Merge branch 'tisaac/feature-fe-geom-dim' into tisaac/plex-flexible-projection

Use the new PetscFECellGeom

Conflicts:
include/petscdmplex.h
include/petscfe.h
src/dm/impls/plex/plexfem.c

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove unused var
Plex+SNES+TS: Complete reorganization of residual evaluation - Now both FE and FV examples use the same method, but there are a bunch of switches which should be eliminated - There is a confusion about IFunction and RHS, but I think they can both be in one function - Added DMPlexSNESGetGeometryFVM() and DMPlexSNESGetGradientFVM() - Added DMPlexGet/RestoreCellFields() and DMPlexGet/RestoreFaceFields() and DMPlexGet/RestoreFaceGeometry() - I think that FV geometry caching needs to be redone - Added DMPlexReconstructGradients_Internal() - Added DMPlexComputeBdResidual_Internal() which does not work for FV - Replaced DMPlexComputeResidualFEM_Internal() with DMPlexComputeResidual_Internal()
Plex: Added DMPlexInsertBoundaryValues() - Unified FE and FV boundary values
Plex: DMPlexProjectFunctionLableLocal() gets discretizations from the DM now
Plex: Added DMPlexComputeGradientFVM()
PetscDS: Fix up some functions to work for both FV and FE
PetscFV: Change PetscFVIntegrateRHSFunction() to get info from PetscDS
TS ex11: There is only one field in our current paradigm - We would need to split Riemann solvers for multiple fields right now
Plex+TS: Remove use of computeGradients in favor of check for dmGrad
TS ex11: Updated interface calls
Plex+TS: Change DMPlexTSGetGradientDM() to automatically construct the gradient info, DMPlexTSSetRHSFunctionLocal() can now be replaced by the DMTS version - Remove unnecessary declarations
Plex+SNES: Add missing declaration
Plex+FE: Removed all use of PetscCellGeometry, Changed FE integration to use PetscFECellGeom
DMSNES+Plex: Added DMPlexSNESGetGeometryFEM() to cache geometry
PetscDualSpace: Remove use of PetscCellGeometry in PetscDualSpaceApply() - Fixed up calls to it for projection into spaces
DMDA: Remove use of PetscCellGeometry in DMDAProjectFunctionLocal()
Plex: Added DMPlexComputeGeometryFEM() and PetscFECellGeom structure
...

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Plex+SNES: Missing declaration

Plex+SNES: Add missing declaration

Merge branch 'prbrune/snes-fascontinuation'

* prbrune/snes-fascontinuation:
SNESFAS: added tau-corrected grid continuation.

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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Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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SNES+DM: Added SNESMonitorFields()
- Activated by -snes_monitor_fields

Merge branch 'prbrune/snes-removegetsetnorm'

* prbrune/snes-removegetsetnorm:
Remove SNESGetFunctionNorm() and SNESSetFunctionNorm().

Remove SNESGetFunctionNorm() and SNESSetFunctionNorm().

The intended replacement is:
1. SNESGetFunction()
2. VecNorm()

snes->norm was going stale, causing some confusion among users. This
way, the

Remove SNESGetFunctionNorm() and SNESSetFunctionNorm().

The intended replacement is:
1. SNESGetFunction()
2. VecNorm()

snes->norm was going stale, causing some confusion among users. This
way, there's no confusion.

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Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

Merge branch 'master' into prbrune/docs-snesmanualupdate

* master:
Doc: fix spelling errors in users manual
superlu_dist determines namemangled based on blas/lapack mangling, NOT fortran manglin

Merge branch 'master' into prbrune/docs-snesmanualupdate

* master:
Doc: fix spelling errors in users manual
superlu_dist determines namemangled based on blas/lapack mangling, NOT fortran mangling
SNESNASM: Explicitly set the NASM type to PC_ASM_BASIC in ASPIN.
SNESNASM: Add missing SNESNASMSet/GetType()
changed prototypes for args for KSPComputeEigenvalues[Explicitly] to arrays and improved manual pages to clarify that arrays are provided by users
update src/mat/examples/tests/ex72.c for reading symmetric matrix in MatrixMarket to petsc binary file
allocate one more space for row data for ml matrix then one might think is correct. This resolves a problem in a user code and won't break anything since it is just space allocated (possibly due to bug in ml).
Revert "metis/parmetis: update to metis-5.1.0/parmetis-4.0.3" There were a couple of reports of breakage of mumps with this update http://lists.mcs.anl.gov/pipermail/petsc-dev/2013-September/012853.html Subject: [petsc-maint] Issue with Metis in PETSC-DEV?
unitialized values outside array size, found by valgrind this example is still funky since it does not seem to handle array sizes properly everywhere
make sure example does not send uninitialized data through MPI to confuse valgrind
make sure no initialized data is sent via MPI to confuse valgrind
create rule for testexamples_SSL to prevent warning in make alltests
variable of wrong type and not even used
cleanup the function prototype representation for pre and post linesearch checking functions and improve documentation minor cleanup of documentation of several basic SNES functions
removed definition of DMADDA and documented removal

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Merge branch 'prbrune/snesnasm-typeinterface'

* prbrune/snesnasm-typeinterface:
SNESNASM: Explicitly set the NASM type to PC_ASM_BASIC in ASPIN.
SNESNASM: Add missing SNESNASMSet/GetType()

SNESNASM: Add missing SNESNASMSet/GetType()

Merge branch 'barry/improve-linesearch-docs'

cleanup the function prototype representation for pre and post linesearch checking functions and improve documentation
minor cleanup of documentation of several basic SNES functions

Fixing merge conflicts in dmregall.

Merged petsc/petsc into master

Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile