Plex+TS: Now the minimum cell radius is held by the Plex
- Its a geometric thing that is stashed

DMTS: Reorganized DMTS for Plex
- Now FVM computation functions look just like FEM
- Riemann solvers are specified to DS, just like f0/f1
- Removed explicit DMPlexTS structure, now just attach to DMT

DMTS: Reorganized DMTS for Plex
- Now FVM computation functions look just like FEM
- Riemann solvers are specified to DS, just like f0/f1
- Removed explicit DMPlexTS structure, now just attach to DMTS
- Changed DMPlexTSSetRHSFunctionLocal()
- Added DMPlexTSComputeRHSFunctionFVM()
- Added minradius to DMTS

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Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex1

Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex11: Fixed calls to DMSetCoordinateSection()
DM: FIxed DMClone() to copy dimension
Plex+DA: Now cell geometry routine can take a PetscFE in order to evaluate at quadrature points - We evaluate isoparametrically at the quadrature points - Changed DMDAComputeCellGeometry() --> DMDAComputeCellGeometryFEM() - Changed DMPlexComputeCellGeometry() --> DMPlexComputeCellGeometryFEM() - Added DMPlexComputeCellGeometryAffineFEM()
DM: Added a embedding dimension, different from the topological dimension - This can now be set in DMSetCoordinateSection(), or it can be automatically determined
Plex: Fix output for ex4
DM: Added DMGetDimPoints() - This replicates DMPlex/DAGetDepthStratum(), but uses the dimension which people have said is more intuitive
DM: Move dimension up into DM - Both DA and Plex had this and I think it makes sense

Conflicts:
src/dm/impls/plex/plexcreate.c

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Merge branch 'knepley/fix-petsc-fv'

* knepley/fix-petsc-fv:
PetscFV: Fully enable other limiters
TS+Plex: Overlap cells were misidentified as ghost cells

Merge branch 'knepley/fix-petsc-fv' into maint

* knepley/fix-petsc-fv:
PetscFV: Fully enable other limiters
TS+Plex: Overlap cells were misidentified as ghost cells

TS+Plex: Overlap cells were misidentified as ghost cells

DM: Added a embedding dimension, different from the topological dimension
- This can now be set in DMSetCoordinateSection(), or it can be automatically determined

DM: Move dimension up into DM
- Both DA and Plex had this and I think it makes sense

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

Merge branch 'knepley/feature-problem-class'

* knepley/feature-problem-class: (40 commits)
PetscDS: Renamed from PetscProblem
ftn-types: fix compilers errors with PetscSection [remove duplicate

Merge branch 'knepley/feature-problem-class'

* knepley/feature-problem-class: (40 commits)
PetscDS: Renamed from PetscProblem
ftn-types: fix compilers errors with PetscSection [remove duplicate code from petscvec*.h90]
PetscSection: Fix Fortran datatypes support
DMPlex: Added quads to cell refiner transform support
DMPlex ex3: Updated to Problem interface
DMDA: Fixed FE projection functions
PetscSection: Fixes for Fortran stubs
DMPlex+TS+Doc: Function docs
PetscSection: Fortran bindings
DMPlex+HDF5: Had revered handedness of transformed periodic coordinates
DMPlex+HDF5: Preserve aspect ratio with remapping of periodic coordinates
DMPlex: Added missing declarations
Sys+DMDT: Added PetscValidFunction()
DMPlex: Fix for DMPlexProjectField()
DMPlex+HDF5: Selectively output fields for viz - Fields with NULL name are ignored
PetscSection: Allow NULL names
DMPlex: Fixes for DMPlexProjectField()
PetscProblem: Added scalar integral (objective function) - Added PetscProblemGet/SetObjective() - Used in PetscFEIntegrate() - Reworked PetscProblemEnlarge_Static()
DM+DT: Adding Fortran bindings
PetscViewer: Added HDF_VIZ format to names
...

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Merge branch 'knepley/feature-problem-class' into knepley/feature-quad-fas

* knepley/feature-problem-class: (38 commits)
PetscSection: Fix Fortran datatypes support
DMPlex: Added quads to cell r

Merge branch 'knepley/feature-problem-class' into knepley/feature-quad-fas

* knepley/feature-problem-class: (38 commits)
PetscSection: Fix Fortran datatypes support
DMPlex: Added quads to cell refiner transform support
DMPlex ex3: Updated to Problem interface
DMDA: Fixed FE projection functions
PetscSection: Fixes for Fortran stubs
DMPlex+TS+Doc: Function docs
PetscSection: Fortran bindings
DMPlex+HDF5: Had revered handedness of transformed periodic coordinates
DMPlex+HDF5: Preserve aspect ratio with remapping of periodic coordinates
DMPlex: Added missing declarations
Sys+DMDT: Added PetscValidFunction()
DMPlex: Fix for DMPlexProjectField()
DMPlex+HDF5: Selectively output fields for viz - Fields with NULL name are ignored
PetscSection: Allow NULL names
DMPlex: Fixes for DMPlexProjectField()
PetscProblem: Added scalar integral (objective function) - Added PetscProblemGet/SetObjective() - Used in PetscFEIntegrate() - Reworked PetscProblemEnlarge_Static()
DM+DT: Adding Fortran bindings
PetscViewer: Added HDF_VIZ format to names
PetscFE+OpenCL: Make more respectable elasticity
PetscFE+OpenCL: Add flag for printing kernel
...

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Merge branch 'knepley/feature-problem-class' into knepley/fix-fe-gpu

* knepley/feature-problem-class: (34 commits)
PetscSection: Fixes for Fortran stubs
DMPlex+TS+Doc: Function docs
PetscSecti

Merge branch 'knepley/feature-problem-class' into knepley/fix-fe-gpu

* knepley/feature-problem-class: (34 commits)
PetscSection: Fixes for Fortran stubs
DMPlex+TS+Doc: Function docs
PetscSection: Fortran bindings
DMPlex+HDF5: Had revered handedness of transformed periodic coordinates
DMPlex+HDF5: Preserve aspect ratio with remapping of periodic coordinates
DMPlex: Added missing declarations
Sys+DMDT: Added PetscValidFunction()
DMPlex: Fix for DMPlexProjectField()
DMPlex+HDF5: Selectively output fields for viz - Fields with NULL name are ignored
PetscSection: Allow NULL names
DMPlex: Fixes for DMPlexProjectField()
PetscProblem: Added scalar integral (objective function) - Added PetscProblemGet/SetObjective() - Used in PetscFEIntegrate() - Reworked PetscProblemEnlarge_Static()
DM+DT: Adding Fortran bindings
PetscViewer: Added HDF_VIZ format to names
PetscFE+OpenCL: Make more respectable elasticity
PetscFE+OpenCL: Add flag for printing kernel
DMPlex: Fixes to DMPlexProjectField()
PetscFE: Fix work arrays
PetscFE+OpenCL: Fix interface updates
DMDT: Fix complex problems
...

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DMPlex+TS+Doc: Function docs

Merged upstream/master to feature-dmmoab

Merge remote-tracking branch 'upstream/master'

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]
gfortran: remove 132 char limit from f90 free-form
SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc
DMPlex-Gmsh: Use trueNumCells when building the coordinate section
Sys: Got guard logic reversed
Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*()
PetscFV: I hate fucking complex
removed ltog scatter from DMDA since functionality can be obtained with gtol scatter and less memory
fix test of DMLocalToGlobalBegin/End and add actual test cases
improve object memory logging for DA, ISLocalToGlobal and ISBLOCK
lower high water mark of constructing parallel scatter by allocating only as much room in svalues as needed
owner in VecScatter construction is the rank, therefor can use PetscMPIInt to hold it do not PetscInt
another reuse of allocated array in 2d/3d DMDA create
improved high water mark of DMDASetups by implementing and using PETSC_USE_POINTER for ISCreateBlock()
PetscFV: Another complex fix
DMPlex+TS: Fixing types
ISIdentity() was wrong for block IS! Indices are NOT scaled by bs
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
...

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Merge branch 'master' into barry/saws-options

Merge branch 'knepley/feature-fv-class'

* knepley/feature-fv-class: (44 commits)
PetscFV: Another complex fix
DMPlex+TS: Fixing types
PetscFV: Straighten out complex types
TS ex11: Fix casts

Merge branch 'knepley/feature-fv-class'

* knepley/feature-fv-class: (44 commits)
PetscFV: Another complex fix
DMPlex+TS: Fixing types
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
PetscFV: Fix Fortran define
PetscFV: Complex fixes
SNES+DM: Added SNESMonitorFields() - Activated by -snes_monitor_fields
PetscFV: Add Fortran types
SNES ex62: Use new DMPlexAddBoundary() interface - Added declaration of DMPlexComputeL2FieldDiff() - Fixed cast
SNES ex12: Fixed Neumann boundary conditions, and moved to new DMPlexAddBoundary interface() - Now do not automatically mark boundary faces
PetscFV: Fixed Fortran bindings
PetscFV+Plex: Refactored to put reconstruction routines in PetscFV_LeastSquares - Added PetscFVComputeGradient() - Added PetscFVLeastSquaresSetMaxFaces() - Moved last squares fitting routines to PetscFV_LeastSquares, and all the work space
PetscLimiter: Add other implementations
TS ex11: Fixed parallel mesh creation - Distribute after physics - Add output for tests
DMPlex: Fixed bug when using refinement from options - Must copy over the point SF
DMPlex: Distribution should copy over BC info
TS ex11: Added refinement tests
TS ex11: Fix boundary conditions after refinement, set types from command line
DMPlex: Added DMPlexCopyBoundary() - Copy boundary conditions after DMRefine() and DMPlexConstructGhostCells()
TS ex11: Specify boundary label
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/plex.c
src/snes/examples/tutorials/ex62.c

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DMPlex+TS: Fixing types

PetscFV: Straighten out complex types

PetscFV+Plex: Refactored to put reconstruction routines in PetscFV_LeastSquares
- Added PetscFVComputeGradient()
- Added PetscFVLeastSquaresSetMaxFaces()
- Moved last squares fitting routines to Pets

PetscFV+Plex: Refactored to put reconstruction routines in PetscFV_LeastSquares
- Added PetscFVComputeGradient()
- Added PetscFVLeastSquaresSetMaxFaces()
- Moved last squares fitting routines to PetscFV_LeastSquares, and all the work space

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TS+Plex: Removed explicit use of "Face Sets" in favor of DMBoundary

DM+TS ex11: Removed redundant code
- Now use geometry from DMPlexTS
- Added DMPlexTSGetGeomtry() and declarations

DMPlex+TS: Massive overhaul
- Added LS capability, but need to move some things over to PetscFV
- Moved geometry setup and gradient setup inside
- Moved InsertBoundaryValues inside
- Switched to sett

DMPlex+TS: Massive overhaul
- Added LS capability, but need to move some things over to PetscFV
- Moved geometry setup and gradient setup inside
- Moved InsertBoundaryValues inside
- Switched to setting the RHSFunction directly so that my context does not get overwritten
- Need to replace use of "Face Sets" with BC information

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TS+DM: Added a Plex traversal for FV methods for RHS