Merge branch 'snes-jac-docfix' of bitbucket:goxberry/petsc

Fix remnant in 'barry/nonlinearsolvertable'

* 'snes-jac-docfix' of bitbucket:goxberry/petsc:
Make SNESJacobianFunction docs & code consi

Merge branch 'snes-jac-docfix' of bitbucket:goxberry/petsc

Fix remnant in 'barry/nonlinearsolvertable'

* 'snes-jac-docfix' of bitbucket:goxberry/petsc:
Make SNESJacobianFunction docs & code consistent.

show more ...

Make SNESJacobianFunction docs & code consistent.

Interface to SNESSetJacobian now includes a function with signature
PetscErrorCode (*J)(SNES,Vec,Mat,Mat,void*) as its fourth argument.
This commit

Make SNESJacobianFunction docs & code consistent.

Interface to SNESSetJacobian now includes a function with signature
PetscErrorCode (*J)(SNES,Vec,Mat,Mat,void*) as its fourth argument.
This commit brings the documentation for SNESJacobianFunction in
line with the SNESSetJacobian interface.

show more ...

Merge branch 'barry/nonlinearsolvertable'

Conflicts:
src/snes/impls/gs/gssecant.c

Merge branch 'master' into barry/nonlinearsolvertable

Conflicts:
include/petscsnes.h

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removed outdated docs and comments on MatStructure usage removed SAME_PRECONDITIONER since no longer used removed unneed use of MatStructure in Schur complement matrix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.

Merge branch 'barry/rm-matstructure-mat-pointer'

Conflicts:
include/petsctao.h

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

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()

SNES/TS still need to be cleaned up to better utilize the new interfaces

show more ...

completed cleanup of removal of matrix pointers to compute jacobian routines

update changes file

fixed tao examples to no longer use Mat* arguments for Jacobian/Hessian etc computations

introduced nonlinear solver HTML table
changed gs and pc in SNES to ngs and npc for consistency and clarity

Merged petsc/petsc into master

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

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

Merge branch 'barry/fix-setfunction-for-snesmf'

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

added faq item for snes matrix-free usage

SNESLineSearch: Fix documentation levels to highlight standard use case

Reported-by: Barry Smith <bsmith@mcs.anl.gov>

remove my silly naming of monitor function passed to SNESMonitorSet() as SNESMonitorFunction

convert to PetscMalloc1()
better handling of string viewer when running out of space

Merge branch 'balay/tao-to-petsc'

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

fixed quote marks for includes to <>

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

Conflicts:
include/makefile

Merge branch 'barry/rm-snesfunction-nonsense'

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