A fix for fieldsplit pcs when using snes virs.

When reset pc fieldsplit saves a copy of the original IS. SNES VIRS then calls a new function, PCFieldSplitRestrictIS, and supplies
the inactive set t

A fix for fieldsplit pcs when using snes virs.

When reset pc fieldsplit saves a copy of the original IS. SNES VIRS then calls a new function, PCFieldSplitRestrictIS, and supplies
the inactive set to create new ISs for the fieldsplit. This is then reindexed and passed down to any nested fieldsplits.

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fixed up formatting of references in manualpages to consistent style

References:
+ 1. - ref1
. 2. - ref2
- 3. - ref3

previously the formatting was varied and ugly

broken nonlinear solver table links fixed

Reported-by: Andrew McRae <A.T.T.McRae@bath.ac.uk>

Also made References: formatting consistent by always listing authors first

begun adding more monitoring functionality to SNESLineSearch

snesvi should only use DM to compute bounds if it can compute bounds
fixes for shashi example, converges to some degree with rs method

Complete update to new PetscOptions interface

Begin renaming the PetscOptions objects for the future where PetscOptions will not be a singleton

Merge branch 'barry/add-mpiu_allreduce'

Merge branch 'stefano_zampini/fix-aspin-create'

Introduce MPIU_Allreduce() to detect cases where all processes that share an MPI comm do not call the same sequence of MPI_Allreduce()
This is a bug that can be difficult to track down.

Suggested-by

Introduce MPIU_Allreduce() to detect cases where all processes that share an MPI comm do not call the same sequence of MPI_Allreduce()
This is a bug that can be difficult to track down.

Suggested-by: Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>
Suggested-by: Patrick Lacasse <placasse@giref.ulaval.ca>

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fix violations of PETSc style guide: Usage of SETERRQ and NULL

SNESASPIN: forgot to reset NEWTONLS and free the data

SNESASPIN: destroy the nonlinear preconditioner (specific to ASPIN) when ASPIN is destroyed

Typo fix contributed by Patrick Sanan

Merge branch 'maint'

SNESUpdateCheckJacobian: make relative norm output syntactically correct

Merge branch 'master' into barry/fix-petscviewer-attempt-2

Merge remote-tracking branch 'origin/knepley/feature-snes-deflation'

* origin/knepley/feature-snes-deflation: (55 commits)
Plex: Correct complex problem
Plex ex12: Now PCMG monitor creates its o

Merge remote-tracking branch 'origin/knepley/feature-snes-deflation'

* origin/knepley/feature-snes-deflation: (55 commits)
Plex: Correct complex problem
Plex ex12: Now PCMG monitor creates its own coarse solutions
Plex ex12: Put in working setting for PCMG coarsening test
XDMF: Now take a bunch of files as input
SNES ex12: Use monitors instead of brute force to monitor errors
SNES ex12: Renumber meshes to match MG numbering
PC+SNES: Attach a level id to subsolvers in a multilevel solve - We should have done this years ago
Plex ex12: Added error output on each level
Plex: Added DMPlexComputeL2DiffVec() - This puts cellwise error integrals in a Vec
Plex: Fix variable init
Add an option to ex12 to dump the coarsened hierarchy to disk.
Plex: Fixed unused variables
Plex: Fixed PetscScalar conversion problem
Plex: Fixed function header
Profile DMCreateInterpolation (nontrivial cost for nonnested meshes)
Replace the arguments for coarsening in ex12 with correct ones
Plex: Using a refinement function
Plex: Added DMPlexGet/SetRefinementFunction() - Use to do non-uniform refinement
Events for DMCoarsen and DMLocatePoints
Update the pragmatic build script to use master, not my branch
...

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added error checking for when PetscViewer is not passed to the standard monitor routines

Reported-by: Garth N. Wells <gnw20@cam.ac.uk>

Removed outdated output in example test file