Merge branch 'maint'

tests: fix buggy shell in makefile [and corresponding output files]

DMPlex + FV: remove leaky references in projection functions

These had already been fixed for FE but I must have missed FV

DMPlexTree: do not skip out of child matrix loops early

Even in the matrix will have size zero rows, we still want to calculate the number of columns,
which is useful for keeping track of offsets of

DMPlexTree: do not skip out of child matrix loops early

Even in the matrix will have size zero rows, we still want to calculate the number of columns,
which is useful for keeping track of offsets of fields

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PetscFV: correct field offsets when limiting gradients

DMP4estTree: ignore negative values when getting/setting vector values for transfer

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()

PetscFV: correct field offsets when calculating gradients

The offsets were originally calculated with respect to the closure of the discretization on a cell, but we only
want offsets that are with r

PetscFV: correct field offsets when calculating gradients

The offsets were originally calculated with respect to the closure of the discretization on a cell, but we only
want offsets that are with respect to the cell-centered variables, which is what the DMPlexPointLocalFieldRead()
funciton provides.

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Merge branch 'maint'

Plex ex1f90: Updated to new DMPlexCreateBoxMesh()

Plex ex18: Updated output for new PetscObject viewing
- Fixed DMPlexCreateBoxMesh() call

Plex ex1: Updated GMsh output

Plex ex1: Updated output for ending newline

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

* master:
Plex ex1: Added another GMsh test
Plex+GMsh: Reader now handles optional PhysicalNames section
Plex ex1: Reorganized test output

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

Merge branch 'knepley/fix-plex-gmsh-reader'

* knepley/fix-plex-gmsh-reader:
Plex ex1: Added another GMsh test
Plex+GMsh: Reader now handles optional PhysicalNames section
Plex ex1: Reorganized

Merge branch 'knepley/fix-plex-gmsh-reader'

* knepley/fix-plex-gmsh-reader:
Plex ex1: Added another GMsh test
Plex+GMsh: Reader now handles optional PhysicalNames section
Plex ex1: Reorganized test output

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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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Merged in mapdes/petsc/gmsh-cell-sets (pull request #481)

plexgmsh: Read Cell Sets as well as Face Sets

DMPlex: Choose default partitioner from [chaco, parmetis, simple]

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

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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Plex ex1: Added another GMsh test

Plex+GMsh: Reader now handles optional PhysicalNames section

Plex ex1: Reorganized test output