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

Merge branch 'knepley/fix-fem-multifield'

* knepley/fix-fem-multifield:
DMDT: Fixed Fortran PetscQuadrature definition
DMPlex ex3: Added Q2 tests - Made DA tests only 2x2 - Changed output format

Merge branch 'knepley/fix-fem-multifield'

* knepley/fix-fem-multifield:
DMDT: Fixed Fortran PetscQuadrature definition
DMPlex ex3: Added Q2 tests - Made DA tests only 2x2 - Changed output format - Quad tests now actually work
DMDA: Added DMDAComputeL2GradientDiff()
PetscSpace: Fixed polynomial derivative evaluation for quads
DMDA: Fix closure operations in 2D
DMPlex: Interpolation cleanup - Remove unused PetscSpace - Fix uninitialized variable
PetscFE: Fix PetscBool handling
SNES ex62: Updated output
DMPlex ex3: Use PetscFECreateDefault() and correct tensor tests
PetscFE: Fix PetscFECreateDefault() - The space should default to tensor on a non-simplex - The quadrature should be tensor Gauss on a non-simplex
DT: Added PetscDTGaussTensorQuadrature()
DT: Added citation for Gloub+Welsch method
PetscSection: Now global section can also be viewed
DMPlex: Allow NULL function for ProjectFunction()
PetscDualSpace: Added doc for PetscDualSpaceApply() - Cherry-picked from df2d8bb
PetscFE: Fixed PetscFECreateDefault() - Setup FE - Minimum quad order - Destroy quad after setting
PetscFE: PetscFECreateDefault() now takes a number of components and a reference cell type - Cherry-picked from a255314
PetscFE: Added PetscFECreateDefault() - Cherry-picked from 8919f5a
PetscFE: Allow lowest order cell Lagrange dual basis functions
DMPlex: Fix preallocation with cell variables - I had an incorrect loop optimization

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

show more ...

Merge branch 'master' into prbrune/matcoloring-greedy

Merge branch 'maint'

* maint:
DTGaussQuadrature: fix weight averaging for npoints=2 and output

Conflicts:
src/dm/dt/examples/tests/ex1.c

DTGaussQuadrature: fix weight averaging for npoints=2 and output

DT: Added PetscDTGaussTensorQuadrature()

DT: Added citation for Gloub+Welsch method

Merge branch 'knepley/feature-plex-fas'

* knepley/feature-plex-fas: (56 commits)
DMPlex: Removed unused variable
DMPlex: Fix for C++ build, small fix for PetscFE
DMPlex: Removed leak from Tria

Merge branch 'knepley/feature-plex-fas'

* knepley/feature-plex-fas: (56 commits)
DMPlex: Removed unused variable
DMPlex: Fix for C++ build, small fix for PetscFE
DMPlex: Removed leak from Triangle
SNES ex12: Two working unstructured FAS solves for the unregularized p-Laplacian
DMPlex: Cleaned up some memory issues
DMPlex: Implement injection - I don't think this should be required
DMPlex: DM interpolation requires the scaling vector for FAS
DMPlex: Can now create a map from coarse to fine vertices - This is currently necessary for FAS, which I think is wrong
DMPlex: Turn off Fortran stub
DMPlex: Fix DMPlexMatSetClosureRefined() - Reject duplicate fine points - Screen out point with dof = 0 - Fix the allocation for fine points
DMPlex: My brain did not work for several days - I have fixed the interpolation code - I think I can reuse that other code for something else
DMPlex: Fix setting Plex options on automatically refined meshed
SNES ex12/31/52/62/72: Use new SNESComputeJacobian() interface
DMPlex: Remove MatStructure from DMPlexComputeJacobianFEM() - Add missing declarations
Sys Logging: Fixes for log detail - Must preserve reduction count - Output objects and memory - Output stage summary
SNES ex12: Fixing things for multilevel - Need to set PetscFE on all coarse grids - Need application context for interpolator construction
SNES ex12: Use PetscFESetUp(), and fix quadrature ref handling
SNES ex52/62: Use PetscFESetUp(), and fix quadrature ref handling
DMPlex ex3: Uses automatic section creation, PetscFESetUp(), and fix quadrature ref handling
DMPlex: Fixing interpolator construction - Fixed definition of rectangular sizes - Use PetscFERefine() - Use special MatSet
...

show more ...

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTransp

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTranspose: fix for lazy block size
mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option.
configure: add FC_DEFINE_FLAG to petscvariables
added a citation for pounders, Stefan finally came through
update to latest netcdf fixes bug that did not allow building on recent Mac OS X
DMPlex: Fixes for CGNS - Fixed loop bounds since CGNS uses closed intervals - Bug with mixed cell types - Typo with coordinates
final updates from nightly tests
fix for countcfunction
removed outdated docs and comments on MatStructure usage removed SAME_PRECONDITIONER since no longer used removed unneed use of MatStructure in Schur complement matrix
removed MatStructure arguments from Tao
fixes for Sundials and fun3d cannot use MPIU_SUM for integer arrays
inplace ILU factorization must update state of inplace matrix to prevent infinite recursion of updating PC
fixes for BDDC by the way not having BDDC always in the testing is going to lead to trouble
the compute Jacobian functions for SNES and TS now do not take a MatStructure flag
KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner if the operator changed in the way that SAME_PRECONDITIONER did with KSPSetOperators()
tracks when Mat's have a change in nonzero structure this information can be used by PC to determine how preconditioners must be rebuilt currently only does an error check if the user said same nonzero pattern but actually changed the pattern
completed cleanup of removal of matrix pointers to compute jacobian routines
makefile: Added 'make includegraph' to create an inclusion dependency graph.
Contrib: Updated include-graph.sh script to ignore *.hh files
...

Conflicts:
src/dm/dt/interface/dt.c

show more ...

Merging master with feature-dmmoab. Only conflict was with SOURCECXX specification under impls/moab/makefile.

Merged petsc/petsc into master

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

DT: PetscQuadrature is now a PetscObject
- Added PetscQuadratureGet/SetData()

Merge branch 'maint'

* maint:
DT: remove spurious printing

Conflicts:
src/dm/dt/interface/dt.c

DT: remove spurious printing

Merge branch 'master' into barry/ts-rhsjacobian-only

Merge branch 'shri/update-SuiteSparse' into shri/external-package-KLU

Conflicts:
conf/test
config/examples/arch-linux-pkgs-dbg-ftn-interfaces.py
config/examples/arch-linux-pkgs-opt.py

add quad support for acos,asin,tgamma

Merge branch 'balay/tao-to-petsc'

Conflicts:
src/snes/impls/fas/fasfunc.c
src/snes/impls/fas/fasgalerkin.c

more (double) case in print statements
some badly formatted code

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
include/makefile

Merge remote-tracking branch 'origin/barry/remove-big-g'

Merge branch 'master' into knepley/feature-mat-zerorowscols-baij