Merge branch 'maint'

Provide additional information in manual pages for line search algorithms

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

MatGetVecs() and KSPGetVecs() replaced with MatCreateVecs() and KSPCreateVecs()
since they are creators not getters

Merge branch 'knepley/fix-snesew-postsolve'

* knepley/fix-snesew-postsolve:
SNES: Eliminating redundant computation in SNESEW convergence check - We did not agree that PCNONE should imply KSP_NORM

Merge branch 'knepley/fix-snesew-postsolve'

* knepley/fix-snesew-postsolve:
SNES: Eliminating redundant computation in SNESEW convergence check - We did not agree that PCNONE should imply KSP_NORM_UNPRECONDITIONED, we could do this for the next release

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Merge branch 'knepley/fix-plex-coords-parallel'

* knepley/fix-plex-coords-parallel:
DMPlex: Incorrect periodicity information
KSP+SNES: Converged output now includes prefix
DMPlex ex4: Fixed t

Merge branch 'knepley/fix-plex-coords-parallel'

* knepley/fix-plex-coords-parallel:
DMPlex: Incorrect periodicity information
KSP+SNES: Converged output now includes prefix
DMPlex ex4: Fixed test output
Mat+Coloring: Greedy coloring fix - Use ocolors[] for off-diagonal piece
PetscSection: Added check for mismatch between SF and Section
DMPlex: DMPlexReplace_Static() fixes - Should share coordinateDM, not just the section, so we get correct SF - Pass on periodicity information
DMPlex: Refinement should create SF before coordinates, so coordinateDM gets correct SF - Also pass on periodicity information
DMPlex: Distribution should create SF before coordinates, so coordinateDM gets correct SF - Also pass on periodicity information

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SNES: Eliminating redundant computation in SNESEW convergence check
- We did not agree that PCNONE should imply KSP_NORM_UNPRECONDITIONED, we could do this for the next release

matlab: fix compiler warnings

KSP+SNES: Converged output now includes prefix

snes->ksp refered to when it did not exist

Traceback (most recent call last):
File "test/test_snes.py", line 155, in testCompJac
self.snes.computeJacobian(x, J)
File "SNES.pyx", line 236, in pe

snes->ksp refered to when it did not exist

Traceback (most recent call last):
File "test/test_snes.py", line 155, in testCompJac
self.snes.computeJacobian(x, J)
File "SNES.pyx", line 236, in petsc4py.PETSc.SNES.computeJacobian
(src/petsc4py.PETSc.c:141969)
Error: error code 85
[0] SNESComputeJacobian() line 2209 in
/Users/dalcinl/Devel/petsc-dev/src/snes/interface/snes.c
[0] KSPSetReusePreconditioner() line 192 in
/Users/dalcinl/Devel/petsc-dev/src/ksp/ksp/interface/itfunc.c
[0] Null argument, when expecting valid pointer
[0] Null Object: Parameter # 1

Reported-by: Lisandro Dalcin <dalcinl@gmail.com>

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changed isams to issaws for code clarity

SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc

A bug was introduced in ddd0b78 that broke nonlinear left preconditioning
due to the MATMFFD instance set up on the outer solve

SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc

A bug was introduced in ddd0b78 that broke nonlinear left preconditioning
due to the MATMFFD instance set up on the outer solver being copied to the
inner. The solver calls SNESSolve() on itself in a loop trying to difference
the preconditioned function. The solution is to set up the matrix-free context
after copying all relative state onto snes->pc, preserving the use case fix
that was the inspiration for the change in ddd0b78.

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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

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PetscObjectUseFortranCallbackXXX() already has PetscFunctionReturn() so remove redundant return 0; from numerious stubs

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

doc: fix getpdflabels to count manual chapters correctly.
Also fix URLs from man pages to manual.pdf

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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Merge branch 'prbrune/removeunwrappedmathfunctions'

* prbrune/removeunwrappedmathfunctions:
Math: fix typo
Added src/sys/examples/tests/ex25.c for PetscScalar and PetscReal wrapping.
Wrapped t

Merge branch 'prbrune/removeunwrappedmathfunctions'

* prbrune/removeunwrappedmathfunctions:
Math: fix typo
Added src/sys/examples/tests/ex25.c for PetscScalar and PetscReal wrapping.
Wrapped tan(),[sin,cos,tan]h() for Real/Scalar, a[sin,cos,tan]() for Real.
Wrapped math.h and quadmath.h functions used in petsc source exempting examples

Conflicts:
include/petscmath.h
src/dm/dt/interface/dt.c
src/ksp/ksp/impls/cg/stcg/stcg.c
src/snes/linesearch/interface/linesearch.c
src/ts/impls/explicit/rk/rk.c

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SNES: snes should pass its snes->jacobian and snes->jacobian_pre to snes->pc

initial arrays that are published to SAWs, otherwise SAWs may access them before PETSc code has put correct values into them

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.

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Merge branch 'master' into barry/nonlinearsolvertable

Conflicts:
include/petscsnes.h