DMPlex: Now for VTK and HDF5 we can put in the correct boundary values if they were registered using DMPlexAddBoundary()

DMPlex: Fix DMPlexGetAdjacency_Internal() to allocate if necessary

Merge branch 'mlange05/feature-plex-multi-faced-cube'

* mlange05/feature-plex-multi-faced-cube:
DMPlex: Fixing c89 incompatibility.
DMPlex: Adding multi-face support in DMPlexCreateCubeBoundary

DMPlex: Added Fortran wrapper for DMPlexComputeCellGeometryFVM()

DMPlex: Added an HDF5 viewer

Merge branch 'knepley/fix-fem-multifield'

* knepley/fix-fem-multifield:
DMDT: Fixed Fortran PetscQuadrature definition
DMPlex ex3: Added Q2 tests - Made DA tests only 2x2 - Changed output format

Merge branch 'knepley/fix-fem-multifield'

* knepley/fix-fem-multifield:
DMDT: Fixed Fortran PetscQuadrature definition
DMPlex ex3: Added Q2 tests - Made DA tests only 2x2 - Changed output format - Quad tests now actually work
DMDA: Added DMDAComputeL2GradientDiff()
PetscSpace: Fixed polynomial derivative evaluation for quads
DMDA: Fix closure operations in 2D
DMPlex: Interpolation cleanup - Remove unused PetscSpace - Fix uninitialized variable
PetscFE: Fix PetscBool handling
SNES ex62: Updated output
DMPlex ex3: Use PetscFECreateDefault() and correct tensor tests
PetscFE: Fix PetscFECreateDefault() - The space should default to tensor on a non-simplex - The quadrature should be tensor Gauss on a non-simplex
DT: Added PetscDTGaussTensorQuadrature()
DT: Added citation for Gloub+Welsch method
PetscSection: Now global section can also be viewed
DMPlex: Allow NULL function for ProjectFunction()
PetscDualSpace: Added doc for PetscDualSpaceApply() - Cherry-picked from df2d8bb
PetscFE: Fixed PetscFECreateDefault() - Setup FE - Minimum quad order - Destroy quad after setting
PetscFE: PetscFECreateDefault() now takes a number of components and a reference cell type - Cherry-picked from a255314
PetscFE: Added PetscFECreateDefault() - Cherry-picked from 8919f5a
PetscFE: Allow lowest order cell Lagrange dual basis functions
DMPlex: Fix preallocation with cell variables - I had an incorrect loop optimization

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

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DMPlex: Switching tests to use the new ExodusII/CGNS file wrappers