running with -snes_monitor_lg_residualnorm cause NEWTONLS to not set its default line search because the setup for lg_residualnorm
used its own optionsbegin and caused OptionsTail() to return when it

running with -snes_monitor_lg_residualnorm cause NEWTONLS to not set its default line search because the setup for lg_residualnorm
used its own optionsbegin and caused OptionsTail() to return when it shouldn't.

This is a hacky fix for one case of a general issue that eventually needs fixing.

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Merge branch 'prbrune/snes-fascontinuation'

* prbrune/snes-fascontinuation:
SNESFAS: added tau-corrected grid continuation.

SNESFAS: SNESFASGetSmoother(Down/Up) and SNESFASGetCoarseSolve prefix fix.

When the user uses the SNESFASGetSmoother*() interfaces to create the smoothers
the prefix is set incorrectly due to the wr

SNESFAS: SNESFASGetSmoother(Down/Up) and SNESFASGetCoarseSolve prefix fix.

When the user uses the SNESFASGetSmoother*() interfaces to create the smoothers
the prefix is set incorrectly due to the wrong outer SNES being passed to
SNESFASCycleCreateSmoother_Private(). The fix is merely to pass the correct one.

Based-on-patch-by: Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>

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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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Remove SNESGetFunctionNorm() and SNESSetFunctionNorm().

The intended replacement is:
1. SNESGetFunction()
2. VecNorm()

snes->norm was going stale, causing some confusion among users. This
way, the

Remove SNESGetFunctionNorm() and SNESSetFunctionNorm().

The intended replacement is:
1. SNESGetFunction()
2. VecNorm()

snes->norm was going stale, causing some confusion among users. This
way, there's no confusion.

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SNESTEST: Fix ancient formatting error in docs.

SNESTEST: Update manual entry notes to say exactly what a user should expect.

SNESNASM: Explicitly set the NASM type to PC_ASM_BASIC in ASPIN.

SNESNASM: Add missing SNESNASMSet/GetType()

create new matrix for each finite difference Jacobian created to prevent triggering errors about new nonzeros entered into matrix

matrices created for storing finite differences for Jacobian must allow new nonzero allocation since do not know preallocation in advance

SNESQN: Fix manual for SNESQNSetRestartType

Reported-by: Patrick Farrell <patrick.farrell@maths.ox.ac.uk>

fixed locations in code where MatStructure argument had not been changed

Most of these were due to code that did not get compiled in tests; also made sure all that code now gets compiled in tests

Merge branch 'prbrune/fix-aspin-mat'

* prbrune/fix-aspin-mat:
SNESASPIN: Test for ex16 with ASPIN
SNESASPIN: Fix for the case of zero iterations

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
...

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SNESASPIN: Fix for the case of zero iterations

In the case where the absolute tolerance is satisfied in the
first subSNES step, the operators are never set on the subKSP,
leading to an error in the

SNESASPIN: Fix for the case of zero iterations

In the case where the absolute tolerance is satisfied in the
first subSNES step, the operators are never set on the subKSP,
leading to an error in the outer KSP iteration. For the sake of
generality, have the ASPIN Jacobian call KSPSolve() instead of
PCApply() when multiplying.

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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

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