Plex: Fixes for analyzer

Plex: Added a new point location type to remove entries which are not found
- This was the default, but its not what DMSwarm wanted and its non-intuitive I agree

DMPlex: construct the correct l2gmap for MatIS using the subdomainSection (for local indexing) and the globalSection

Update ComputeJacobian to set the closure in the local matrix

Plex: Allow FEM interpolation inside DMInterpolation

Plex: Changed Get/RestoreFaceFields() and Get/RestoreFaceGeometry() to return the number of active faces
- This fixes a long-standing bad access in FV, although the values were never actually used.

Plex: Fixed incredibly stupid bug in Jacobian computation

DM: Added mode to DMLocatePoints() to change failure behavior
- Implement to NEAREST mode in Plex for 2D simplices
- Added DMPlexCLosestPoint_Internal()

DMPlex: consistently ignore parent faces in FVM computations

We were sometimes making them exist with 0. values, but not consistently, so the layout
was changing between different functions, leading

DMPlex: consistently ignore parent faces in FVM computations

We were sometimes making them exist with 0. values, but not consistently, so the layout
was changing between different functions, leading to values going to the wrong places

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DMPlexSNES: a hack to get face fields for nonconforming elements

I think what I have written now doesn't work for discontinuous finite elements, but otherwise is right

Plex+FV: Integrated changes for FV support with multiple fields

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary c

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary commitid] - and dirname in tarball
Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES
CUDA: Added external declaration for cuBLAS handle.
docs: fix reference to KSP_Create in parent commit
Add information on PETSC_EXTERN and PETSC_INTERN to developers manual
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Configure: Fix check for spaces in PETSC_DIR
Plex: Updated examples to new DMPlexCreateBoxMesh()
sick of failure due to incorrect master branch
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Examples that require Fortran to compile but were listed in tests that did not require Fortran
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
...

Conflicts:
src/dm/impls/plex/makefile
src/snes/utils/dmplexsnes.c

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Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES

DMPlexTS, DMPlexSNES: cache in the dm instead of the dmts, dmsnes objects

DMPlex: move FV methods out of DMPlexSNES and into their own file

DMPlex: cache FVM data

Plex: Fixed ResconstructGradients_Internal() to take an FVM and to work in multifield problems
- ApplyLimiter_Internal() now can limit an FV field within a multifield problem

Plex: When forming Jacobian, just use identity for FV fields

Plex: Only compute Jacobian matrix if point wise functions for it are specified
- Now we can use -snes_mf_operator with a constructed preconditioned matrix and MF Jacobian action

Merge branch 'knepley/feature-ts-mass-matrix'

* knepley/feature-ts-mass-matrix:
Plex: Removed unused variables

# Please enter a commit message to explain why this merge is necessary,
# especially

Merge branch 'knepley/feature-ts-mass-matrix'

* knepley/feature-ts-mass-matrix:
Plex: Removed unused variables

# 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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Plex: Removed unused variables

Plex+SNES: Fixed kernels for Jacobian action

Merge branch 'knepley/feature-ts-mass-matrix' into knepley/fix-petscfe-kernels-ts

* knepley/feature-ts-mass-matrix:
TS ex32: Added a heat equation example - Not yet working, but checking mass matr

Merge branch 'knepley/feature-ts-mass-matrix' into knepley/fix-petscfe-kernels-ts

* knepley/feature-ts-mass-matrix:
TS ex32: Added a heat equation example - Not yet working, but checking mass matrix now
Plex+SNES: Added DMPlexSNESComputeJacobianActionFEM() - And an internal version

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Plex+SNES+TS: Pass time and shift down into residual and Jacobian kernels, and the boundary kernels
- Added time into ComputeRHS/IFunction

Plex+SNES: Added DMPlexSNESComputeJacobianActionFEM()
- And an internal version

doc fixes