update manual pages for context set and get routines regarding use from Fortran and defining interface for them

LG monitors: Simplify KSP/SNES residual monitors

Remove routines {KSP|SNES}MonitorLG[[True]ResidualNorm]Destroy() and use
PetscDrawLGDestroy() for the monitor destroy routine.

LG monitors: Simplify handling of LG contexts

LG monitors: Use KSP/SNES communicators to create the PetscDraw contexts

Merge branch 'barry/xml-nested-logging'

improved viewing of fractional counts in xml nested log viewing
fixed bug in output of doubles to xml nested log files

added SNESObjectiveFunction evaluation for logging. This issue was

Reported-by

improved viewing of fractional counts in xml nested log viewing
fixed bug in output of doubles to xml nested log files

added SNESObjectiveFunction evaluation for logging. This issue was

Reported-by: Ed Bueler <elbueler@alaska.edu>

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if a SNESSolve() fails during grid sequencing then the SNES returns rather than continuing to solve on finer grids

Turn off error generation if incorrect memory preallocation for SNESComputeJacobianDefault()
because user will not in general set it correctly for this computation

Merge branch 'maint'

SNES function evaluations were not counted for certain Jacobian computations

Reported-by:Ed Bueler <elbueler@alaska.edu>

Merge branch 'master' into jed/process-options-handler

added error checking for when PetscViewer is not passed to the standard monitor routines

Reported-by: Garth N. Wells <gnw20@cam.ac.uk>

Removed outdated output in example test file

Options: pass PetscOptions* to options handlers

PetscObjectAddOptionsHandler now takes an event handler that includes a
PetscOptions argument. PetscObjectProcessOptionsHandlers requires this
as inp

Options: pass PetscOptions* to options handlers

PetscObjectAddOptionsHandler now takes an event handler that includes a
PetscOptions argument. PetscObjectProcessOptionsHandlers requires this
as input.

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initial locks with concurrencykit and OpenMP

cleanup of many monitors that used nonthread safe constructors when no viewer passed in

cleanup of examples that generated unused variable messages when

initial locks with concurrencykit and OpenMP

cleanup of many monitors that used nonthread safe constructors when no viewer passed in

cleanup of examples that generated unused variable messages when compiled with --with-log=0

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One now passes the nullspace in the matrix for a linear system as the first Amat argument to KSPSetOperators, SNESSetOperators, TSSetIJacobian() not the second pmat argument

This allows nesting of K

One now passes the nullspace in the matrix for a linear system as the first Amat argument to KSPSetOperators, SNESSetOperators, TSSetIJacobian() not the second pmat argument

This allows nesting of KSP/PC where the matrix is singular but the matrix passed to construct the preconditioner (the pmat) is not singular

Reported-by: Stephan Kramer <s.kramer@imperial.ac.uk>

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MatMFFD doesn't need to have its own null space management
cherry-picked from 39601f4 (barry/remove-matmffdaddnullspace/master)

Add Fortran stub for SNESSetUpdate()

Reported-by: John O'Sullivan <jp.osullivan@auckland.ac.nz>

fixed definition of active constraints to only include f > 0 or f < 0 to match citation
removed dead vi examples
removed dead vi routine
updated vi examples output
added command line option to zero e

fixed definition of active constraints to only include f > 0 or f < 0 to match citation
removed dead vi examples
removed dead vi routine
updated vi examples output
added command line option to zero equality of x[] value with its constraint instead of hardwired 1.e-8

Reported-by: Asbjørn Nilsen Riseth <riseth@maths.ox.ac.uk>

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changed second argument of PetscObjectViewFromOptions() to PetscObject and all routines that use this routine

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED inste

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED instead of generating an error that stops the program. In response to Issue 96. This includes failures in MatCreateSNESMF() applications due to domain errors. The mechanism to propagate some errors is by setting Info or Nan into the output vector and using the norm or inner product reductions in SNES or KSP to propagate the error condition to all processes and then handling them immediately after the norm or inner product.

This allows, for example, ODE integrators to try again with a smaller time-step if the PCSetUp failed instead of requiring a complete restart of the run with other options.

Currently some error conditions, such as function domain error in a line search may not get progated up using the correct SNESConvergedReason

See src/snes/examples/tests/ex69.c for the handling of several conditions

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Merge branch 'barry/add-ksp-total-iterations/master'

allow SNESComputeFunction() to put Nan or Inf into resulting functions so
that they may be caught by SNESLineSearch() and other SNES routines and return up to
TS so that TS can recover by cutting the

allow SNESComputeFunction() to put Nan or Inf into resulting functions so
that they may be caught by SNESLineSearch() and other SNES routines and return up to
TS so that TS can recover by cutting the time-step etc

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PetscHeaderCreate: Shorten argument list and optimize memory allocation

* Remove type arguments from the macro
* Use a single memory allocation call instead of three

fixed missing CHKERRQ() detected by clang's --analyze

fix ex5.c so SNES counts linear solve over all grid sequencing steps to match cummulative counts of linear solver