SNES: Allow SNESTestJacobian() to function without calling SNESSolve()

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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SNES: Initialize memory

Introduce logging of memory usage to the PETSc event logging infrastructure.

The logging can be turned on and viewed with the options -log_view -log_view_memory

The logging requires the use of the

Introduce logging of memory usage to the PETSc event logging infrastructure.

The logging can be turned on and viewed with the options -log_view -log_view_memory

The logging requires the use of the PETSc malloc so may slow the runs slightly but since it is not
doing error checking of the memory it should not slow down the computations significently.

Four pieces of information about memory are logged and display in four additional columns in the table.
They are documented in the output above the table. Each column provides a particular "view" of the
memory usage in the event and they complement each other.

This should make it much easier for developers focusing on memory usage in their implementations
to understand the usage in the code, where the memory is being utilized, how it scales with problem size and number of processes etc.

Commit-type: feature

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Merged in barry/cleanup-petscstringviewer (pull request #1630)

Work on PetscViewerString. Fix use of PetscInt -> size_t, add new functionality, add usage by basic solver objects, add test case

Work on PetscViewerString. Fix use of PetscInt -> size_t, add new functionality, add usage by basic solver objects, add test case

Commit-type: style-fix, feature, documentation, example

SNESLineSearch should only be created and used if the SNES type requires the line search

Previously the line search was created for all solver and and SNESLineSearchSetFromOptions()
and SNESLineSear

SNESLineSearch should only be created and used if the SNES type requires the line search

Previously the line search was created for all solver and and SNESLineSearchSetFromOptions()
and SNESLineSearchView() called for all solvers, even those that never used it,
leading to confusion for users

Commit-type: feature, documentation
Reported-by: Robert Nourgaliev <nourgaliev1@llnl.gov>

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Deprecate old {Mat|PC|KSP}ComputeExplicitOperator in favor of {Mat|PC|KSP}ComputeOperator

{Mat|PC|KSP}ComputeExplicitOperator: add extra argument for matrix type

Merge remote-tracking branch 'origin/maint'

The SNESNASM nonlinear preconditioner doesn't ever use the KSP solver therefor
should never turn on the usesksp flag. The setting of this flag made the SNESASPIN solver
that uses the SNESNASM solver

The SNESNASM nonlinear preconditioner doesn't ever use the KSP solver therefor
should never turn on the usesksp flag. The setting of this flag made the SNESASPIN solver
that uses the SNESNASM solver incorrectly have SNESNASM process the options for the
KSP and view it in SNESView() which could lead to users incorrectly believing the
solver was being used. Also added more text to the manual pages for these objects
to clarify how they function and interact with the Jacobian.

Commit-type: bug-fix, documentation

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Merged in knepley/feature-poiseuille-example (pull request #1446)

Knepley/feature poiseuille example

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Don't call KSPCreate() and KSPSetFromOptions() in SNESSetFromOptions() if
the SNES method doesn't use KSP.

Calling the KSPSetFromOptions() processes the KSP options so users may think
they are actua

Don't call KSPCreate() and KSPSetFromOptions() in SNESSetFromOptions() if
the SNES method doesn't use KSP.

Calling the KSPSetFromOptions() processes the KSP options so users may think
they are actually being used, instead it will now print out a warning in
debug mode that the KSP options have been skipped. Also updated to test
harness cases that used -ksp_monitor_short when it wasn't really being used

Commit-type: testing-fix, style-fix, feature

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DM+DS: Exact solution functions should also carry contexts

Use new vector read-lock function names

The new one are VecLockReadPush, VecLockReadPop, VecSetErrorIfLocked

Merge branch 'knepley/feature-snes-patch' [PR #1332]

* knepley/feature-snes-patch:
Implement SNESPATCH, a SNES for the topological construction of nonlinear relaxation methods.