Plex: Allow FEM interpolation inside DMInterpolation

Merge branch 'knepley/feature-dm-point-location-failure'

* knepley/feature-dm-point-location-failure:
Plex: Fixed declaration and complex conversion
DM: Added mode to DMLocatePoints() to change

Merge branch 'knepley/feature-dm-point-location-failure'

* knepley/feature-dm-point-location-failure:
Plex: Fixed declaration and complex conversion
DM: Added mode to DMLocatePoints() to change failure behavior - Implement to NEAREST mode in Plex for 2D simplices - Added DMPlexCLosestPoint_Internal()

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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

Merge branch 'knepley/fix-plex-mf-prec'

* knepley/fix-plex-mf-prec: (26 commits)
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Plex: Updated examp

Merge branch 'knepley/fix-plex-mf-prec'

* knepley/fix-plex-mf-prec: (26 commits)
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Plex: Updated examples to new DMPlexCreateBoxMesh()
TS ex11: Fixed output for new ROSW
Plex: Forgot internal declaration
Plex: Fixed ComputeIntegral() to work with FVM - May still have a bug, not sure
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
PetscFV: Added -petscfv_compute_gradients
SNES ex12: Fixed output for NGS
PetscDS: Added GetFieldIndex() and GetFieldSize() - Fix to accept FV as well
Plex: Forgot to eliminate PetscRealPart() after type change
Plex: fix line geometry for localized
Plex: fix section access to last commit
DMPlex: fix rectanlge geometry for localized
DMConvert_p4est_plex: set projection height early, so it passes to coordinate dm
DMLocalizeCoordinates(): make more flexible and targeted
Plex: When forming Jacobian, just use identity for FV fields
Plex+FE: Added missing FV dual space
PetscFE: If all Jac pointwise functions are NULL, do not evaluate
DMP4est: change order of setting projection height and localizing coordinates
...

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

DMPlex: cache FVM data

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

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

Merge branch 'master' into barral/feature-dmplex-adapt

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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Merge branch 'knepley/fix-petscfe-kernels-ts'

* knepley/fix-petscfe-kernels-ts:
PetscFE+OpenCL: Fixed OpenCL residual eval for new interface
Plex+SNES: Fixed kernels for Jacobian action
Plex+S

Merge branch 'knepley/fix-petscfe-kernels-ts'

* knepley/fix-petscfe-kernels-ts:
PetscFE+OpenCL: Fixed OpenCL residual eval for new interface
Plex+SNES: Fixed kernels for Jacobian action
Plex+SNES+TS: Pass time and shift down into residual and Jacobian kernels, and the boundary kernels - Added time into ComputeRHS/IFunction
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: 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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Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()
Update the xSDKTrilinos test message to use interactive session and ctest
gcc6: fix comple warnings with -Wmisleading-indentation
fix compile warning
bugfix for MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable()
minor formatting cleanup of gamg.c
add ml example to tutorials page for xsdk
bugfix of MatDuplicate for mpiaij matrix product Reported-by: Miorelli, Federico <Federico.Miorelli@cgg.com>
The deprecated -log_summary_exclude was still being used when it should have been -log_exclude
cpardiso: requires mkl_blacs so check for that. Also common code to detect MKL for both pardiso and cpardiso
cpardiso: fix segv and memory leaks
resume MatGetSubMatrix_SeqSBAIJ() because it cannot share routine with BAIJ due to cast
fix bad relative links
replace MatSeqBAIJSetPreallocation_SeqBAIJ with MatSeqBAIJSetPreallocation to skip this call when input mat is sbaij type
fix a variety of set but not used variables in examples detected by clang static analyzer
removed declared but not used variable
ANL Report formatting requires listing authors by affiliation
DMP4est: uncrustify
DMP4est: remove memset()
...

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