Fixes for doctext update

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some Pets

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some PetscMalloc*()
3) Eliminated unneeded PetscCalloc*()
4) Removed some memory allocations and copies in MatFDColoringSetUp(), added local variables for better compiler optimization
5) Added MatSetValues_SeqAIJ_SortedFull(), added MatSetOption(MAT_SORTED_FULL)
6) Optimized DMCreateMatrix_DA_*AIJ for nonperiodic case to automatically have sorted columns (faster MatSetValues() times)
7) Eliminated call to PetscMemzero() in PetscFree()

Commit-type: style-fix, feature

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Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

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Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but not from examples).

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 -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find src -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/d' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/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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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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Merge remote-tracking branch 'origin/maint'

Missing SNESCheckFunctionNorm() in the Newton TR solver could result infinite loop on
Nan/Inf if user input is Nan/Inf

Commit-type: bug-fix
Reported-by: Heeho Park <heepark@sandia.gov>

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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Allow user provided KSP convergence test to be used by KSP called from SNESNEWTONTR

Previously SNESNEWTONTR was hardwired to call the default KSP convergence test and
then its own special test, inst

Allow user provided KSP convergence test to be used by KSP called from SNESNEWTONTR

Previously SNESNEWTONTR was hardwired to call the default KSP convergence test and
then its own special test, instead pass down whatever convergence test was set for
the KSP and use that one followed by the special test

Change test case to specifically look for requested string only
Prevents the need for alt files due to different convergence history
with different precisions and compilers

Commit-type: bug-fix, feature, example, portability-fix, testing-fix
Reported-by: Robert Nourgaliev <nourgaliev1@llnl.gov>
Reported-by: nightly tests

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Merged in barry/fix-nasm-uses-ksp/maint (pull request #1557)

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

Merged in barry/fix-nasm-uses-ksp/maint (pull request #1557)

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 KS

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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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SNESQN: fix location of update calls

As per the documentation, the update callback is called at the beginning of each step

fix missing CHKERRQ

Missing ierr and incorrect use of upsweep in help message

Commit-type: style-fix, documentation

Merge branch 'master' of bitbucket.org:petsc/petsc

Fix documentation that used outdated SNESGetPC() SNESSetPC()

Commit-type: documentation

Revert the function name where it is referenced