Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Merge from doc-fixes branch

Fixes for doctext update

Merged in barry/optimize-aij-da (pull request #1762)

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

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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Merge remote-tracking branch 'origin/barry/add-petscarrayxxx-ops' [PR #1771]

Added MatUpdateMPIAIJWithArrays()

Commit-type: optimization, feature, example
Reported-by: Hong Zhang <hongzhang@anl.gov>

Merged in barry/update-collective-on (pull request #1744)

Update the use of Collective on in the manual pages to reflect the new style

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Merge remote-tracking branch 'origin/psanan/docs-remove-manconcepts' [PR #1733]

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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Merged in jkruzik/petsc/jkruzik/feature-matcomposite-additions (pull request #1676)

MATCOMPOSITE improvements

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.a

Merged in jkruzik/petsc/jkruzik/feature-matcomposite-additions (pull request #1676)

MATCOMPOSITE improvements

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

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Merged in barry/feature-matcreateconstantdiagonal (pull request #1678)

Introduces a new Mat class that consists of a single constant value for each enrty of the diagonal.

set MatStructure

add MatCompositeMergeType

Introduces a new Mat class that consists of a single constant value for all entries of the diagonal.

Very light-weight matrix class suports factorization, SSOR, MatMult(), MatShit(), MatScale()
Usef

Introduces a new Mat class that consists of a single constant value for all entries of the diagonal.

Very light-weight matrix class suports factorization, SSOR, MatMult(), MatShit(), MatScale()
Useful for IMEX methods when the user provides on a RHSJacobian

Commit-type: feature

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rename GetNmat to GetNumberMat

Merged in dalcinl/fix-clang-warnings (pull request #1671)

Fix clang warning -Wextra-semi-stmt

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

rename GetNMat to GetNmat

get composite type

Fix clang warning -Wextra-semi-stmt

https://clang.llvm.org/docs/DiagnosticsReference.html#wextra-semi-stmt

warning: empty expression statement has no effect;
remove unnecessary ';' to silence this

Fix clang warning -Wextra-semi-stmt

https://clang.llvm.org/docs/DiagnosticsReference.html#wextra-semi-stmt

warning: empty expression statement has no effect;
remove unnecessary ';' to silence this warning [-Wextra-semi-stmt]
ierr = PetscOptionsTail();CHKERRQ(ierr);
^

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allow merging from left

get ith matrix

add counter for number of matrices

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