DMPlex: Fixed compiler problems with complex

DMPlex: Fix DMPlexComputeCellGeometry() to handle lower dimensional cells
- Now I call DMPlexGetLabelValue() for depth each time, which might be too expensive. We could stash the depth label pointer

DMPlex: Fixed error in projection from 3D to 2D
- Need to check for case where normal is already z

DMPlex: Adding boundary integration
- Added a boundary integration input to DMPlexSetFEMIntegration(), this also takes cell normals
- Added an integrateBdResidualFEM() function to DMPlex
- f0 and f1

DMPlex: Adding boundary integration
- Added a boundary integration input to DMPlexSetFEMIntegration(), this also takes cell normals
- Added an integrateBdResidualFEM() function to DMPlex
- f0 and f1 for boundary integration take the cell normal as an argument (right now not used)
-

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DMPlex: Fixed cell inversion for TetGen to commute with mesh interpolation

removed path argument to XXXInitializePackage() and XXXRegister()

segbuffer: add PetscSegBufferGetInts() to encourage use of PETSC_RESTRICT

segbuffer: create wrapper structure

The old structure exposed the linked list property of the implementation.
Now we have a simple wrapper structure so that implementation detail is
not leaked. This

segbuffer: create wrapper structure

The old structure exposed the linked list property of the implementation.
Now we have a simple wrapper structure so that implementation detail is
not leaked. This will also make it possible to implement some thread-safe
operations.

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Merge branch 'knepley/plex-surface-integration' into knepley/plex

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic b

Merge branch 'knepley/plex-surface-integration' into knepley/plex

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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DMPlex: Added integration over boundary to DMPlexComputeResidualFEM()
- Added quadBd, f0/1BdFuncs to PetscFEM struct
- Needs to be tested

DMGetLocalToGlobalMapping_*: normalize names from DMCreateLocalToGlobalMapping_*

Merge branch 'jed/plex-scalable-partition-closure' of bitbucket.org:petsc/petsc into knepley/plex

DMPlex ex7: Orientations now working properly
- Added check for inverted cells
- Added check that vertex cones match for interpolated and non-interpolated meshes
- Fixed hex and tet tests
- Support r

DMPlex ex7: Orientations now working properly
- Added check for inverted cells
- Added check that vertex cones match for interpolated and non-interpolated meshes
- Fixed hex and tet tests
- Support reading ExodusII files and use mesh generators

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DMPlex: Changed orientation convention and fixed many bugs
- Tetrahedra now all have outward facing normals
- We have to flip input from TetGen and ExodusII
- Hexahedra now all have outward facing

DMPlex: Changed orientation convention and fixed many bugs
- Tetrahedra now all have outward facing normals
- We have to flip input from TetGen and ExodusII
- Hexahedra now all have outward facing normals
- We have to flip input from ExodusII
- Fixed bug with orientation -1 (now encoded as -faceSize)
- Fixed parallel bug with DMPlexInterpolate()
- Fixed determinant calculation for Tet and Hex
- Fixed bug with reversing orientation, now must also start on the opposite vertex
- This solution in GetTransitiveClosure() is suboptimal, should change the definition of negative orientation

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DMPlexCreatePartitionClosure: replace quadratic algorithm

This implementation uses a PetscBT to avoid duplicates and incrementally
packs a PetscSegArray with the points needed by each rank.

This fu

DMPlexCreatePartitionClosure: replace quadratic algorithm

This implementation uses a PetscBT to avoid duplicates and incrementally
packs a PetscSegArray with the points needed by each rank.

This function used to dominate run-time when loading meshes in parallel
and is now a negligible fraction of run time.

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DMPlex: Fix default |J| for DMPlexComputeCellGeometry()

DMPlex: Fix for cell geometry (unbelievable screwup)

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

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()

DMPlexDistribute: fix label distribution

This old code was not advancing to the next label when it finds "depth"
(which is not distributed), thus it just compared "depth" multiple times
and never ch

DMPlexDistribute: fix label distribution

This old code was not advancing to the next label when it finds "depth"
(which is not distributed), thus it just compared "depth" multiple times
and never checked the other label names.

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DMPlexVTKWriteAll_VTU: fix writing vertex data

dmplex: doc fixes [nightlybuilds]

doc: nightlybuild fixes