Merge branch 'knepley/fix-plex-regression'

* knepley/fix-plex-regression:
SNES ex62: Solver jitter
SNES ex62: Newline at the end of output
TS ex11: It looks like Toby's fixes have slightly cha

Merge branch 'knepley/fix-plex-regression'

* knepley/fix-plex-regression:
SNES ex62: Solver jitter
SNES ex62: Newline at the end of output
TS ex11: It looks like Toby's fixes have slightly changed the shallow water example
TS ex32: Add output
Plex ex17: Updated to new point location interface
Plex: Must initialize interpolation elemMat since I only set the component diagonal
SNES ex12: Fixed tolerance in FAS runs
SNES ex12: Why did the ASM regression change?
SNES ex12: Corrected cheby options
SNES ex12: Added p4est output
SNES ex12: Updated output for changed GAMG settings
SNES ex12: Updated output for newline at end
Fortran: Missing if body in #define
Draw: Missing 'do' in incomprehensible #define

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Plex: Must initialize interpolation elemMat since I only set the component diagonal

Merge branch 'tisaac/dm-boundary-in-ds'

Boundary conditions are better conceptually matched to the PetscDS,
which holds the equations, than to the DM. This makes it easier to
share the same problem

Merge branch 'tisaac/dm-boundary-in-ds'

Boundary conditions are better conceptually matched to the PetscDS,
which holds the equations, than to the DM. This makes it easier to
share the same problem between different meshes, such as in a hierarchy.

* tisaac/dm-boundary-in-ds:
PetscDS: fix examples affected by moving boundaries
builder.py: skip empty targets
DMPlex: don't copy coordinates to self
SNES ex69: fix recent PetscDS changes
DMSetDS(): reference, then destroy
PetscDS: fix _Basic creation and destruction
PETSC_DEPRECATED in source files doesn't play well with fortran interfaces
DM: switch to using PetscDS boundary in examples
PetscDS: add missing PetscDSCopyBoundary, fix copy loops
DM: set PetscDS from options in DMSetFromOptions()
DM: protect against changing prob when populating boundary
DM, PetscDS: remove redundant boundary representations
DM: transfer boundary methods to PetscDS
PetscDS: start creating parallel for DMBoundary

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Plex+Doc: Added page for DMPlexInsertBoundaryValues()

PetscDS: add missing PetscDSCopyBoundary, fix copy loops

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize t

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize the amount of code that is specialized to the
different DMs, and in the future more work can be done to improve this
interface.

* tisaac/ts-ex11-amr: (62 commits)
DMP4est: type fix
Plex: Fixes for analyzer
DMP4est: update snes ex12 regressions
DMPlex: fix parent/child interpolation with numFields > 0
DMP4est: also compute anyChange for uniformly refined/coarsened meshes
TS ex11: fix command line for AMR without computed gradients
TS ex11: remove gradient reconstruction from adaptivity requirements
DMPlexTree: some compilers want this var initialized
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.
DMPlexTS: removed unused variables
DMPlex/DMP4est: small fixes for next warnings and errors
SNES ex36 and ex52: These do not work anymore
DMPforestGetTransferSF_Point(): try to match parents
PetscViewerHDF5: destroy old file data if setting new filename
DMPlex + FV: remove leaky references in projection functions
Plex: Fixed incredibly stupid bug in Jacobian computation
PetscViewer HDF5: added get name method
DMPlexTree: do not skip out of child matrix loops early
PetscFV: correct field offsets when limiting gradients
DMP4estTree: ignore negative values when getting/setting vector values for transfer
...

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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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DMPlex + FV: remove leaky references in projection functions

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

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

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

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: Remove unused variables

Plex: Fixed ComputeIntegral() to work with FVM
- May still have a bug, not sure

Plex: Forgot to eliminate PetscRealPart() after type change

Merge branch 'tisaac/dmp4est-set-periodic-domain' into knepley/fix-plex-mf-prec

* tisaac/dmp4est-set-periodic-domain:
Plex: fix line geometry for localized
Plex: fix section access to last commi

Merge branch 'tisaac/dmp4est-set-periodic-domain' into knepley/fix-plex-mf-prec

* tisaac/dmp4est-set-periodic-domain:
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
DMP4est: change order of setting projection height and localizing coordinates
DMP4est: prefer [0,L) for periodic coordinates
Plex: more descriptive debugging

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Plex+FE: Added missing FV dual space

Merge branch 'tisaac/plex-descriptive-debug' into tisaac/dmp4est-set-periodic-domain

* tisaac/plex-descriptive-debug:
Plex: more descriptive debugging

Plex: more descriptive debugging

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'tisaac/dm-locate-points-sf'

* tisaac/dm-locate-points-sf:
Plex: missed in IS
DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

Merge branch 'tisaac/dmp4est-feature-injection'

* tisaac/dmp4est-feature-injection: (27 commits)
DMP4est: linear solve regression tests
DMP4est: regression tests for exact interpolation/injectio

Merge branch 'tisaac/dmp4est-feature-injection'

* tisaac/dmp4est-feature-injection: (27 commits)
DMP4est: linear solve regression tests
DMP4est: regression tests for exact interpolation/injection
PetscDualSpace: create height subspaces at setup.
DMClone(): get agreement on cloning coordinates
DMP4est: bump number of procs in regression test
DMP4est: fix memory leaks
DMP4est: added diagnostic views
DMP4est: adding regression tests
SNES tutorials ex12: added RUN_EXACT, solve from exact solution
DMPlex: memory clean up in Injector/InterpolatorTree routines
DMP4est: use DMCoarsen_Forest
DMPlexComputerInterpolatorTree(): restore another work array
DMPlexAnchorsModifyMat(): restore work arrays
DMPlexComputeInjectorTree(): fix local / off-process bounds
DMPlexComputeInjectorTree(): more fixes
DMPlexComputeInjectorTree(): fix coarse/fine char mixup
DMPlexComputeInjectorTree() compiles
WIP: DMPlexComputeInjectorTree()
Plex tests ex3: added regression tests for injectors
DMPlex tests ex3: fix viewing, creating injectors
...

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Merge branch 'sanderarens/fix-plex-neumann-bc'

* sanderarens/fix-plex-neumann-bc:
SNES ex77: Test now passing - Fixed memory leak - Use parser for numeric output
SNES ex77: Added test from Sande

Merge branch 'sanderarens/fix-plex-neumann-bc'

* sanderarens/fix-plex-neumann-bc:
SNES ex77: Test now passing - Fixed memory leak - Use parser for numeric output
SNES ex77: Added test from Sander - Does not work yet
SNES ex77: add small penalty term to Lagrangian density. This speeds up the linear solver convergence a lot and also allows for larger pressure loadings.
SNES ex62: Fixed output for proper block sizes
DM: pass down block size to subIS when creating a subDM.
SNES ex77: delete some unused variables.
SNES ex77: call DMPlexLabelComplete for correct Dirichlet bc's.
SNES+Plex: Add checks for valid IS after calls to DMLabelGetStratumIS.
SNES ex77: check if IS from DMGetStratumIS is a valid pointer as it can be NULL if used in parallel.
SNES: Add ex77: nonlinear elasticity with pressure loading
Plex: R should be a proper rotation from \hat z to n
SNES+Plex: Allow for multiple label values per boundary condition in BdResidual/BdJacobian
SNES+Plex: Fix the dimensions in BdResidual/BdJacobian

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