Merged petsc/petsc into rmills/petsc master.

DMPlex: Update calls to DMPlexMatSetClosure() to eliminate default arguments

Merge branch 'maint'

* maint:
changes/34.html: document stricter MatRestoreRow/MatRestoreRowIJ
Cannot use PETSC_COMM_WORLD in library code
DMPlex: Removed PETSC_COMM_WORLD from code
Fix VecS

Merge branch 'maint'

* maint:
changes/34.html: document stricter MatRestoreRow/MatRestoreRowIJ
Cannot use PETSC_COMM_WORLD in library code
DMPlex: Removed PETSC_COMM_WORLD from code
Fix VecSetDM() to accept dm=NULL

show more ...

DMPlex: Removed PETSC_COMM_WORLD from code

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory corruption occurs otherwise
DMPlex: All quadrilateral geometry tests working
DMPlex: remove unused variable
DMPlex: Hexahedron geometry tests now pass
DMPlex: More geometry work
DMPlex: use PETSC_HAVE_TGAMMA to get the build working on windows
configure: add test for tgamma() [this is missing on windows]
DMPlex: Added random transform tests for tets - Fixed memory leak
DMPlex: Fixed 3D geometry
DMPlex: FVM geometry tests now work for triangles
DMPlex: one more win32/complex fix
DMPlex: Enhanced geometry tests - Added random transforms of the reference triangle in 2D
DMPlex: Fixed complex problems in geometry calculation
DMPlex: Fixed Fortran test output
DMDT: M_PI --> PETSC_PI
DMPlex: Reorganized geometry testing
TS ex11: Put in 3D inflow and outflow ids from the command line
DMPlex: Added DMPlexRestoreCone/Support() to F90 interface definition header - Also added to test ex1f90
TS ex11: Need to make these ids input from the command line
DMPlex: Add Fortran bindings
DMPlex: Reorder tet output since I order tets differently
Builder: Link Fortran examples with Fortran linker
DMPlex: Fixed leak in example
DMPlex: Tutorial now shows how to output VTK
PetscViewer: Added VTK type for Fortran
DMPlex: Remove parameter names from prototype
DMPlex: Geometry fixes for C++ complex
DMAKKT: Remove from build
DMPlex: Now DMPlexCreateSection() only has an F90 interface
SNES: add Fortran bindings to DMSNESSet{Function,Jacobian}
SNES: remove superfluous casting in DM local Fortran bindings
SNES: compile zdmlocalsnesf.c
DMDT: Fix Fortran wrapper
DMPlex: Added Fortran interface for DMPlexMatSetClosure()
PetscSection: Added docs, enabled Fortran wrappers
DM: Added Fortran bindings for DMSNESSetFunction/JacobianLocal()
SNES ex12: Looks like 3D Neumann conditions are working
DMPlex: Fix volume determination for 2D in 3D
DMPlex: Better error reporting
SNES ex12: Boundary integration seems to work in 2D
DMPlex+FEM: Fix for boundary integration
TS ex11: Better error reporting
DMPlex ex8: Added FVM geometry tests
DMPlex: Fixed FVM geometry for 2D in 3D
SNES ex62: Now using PetscDT quadrature
DMDT: Translated FIAT's Gauss-Jacobi quadrature
DMPlex: Fix geometry tests - Fix tests for 2D projection
DMPlex: Geometry fixes
DMPlex: Small fixes for geometry
DMPlex: Fixed damn prototype
PetscSection: Added VecSetValuesSectionF90() - Fixed bug in Vec Fortran header
DMPlex: Added Fortran defines for additional insert modes
DMPlex: Silence warning in DMPlexInvertCells_Internal()
DMPlex: Functions passed to evaluation routines now return void and pass results in arguments
DMPlex: Now we give an explicit embedding dimension to the FVM geometry methods
DMPlex: Fixed complication with complex - Started to add 3D geometry stuff
TS ex11: Replace edge geometry with call to DMPlexComputeCellGeometryFVM()
DMPlex: Added normal argument to DMPlexComputeCellGeometryFVM() - This is only calculated for faces - Added calculation for faces in 2D
DMPlex: Damn makefiles
DMPlex: Added declaration for DMPlexCreateCGNS()
TS ex11: Reorganized computation of geometry in preparation for 3D
Builder: Now individual tests can have requirements - The key is 'requires', and it takes a list of package names - Also fixed up showSingleRun()
TS ex11: Use new DMPlexComputeCellGeometryFVM()
DMPlex: Added DMPlexComputeCellGeometryFVM() - Added internal volume methods
DMPlex: fix const and int vs. PetscInt
DMPlex: Better error reporting
DMPlex+ExodusII: Fixed reading of quads - Was broken by 2e1b13c25062c3c40593ce7412c5cd227259ade7
DMPlex: Hex cell geometry was broken - I don't see how this test passed before
DMPlex: Regression cleanup
DMPlex: Regression cleanup
SNES ex12: Fixed sign for Neumann BC
DMPlex+FEM: The dimension does not change for boundary elements
DMPlex: Geometry now works for boundary elements
DMPlex+FEM: Fixed quadrature coordinate handling for boundary integrals
SNES ex12: Reorganized tests, still working on Neumann conditions - Fixed boundary face label
DMPlex: Turn off CGNS by default
DMPlex: Added 1D cell geometry
DMPlex: DMPlexCreateCGNS()
DMPlex: Updated test ex1 output
DMPlex: Fixed compiler problems with complex
SNES ex12: Now does boundary integration - Still not verifying exact solution for Neumann conditions
DMPlex: Fix DMPlexComputeCellGeometry() to handle lower dimensional cells
DMPlex: Fixed error in projection from 3D to 2D - Need to check for case where normal is already z
DMPlex: Adding boundary integration
DMPlex: Fixed cell inversion for TetGen to commute with mesh interpolation
SNES ex12: Cleaning up ex12 testing
DMPlex: Added integration over boundary to DMPlexComputeResidualFEM() - Added quadBd, f0/1BdFuncs to PetscFEM struct - Needs to be tested
FEM Generation: We now allow a *_bd.h header that holds boundary discreization
Builder: Fixed regression requirements
Builder: Fixed specification of multiple tests to run
DMPlex ex7: Orientations now working properly
DMPlex: Changed orientation convention and fixed many bugs
SNEX ex12: Ignore generated headers
SNEX ex12 and ex52: Remove CTetGen warnings from test output - Fixed this in CTetGen repository
DMPlex: Fix default |J| for DMPlexComputeCellGeometry()
DMPlex: Fix for cell geometry (unbelievable screwup)
DMPlex ex7: Check that |J| is nonzero for each cell in interpolated mesh
DMPlex: Allow DMPlexComputeCellGeometry() to work with interpolated meshes
DMPlex: Added prototype for DMPlexCopyCoordinates(), and docs for that and DMPlexInterpolate()
DMPlex: Added F90 interface for DMPlexComputeCellGeometry()

Conflicts:
include/petscdmplex.h

show more ...

DMPlex: Remove parameter names from prototype

DMPlex: Better error reporting

DMPlex: Functions passed to evaluation routines now return void and pass results in arguments

DMPlex+FEM: The dimension does not change for boundary elements

DMPlex: Adding boundary integration
- Added a boundary integration input to DMPlexSetFEMIntegration(), this also takes cell normals
- Added an integrateBdResidualFEM() function to DMPlex
- f0 and f1

DMPlex: Adding boundary integration
- Added a boundary integration input to DMPlexSetFEMIntegration(), this also takes cell normals
- Added an integrateBdResidualFEM() function to DMPlex
- f0 and f1 for boundary integration take the cell normal as an argument (right now not used)
-

show more ...

Merged petsc/petsc into rmills/petsc master

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which
drop the string name argument.

* barry/rm-xxxregisterdynamic: (82 commits)
...

Conflicts:
src/ts/interface/tsregall.c

show more ...

Merge branch 'knepley/plex-surface-integration' into knepley/plex

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic b

Merge branch 'knepley/plex-surface-integration' into knepley/plex

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

show more ...

DMPlex: Added integration over boundary to DMPlexComputeResidualFEM()
- Added quadBd, f0/1BdFuncs to PetscFEM struct
- Needs to be tested

Merge branch 'master' into barry/ams

Conflicts:
include/petscviewer.h
src/sys/classes/viewer/interface/viewreg.c
src/sys/threadcomm/interface/threadcomm.c

Merge branch 'master' of bitbucket.org:petsc/petsc into knepley/plex

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

Merge branch 'balay/nightlybuild-fixes'

dmplex: doc fixes [nightlybuilds]

Merge branch 'balay/nightlybuild-fixes'

doc: nightlybuild fixes

Merge branch 'master' into tautges/dmmoab

* master: (24 commits)
testexamples: support *.cxx
...

DMPlex: Moved out Preallocation and FEM support to other files

Hg-commit: b2561291e574ff9a0f8a073426e136d4a44a4dde