refactored LMVM matrix names for Broyden-class methods

SNESQN harmonization with MATLMVM objects

Merge branch 'tchen01/ksp-pipeprcg' into 'master'

add pipelined predict-and-recompute CG variant

See merge request petsc/petsc!2442

add pipelined predict-and-recompute CG variant

This is a new CG variant which (pipelined predict-and-recompute CG) allows the global reductions and matrix vector products in each iteration to occur

add pipelined predict-and-recompute CG variant

This is a new CG variant which (pipelined predict-and-recompute CG) allows the global reductions and matrix vector products in each iteration to occur simultaneously.
The numerical properties may be better than pipecg.

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Merge branch 'master' into 'stefanozampini/sfwin-reuse-win'

# Conflicts:
# config/BuildSystem/config/packages/MPI.py

Merge branch 'jolivet/feature-hpddm-deflation' into 'master'

Add KSPHPDDM[Set|Get]DeflationSpace

See merge request petsc/petsc!2426

Add KSPHPDDM[Set|Get]DeflationSpace

Merge branch 'mark/fix-viewfromoptions' into 'master'

prototype for ViewFromOptions macro-->functions

See merge request petsc/petsc!2083

prototype for ViewFromOptions macro-->functions

Merge branch 'master' into 'master'

Add --download-hpddm

See merge request petsc/petsc!1994

--download-hpddm for PCHPDDM and KSPHPDDM

Merge branch 'pr1819/jkruzik/feature-pcdeflation/master' [PR #1819]

* pr1819/jkruzik/feature-pcdeflation/master:
PCDeflation.
Implements multilevel deflation preconditioner that can shift part of th

Merge branch 'pr1819/jkruzik/feature-pcdeflation/master' [PR #1819]

* pr1819/jkruzik/feature-pcdeflation/master:
PCDeflation.
Implements multilevel deflation preconditioner that can shift part of the spectrum to a predefined value.

Given a full rank deflation matrix W, the deflation preconditioner uses projections Q = W*(W'*A*W)^{-1}*W' and P = I - Q*A.
It computes computes initial guess x0 = x_{-1} - Q*r_{-1} which is the solution on the deflation space.
The preconditioner application consists of P*M^{-1} + factor*Q, where M^{-1} is an additional preconditioner.

See the documentation for PCDEFLATION above PCCreate_Deflation for more detailed description.

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remove SetPC SetCoarseKSP

set coarse probelm ksp

support dynamic tolerance

Merge branch 'maint'

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

Commit-type: portability-fix

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

Merged in barry/update-deprecate-functions (pull request #1654)

Change PETSC_DEPRECATED to PETSC_DEPRECATED_FUNCTION and PETSC_DEPRECATED_TYPEDEF for code clarity

Change PETSC_DEPRECATED to PETSC_DEPRECATED_FUNCTION and PETSC_DEPRECATED_TYPEDEF for code clarity

and to make the macros match the ones for ENUM and MACRO. Add version information for almost all de

Change PETSC_DEPRECATED to PETSC_DEPRECATED_FUNCTION and PETSC_DEPRECATED_TYPEDEF for code clarity

and to make the macros match the ones for ENUM and MACRO. Add version information for almost all deprecations
in a single consistent format. Remove a couple of unneeded deprecated functions that could be inlined.

Commit-type: style-fix

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Merged in barry/fix-naming-cg-methods (pull request #1650)

Fixed inconsistent naming with CG methods for TR

Approved-by: Matthew Knepley <knepley@gmail.com>

Fixed inconsistent naming with CG methods for TR

Some of the KSPXXX macros for xxx had an inconsisten KSPCGXXX that was not in the string xxx name
The KSPCGXXX was used for KSPCreate_CGXXX() but the

Fixed inconsistent naming with CG methods for TR

Some of the KSPXXX macros for xxx had an inconsisten KSPCGXXX that was not in the string xxx name
The KSPCGXXX was used for KSPCreate_CGXXX() but the other method functions were missing the CG, for example, KSPSolve_XXX()
(these meant using tags to find functions was cumbersome due to the special cases)
Missing Fortran macro

Removed the extraneous CG from the macros and the function usage; now all macros and functions have consistent PETSc style usage
that match the string names
Added deprecation messages for out-dated use
Added new configure check for PETSC_DEPRECATED_MACRO

I decided to remove the CG from the KSPCGXXX instead of adding a cg to the string name because 1) it was not possible to deprecate
the string names at compile time, we would have to have runtime warnings. 2) the string names are shorter, 3) the stcg already
had a cg (at the end and not the beginning) and that would have to be removed or we'd have the absurd cgstcg. If starting from
sratch today not worrying about legacy I would have all the string names begin with cg consistently (and naturally the KSPXXX would
have them as well), but for legacy reasons we have the current naming which is not ideal because it does not clearly
indicate which methods are CG methods. (We have this problem with other subclasses in PETSc also).

Commit-type: style-fix

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Merged in barry/rm-kspsettablevel (pull request #1627)

Remove unneeded and unused KSP functions that replicate PetscObject functions

Approved-by: Matthew Knepley <knepley@gmail.com>