Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Plex+TS: Allow U_t to have positive sign in IFunction

Removed unused variables

Plex+SNES+TS: Better way to tell if we are implicit

Plex+SNES+TS: Use PetscDS interface for implicitness

Plex+SNES: Preliminary handling of implicitness
- FVM is always explicit except for a time derivative
- FEM is always implicit
- I will allow the user to override this soon

SNES+Plex: Fixed FEM face interpolation
- Now works for any order

SNES+Plex: Fixed face field tabulation when one cell is an FV ghost cell

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

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

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'knepley/fix-vec-readonly'

* knepley/fix-vec-readonly:
Plex: Added read-only Vec fixes for point location and interpolation
Mat: Added read-only Vec fixes for MATDENSE

Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Plex: Added read-only Vec fixes for point location and interpolation

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Merge branch 'tisaac/feature-gamg-extensible' into barry/experiment

Conflicts:
src/ksp/pc/impls/gamg/gamg.h

Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
Plex: Preserve periodicity

Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
Plex: Preserve periodicity when adding ghost cells
Plex: Fixed DMPlexGetGlobalFieldOffset_Private() in optimized mode
Plex+SNES: Offset should be into field components, not basis functions
Plex+SNES: Add guards for optional arrays
DS: Added PetscDSGetComponentOffset(), Added to petsc.h
Plex+TS: FVM RHS computation uses a global F
Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term
Plex: Added DMPlexPointGlobalFieldRead/Ref()
Plex+SNES: Fixed DMPlexGetFaceFields() - It returns field values, not coefficients - FE evaluation is now done
FV: In PetscFVIntegrateRHSFunction(), the arguments are field values, not coefficients
FE: Added EvaluateFaceFields() to FE fields at face centroids
Plex: Added DMPlexPointLocalFieldRead()
FE: Have a standard tabulation at face centroids
Plex: Copy BC for hierarchical refinement
FE: Allow P0 over 1D cells
Plex+FV: Fixed BC with gradient calculation
Plex ex1: Move overlap computation after SetFromOptions
Plex: DMPlexDistribute() no longer calls DMSetFromOptions() - Fixed examples
...

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Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Doe

Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Does SF stratification by depth, not by dimension - The old code numbered cells after vertices
Plex+SNES: Fixes for nonzero cStart
cannot call PetscObjectGetName() on a subset of the MPI processes
MatView() with some matrix formats and ASCII_MATLAB did not print correct matrix name
Plex: Preserve periodicity when adding ghost cells
Plex: Fixed DMPlexGetGlobalFieldOffset_Private() in optimized mode
Plex+SNES: Offset should be into field components, not basis functions
Plex+SNES: Add guards for optional arrays
DS: Added PetscDSGetComponentOffset(), Added to petsc.h
Plex+TS: FVM RHS computation uses a global F
Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term
Plex: Added DMPlexPointGlobalFieldRead/Ref()
Plex+SNES: Fixed DMPlexGetFaceFields() - It returns field values, not coefficients - FE evaluation is now done
FV: In PetscFVIntegrateRHSFunction(), the arguments are field values, not coefficients
FE: Added EvaluateFaceFields() to FE fields at face centroids
Plex: Added DMPlexPointLocalFieldRead()
FE: Have a standard tabulation at face centroids
Plex: Copy BC for hierarchical refinement
FE: Allow P0 over 1D cells
Plex+FV: Fixed BC with gradient calculation
...

Conflicts:
config/builder.py

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Plex+SNES: Fixes for nonzero cStart

Plex+SNES: Offset should be into field components, not basis functions

Plex+SNES: Add guards for optional arrays

Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term

Plex+SNES: Fixed DMPlexGetFaceFields()
- It returns field values, not coefficients
- FE evaluation is now done

FE+FV: When mixing, FE should ignore hybrid (ghost) cells which FV uses for BC, and FV should evaluate on cells
- When creating default section, FE should not run over hybrid cells
- In DMPlexCompute

FE+FV: When mixing, FE should ignore hybrid (ghost) cells which FV uses for BC, and FV should evaluate on cells
- When creating default section, FE should not run over hybrid cells
- In DMPlexComputeResidual_Internal(), FE should not run over hybrid cells
- In EvaluateFieldJets(), FV does cellwise constant evaluation (should work in linear but demands per cell lookup which should be worked into the interface)
- In DMPlexProjectFunctionLabelLocal(), DMProejctFunctionLocal(), DMProjectFieldLocal(), DMPlexComputeL2Diff(), DMPlexComputeL2GradientDiff(), DMPlexComputeL2FieldDiff(), DMPlexComputeIntegralFEM(), DMPlexCompute InterpolatorFEM(), and DMPlexComputeInjectorFEM(), do not loop over hybrid cells
- Protect use of ghost label in DMPlexComputeGeometryFVM()

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Plex+SNES: Need to initialize residual arrays when mixing FE and FV