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

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

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

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

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

* knepley/feature-ts-fem+fvm-example: (32 commits)
Plex: Fix printf
Plex: Use DMGetCoordinateDim() instead of a calculation
Plex: Added routin

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

* knepley/feature-ts-fem+fvm-example: (32 commits)
Plex: Fix printf
Plex: Use DMGetCoordinateDim() instead of a calculation
Plex: Added routine to view geometry
TS ex18: Added new tests
TS ex18: Updated test output
TS ex18: Add support for functionals
TS ex18: Global field offsets depend on the point since we allow constraints
TS ex18: Move view to after LocalizeCoordinates()
Plex+HDF5: Fixed uninitialized variable
TS ex18: Advection tests working
Plex: Fixed integration with Toby's code that handles sub manifold interpolation - Needed to check for cEndInterior from adding ghost cells
TS ex18: Updated output
TS ex18: Trying out implicit and explicit TS - Added another test with implicit TS
TS ex18: Updated output
SNES ex62: Updated output for new Plex distribution
Plex: Fix leak - No need for extra BC copy
TS ex18: All examples now working - Added ability to use zero velocity - Fixed coordinate localization
TS ex18: Cast boundary values function
TS ex18: Fixes outflow boundary condition - Must index into vector of all field values
TS ex18: Added another advection test
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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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Plex: Use DMGetCoordinateDim() instead of a calculation

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
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Conflicts:
config/builder.py

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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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Merge branch 'master' into mlange/refactor-plex-distribute

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_1.out
src/dm/impls/plex/examples/tests/output/ex12_2.out

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

Merge remote-tracking branch 'origin/tisaac/plex-flexible-projection'

* origin/tisaac/plex-flexible-projection:
PetscDualSpace: Fixed function signature
Plex: update libraries for ex3
Plex: mo

Merge remote-tracking branch 'origin/tisaac/plex-flexible-projection'

* origin/tisaac/plex-flexible-projection:
PetscDualSpace: Fixed function signature
Plex: update libraries for ex3
Plex: move DMPlexProjectionFunction() back to libdm
Plex: use -dm_plex_max_projection_height in non-conforming examples
Plex: fixed a typo in DMPlexProjectFunctionLocal()
Plex: added DMPlexComputeProjection3Dto1D_Internal()
Plex: fixes to recent merge
PetscFE: added dim, dimEmbed to PetscFECellGeom
Plex: skip empty loops for empty dual spaces
DualSpace: 0-order Lagrange spaces do not have dual spaces for height > 0.
Plex: protect against field projection with height > 0.
Plex: start implementing projection with height > 0.
PetscDualSpace: added PetscDualSpaceGetHeightSubspace()
Plex: added DMPlexGet/SetMaxProjectionHeight()

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

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Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLoc

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLocalToGlobalBegin/End in examples removed to prevent cut and paste repeats of their use
openmpi: update to version 1.8.3
added more movies and pubs
more movies
MatGetDiagonalBlock() can be called before matrix is assembled
added a couple more movies/images
PetscLogEventGetId() was missing public prototype
simply output from make streams benchmark test
c2html: fixup so that C2HTML make variable is set [similar to cmake.py]
chaco: current blas test does'nt work with Cray CC [which automatically links with blas] and linux - where -lm needs to be listed explicitly. Switch the test to check if we are using PETSc modifled chaco
builddist: always install c2html/sowing
argonne logo for users manual cover
Remove PETSC_HAVE_CUSP_SMOOTHED_AGGREGATION, use PETSC_HAVE_CUSP instead.
mpich: use older tarball with cygwin/gnu compilers
updated information about packages PETSc can use in users manual
Updated users manual to latest ANL Report format requirements
mpich: update to mpich-3.1.3.tar.gz - remove -download-mpich-mpe [mpich no longer packages mpe] - remove -download-mpich-shared. It was added as a split from --with-mpi-shared to --known-mpi-shared and --download-mpich-shared in 50237a55163f90ac7341b723c6422dfa1dbce792 removing this gives back the control of shared=0/1 to package.py - remove download_solaris as the new tarball works with both gcov and on solaris - remove MPICHInstall() [and use GNUPackage.Install()] as the new tarball fixes 'make clean' requiring sudo
added more images and PETSc pubs
Doc: More refs
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Plex: added DMPlexComputeProjection3Dto1D_Internal()

Uses Frisvad's basis completion,
http://www.imm.dtu.dk/~jerf/papers/abstracts/onb.html

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: Added DMPlexComputeGradientFVM()

Plex: Added DMPlexComputeGeometryFEM() and PetscFECellGeom structure

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

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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Plex: Fix for isoparametric geometry

Plex: Complex fix

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() --> DMDACo

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()

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

Merge branch 'stefano_zampini/pcbddc-maint' into stefano_zampini/pcbddc_deluxe

Merge remote-tracking branch 'origin/irving/doc-cleanup'

Conflicts:
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexgeometry.c
src/snes/examples/tutorials/ex62.c

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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