Merge branch 'master' into barry/ksp-converged-reason-viewer

Conflicts:
src/sys/objects/options.c

Merge branch 'knepley/feature-plex-assembly-fortran'

* knepley/feature-plex-assembly-fortran:
DMPlex+SNES: Added Fortran bindings for assembly
SNES: Added DMPlex assembly declarations
PetscFV:

Merge branch 'knepley/feature-plex-assembly-fortran'

* knepley/feature-plex-assembly-fortran:
DMPlex+SNES: Added Fortran bindings for assembly
SNES: Added DMPlex assembly declarations
PetscFV: Moved struct defintions to type header

show more ...

DMPlex+SNES: Added Fortran bindings for assembly

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
...

show more ...

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
...

show more ...

Plex+SNES: Volumes are PetscReal

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 abo

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()

show more ...

Plex+FE: Removed all use of PetscCellGeometry, Changed FE integration to use PetscFECellGeom

DMSNES+Plex: Added DMPlexSNESGetGeometryFEM() to cache geometry

Plex+SNES+TS: Moved residual computation to solver utilities

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

show more ...

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()

show more ...

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

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
...

show more ...

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

show more ...

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

show more ...

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

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