DMPlex: Fix hybrid bounds for interpolated mesh with cohesive cells

DMPlex: Fixes for cohesive label reconstruction
- Do not put cohesive edges in labels
- Do not reconstruct "depth" label

DMPlex: Fixed cohesive submesh SF
- I misclassified points which were not owned in the original mesh, but are owned in the submesh

DMPlex: Fixed bug with cohesive submesh SF
- Needed to put in owned subpoints since they do not come from leaves OR from the original mesh

DMPlex: Fix out of bounds access for empty mesh

DMPlex: Fixed creation of PetscSF in DMPlexCreateCohesiveSubmesh_Uninterpolated()
- Could not assume that original owner of subvertex owned it in submesh because it might have no subcells
- Needed to

DMPlex: Fixed creation of PetscSF in DMPlexCreateCohesiveSubmesh_Uninterpolated()
- Could not assume that original owner of subvertex owned it in submesh because it might have no subcells
- Needed to redetermine ownership of subpoints

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DMPlex: Initializeremote locations when calculating SF for submesh

DMPlex: FIxed hang in DMPlexCreateCohesiveSubmesh()

DMPlex: Now a label can be used to restrict the points for a cohesive submesh
- Added label and value arguments to DMPlexCreateCohesiveSubmesh()

DMPlex: Added PetscSF creation to DMPlexCreateCohesiveSubmesh_Uninterpolated()
- Added DMPlexFilterPoint_Internal()
- Still need this for the interpolated variant

DMPlex: Remove dead code

Merged petsc/petsc into rmills/petsc master.

DMPlex: Removed aggressive checks for cohesive cells
- How should we handle extraction in parallel?

DMPlex: Allow submesh creation with empty mesh and empty label

DMPlex: Fixed face definition in tetrahedra and hexahedra for new orientation

Merge branch 'knepley/pylith'

* knepley/pylith:
DMPlex: Fixed bug in DMPlexOrient() - Must visit faces in BFS order so that all comparisons are in a connected component of the mesh
DM: Fix leak

Merge branch 'knepley/pylith'

* knepley/pylith:
DMPlex: Fixed bug in DMPlexOrient() - Must visit faces in BFS order so that all comparisons are in a connected component of the mesh
DM: Fix leak when creating global section
DMPlex: Fix allocation for embedded submesh
DMPlex: Removed debugging prints
DMPlex: Fix leak in interpolation
DMPlex: Added DMPlexOrient() which correctly orients a set of adjacent cells - You need this when extracting an embedded submesh
DMPlex: Fix memory management in submesh creation

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DMPlex: Fix allocation for embedded submesh

Merge branch 'knepley/pylith' of bitbucket.org:petsc/petsc into knepley/pylith

# By Jed Brown (2) and Satish Balay (1)
# Via Jed Brown
* 'knepley/pylith' of bitbucket.org:petsc/petsc:
DMPlex: fix

Merge branch 'knepley/pylith' of bitbucket.org:petsc/petsc into knepley/pylith

# By Jed Brown (2) and Satish Balay (1)
# Via Jed Brown
* 'knepley/pylith' of bitbucket.org:petsc/petsc:
DMPlex: fix initialization of variables in degenerate case
DMPlex: add missing PetscFunctionBegin
DMPlex: fix compile warning on bsd

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DMPlex: Fix memory management in submesh creation

Merge branch 'knepley/pylith'

* knepley/pylith:
DMPlex: fix initialization of variables in degenerate case
DMPlex: add missing PetscFunctionBegin
DMPlex: fix compile warning on bsd

DMPlex: fix initialization of variables in degenerate case

This was misdiagnosed as a buggy compiler warning in 390f8ca65451.

DMPlex: add missing PetscFunctionBegin

DMPlex: fix compile warning on bsd

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory corruption occurs otherwise
DMPlex: All quadrilateral geometry tests working
DMPlex: remove unused variable
DMPlex: Hexahedron geometry tests now pass
DMPlex: More geometry work
DMPlex: use PETSC_HAVE_TGAMMA to get the build working on windows
configure: add test for tgamma() [this is missing on windows]
DMPlex: Added random transform tests for tets - Fixed memory leak
DMPlex: Fixed 3D geometry
DMPlex: FVM geometry tests now work for triangles
DMPlex: one more win32/complex fix
DMPlex: Enhanced geometry tests - Added random transforms of the reference triangle in 2D
DMPlex: Fixed complex problems in geometry calculation
DMPlex: Fixed Fortran test output
DMDT: M_PI --> PETSC_PI
DMPlex: Reorganized geometry testing
TS ex11: Put in 3D inflow and outflow ids from the command line
DMPlex: Added DMPlexRestoreCone/Support() to F90 interface definition header - Also added to test ex1f90
TS ex11: Need to make these ids input from the command line
DMPlex: Add Fortran bindings
DMPlex: Reorder tet output since I order tets differently
Builder: Link Fortran examples with Fortran linker
DMPlex: Fixed leak in example
DMPlex: Tutorial now shows how to output VTK
PetscViewer: Added VTK type for Fortran
DMPlex: Remove parameter names from prototype
DMPlex: Geometry fixes for C++ complex
DMAKKT: Remove from build
DMPlex: Now DMPlexCreateSection() only has an F90 interface
SNES: add Fortran bindings to DMSNESSet{Function,Jacobian}
SNES: remove superfluous casting in DM local Fortran bindings
SNES: compile zdmlocalsnesf.c
DMDT: Fix Fortran wrapper
DMPlex: Added Fortran interface for DMPlexMatSetClosure()
PetscSection: Added docs, enabled Fortran wrappers
DM: Added Fortran bindings for DMSNESSetFunction/JacobianLocal()
SNES ex12: Looks like 3D Neumann conditions are working
DMPlex: Fix volume determination for 2D in 3D
DMPlex: Better error reporting
SNES ex12: Boundary integration seems to work in 2D
DMPlex+FEM: Fix for boundary integration
TS ex11: Better error reporting
DMPlex ex8: Added FVM geometry tests
DMPlex: Fixed FVM geometry for 2D in 3D
SNES ex62: Now using PetscDT quadrature
DMDT: Translated FIAT's Gauss-Jacobi quadrature
DMPlex: Fix geometry tests - Fix tests for 2D projection
DMPlex: Geometry fixes
DMPlex: Small fixes for geometry
DMPlex: Fixed damn prototype
PetscSection: Added VecSetValuesSectionF90() - Fixed bug in Vec Fortran header
DMPlex: Added Fortran defines for additional insert modes
DMPlex: Silence warning in DMPlexInvertCells_Internal()
DMPlex: Functions passed to evaluation routines now return void and pass results in arguments
DMPlex: Now we give an explicit embedding dimension to the FVM geometry methods
DMPlex: Fixed complication with complex - Started to add 3D geometry stuff
TS ex11: Replace edge geometry with call to DMPlexComputeCellGeometryFVM()
DMPlex: Added normal argument to DMPlexComputeCellGeometryFVM() - This is only calculated for faces - Added calculation for faces in 2D
DMPlex: Damn makefiles
DMPlex: Added declaration for DMPlexCreateCGNS()
TS ex11: Reorganized computation of geometry in preparation for 3D
Builder: Now individual tests can have requirements - The key is 'requires', and it takes a list of package names - Also fixed up showSingleRun()
TS ex11: Use new DMPlexComputeCellGeometryFVM()
DMPlex: Added DMPlexComputeCellGeometryFVM() - Added internal volume methods
DMPlex: fix const and int vs. PetscInt
DMPlex: Better error reporting
DMPlex+ExodusII: Fixed reading of quads - Was broken by 2e1b13c25062c3c40593ce7412c5cd227259ade7
DMPlex: Hex cell geometry was broken - I don't see how this test passed before
DMPlex: Regression cleanup
DMPlex: Regression cleanup
SNES ex12: Fixed sign for Neumann BC
DMPlex+FEM: The dimension does not change for boundary elements
DMPlex: Geometry now works for boundary elements
DMPlex+FEM: Fixed quadrature coordinate handling for boundary integrals
SNES ex12: Reorganized tests, still working on Neumann conditions - Fixed boundary face label
DMPlex: Turn off CGNS by default
DMPlex: Added 1D cell geometry
DMPlex: DMPlexCreateCGNS()
DMPlex: Updated test ex1 output
DMPlex: Fixed compiler problems with complex
SNES ex12: Now does boundary integration - Still not verifying exact solution for Neumann conditions
DMPlex: Fix DMPlexComputeCellGeometry() to handle lower dimensional cells
DMPlex: Fixed error in projection from 3D to 2D - Need to check for case where normal is already z
DMPlex: Adding boundary integration
DMPlex: Fixed cell inversion for TetGen to commute with mesh interpolation
SNES ex12: Cleaning up ex12 testing
DMPlex: Added integration over boundary to DMPlexComputeResidualFEM() - Added quadBd, f0/1BdFuncs to PetscFEM struct - Needs to be tested
FEM Generation: We now allow a *_bd.h header that holds boundary discreization
Builder: Fixed regression requirements
Builder: Fixed specification of multiple tests to run
DMPlex ex7: Orientations now working properly
DMPlex: Changed orientation convention and fixed many bugs
SNEX ex12: Ignore generated headers
SNEX ex12 and ex52: Remove CTetGen warnings from test output - Fixed this in CTetGen repository
DMPlex: Fix default |J| for DMPlexComputeCellGeometry()
DMPlex: Fix for cell geometry (unbelievable screwup)
DMPlex ex7: Check that |J| is nonzero for each cell in interpolated mesh
DMPlex: Allow DMPlexComputeCellGeometry() to work with interpolated meshes
DMPlex: Added prototype for DMPlexCopyCoordinates(), and docs for that and DMPlexInterpolate()
DMPlex: Added F90 interface for DMPlexComputeCellGeometry()

Conflicts:
include/petscdmplex.h

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Merge branch 'knepley/pylith'

* knepley/pylith:
DMPlex: Add missing declaration - This should merge alright with the other branch which fixes it
DMPlex: Submesh fixes - Coordinates must use a fi

Merge branch 'knepley/pylith'

* knepley/pylith:
DMPlex: Add missing declaration - This should merge alright with the other branch which fixes it
DMPlex: Submesh fixes - Coordinates must use a field - Allow same subpointMap to be specified again
DMPlex: Fix submesh marking for uninterpolated meshes - This now works for embedded submeshes
DMPlex: Interpolation corner cases - Do not interpolate a 1D mesh - No need to copy coordinates of the same DM
DMPlex: Interpolation of a submesh now starts at the faces - Do not know a better way to do this right now
DMPlex: Fix error in work space allocation
ISieve: Coordinate conversion should add a field

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