SNES: Now work vectors come from the DM

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Ste

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Stefano
fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
MatSchurComplement: Must initialize KSP package
bib: fix inbook citation
Bib: Updated some refs
SNES: fix copy/paste in man page
fortran: fix KSPCONVERGEDDEFAULT and SNESCONVERGEDSKIP in fortran includes
Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used
PCGAMG: remove distracting comment
KSP ex49: restrict near-null space for elasticity example with sym BC
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
Fix accidental creation of the matrices in SNESNCG used for linear analogue LS.
PCGAMG: add man page for PCGAMGType
fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()
rm //
Sys: new_ir changed from PetscInt to PetscObjectState - so fix mallocs to use the new type
SNES: Fixed package init in SNESLineSearchCreate()
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex5.c
src/dm/impls/plex/plex.c
src/dm/interface/dm.c

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Merge branch 'jed/converged-default-and-skip'

This process started with SNESDefaultConverged -> SNESConvergedDefault
in v3.4, but the other parts have been added piecemeal. Deprecation
support in C

Merge branch 'jed/converged-default-and-skip'

This process started with SNESDefaultConverged -> SNESConvergedDefault
in v3.4, but the other parts have been added piecemeal. Deprecation
support in C interface.

* jed/converged-default-and-skip:
SNES and KSP: add deprecation for *DefaultConverged and *SkipConverged
KSP: rename KSPDefaultConverged* to KSPConvergedDefault*
KSP: rename KSPSkipConverged -> KSPConvergedSkip
SNES: document SNESSkipConverged -> SNESConvergedSkip
snes->ttol to be used only in convergence tests.
Renamed SNESKSPEW_Pre/PostSolve --> KSPPre/PostSolve_SNESEW.
Renamed SNESSkipConverged --> SNESConvergedSkip.

Conflicts:
include/petscsnes.h
src/docs/website/documentation/changes/dev.html

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Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

Renamed SNESSkipConverged --> SNESConvergedSkip.

Merged petsc/petsc into rmills/petsc master.

Merge branch 'jed/stack-call-blas'

Fix performance bug that calling BLAS takes an amount of time dependent
on the number of memory allocations that the program has made.

* jed/stack-call-blas:
Pe

Merge branch 'jed/stack-call-blas'

Fix performance bug that calling BLAS takes an amount of time dependent
on the number of memory allocations that the program has made.

* jed/stack-call-blas:
PetscStackCallBLAS: new macro instead of PetscStackCall (skip CHKMEMQ)
Stack: consolidate handling of PetscStack

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PetscStackCallBLAS: new macro instead of PetscStackCall (skip CHKMEMQ)

When CHKMEMQ occurs on every call to BLAS or Lapack, we sometimes see
unacceptable performance degradation (orders of magnitude

PetscStackCallBLAS: new macro instead of PetscStackCall (skip CHKMEMQ)

When CHKMEMQ occurs on every call to BLAS or Lapack, we sometimes see
unacceptable performance degradation (orders of magnitude).
PetscStackCallBLAS is currently identical to PetscStackCall except for
skipping CHKMEMQ, but such checking could be made optional in the
future.

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Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

made public several private KSP and SNES methods that may be used by plugin KSP and SNES classes written by users

Hg-commit: 0d6205a1c0feb0cbd5a40a08327fe43345c19792

fixed function names with Default to match new standard (which I just wrote)
fixed a few more functions that should be PETSC_INTERN

Hg-commit: 87889fe4f6d4e8d0963adcc79d438e75330601c6

added PetscObjectComm() and used it to replace (((PetscObject)obj)->comm)

Hg-commit: 3da37c458124ad48ae939f4e9823e4430ee0b8be

removed PETSC_NULL from C and Fortran (except declaration in C for backward compatibility). Kept PETSC_NULL_xxx for Fortran
Fixed a few bugs where PETSC_NULL had been used incorrectly.

Hg-commit: 05

removed PETSC_NULL from C and Fortran (except declaration in C for backward compatibility). Kept PETSC_NULL_xxx for Fortran
Fixed a few bugs where PETSC_NULL had been used incorrectly.

Hg-commit: 054705a517d7f4388a8a084415d7478cbe95dff4

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wrapped LAPACK calls in PetscStackCall()

Hg-commit: 9cee7ca55a1199d641b77bd38e3a2ece2cb4320b

commit after merge

Hg-commit: ebb357f10b0c83746021a2f5d6008cb620ae37d0

Uncrustified src/snes/*

Hg-commit: 0b89af55379cc95040ca47c4c1f8000d6a978df2

Reformatted: "Do not put a blank line immediately before PetscFunctionReturn;"

Hg-commit: c8a41c455986e732d0ea0513d7162a54daffaece

updated PetscBLASIntCast() to return an error code

Hg-commit: 57d88da2280bc54336c931f5cac9a473f8f9a031

commit aftr merge

Hg-commit: 854807b200896ff0e3d6fb344a549ed1a2b93850

Style improvements: braces around 'else', partial '){' -> ') {'

Hg-commit: adc31fe870178bcba56a29e10981c8f8716a006a

fixed rest of mising CHKERRQ() fixed a few unused but set variables

Hg-commit: 4acc0881334451e4d784ba0aa3b37fae2f983d1f

-ts_monitor_solution and -ts_monitor_draw now create private draw window instead of using common

Hg-commit: 8be320aece161ad7864be14c71303784f1c836df

Commit after merge

Hg-commit: 29c41d281e3ece3127c753661dccfd04e452b7f8

removed trailing blanks from source code
added rule rmtrailingblanks accessible via make ACTION=remtrailingblanks tree

Hg-commit: 6e3652165d48aa5f3e94dd66bf607adea6fac27a

code to match PETSc style guide for if (xxx) for (xxx) sizeof(xxx)

Hg-commit: 01e0d19bcd83a980fb5e8e32b294a95da72b405f