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

show more ...

Deprecate old {Mat|PC|KSP}ComputeExplicitOperator in favor of {Mat|PC|KSP}ComputeOperator

{Mat|PC|KSP}ComputeExplicitOperator: add extra argument for matrix type

Merged in knepley/feature-snes-check-split (pull request #1553)

Knepley/feature snes check split

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

Fixing variable name

Plex+SNES: Remove check for small value

DM: Changed printing of Taylor test monitor

SNES+Plex: Update output for new check

Capitalize Enum types

Fixes for Barry's review in pr1451 and others

Revert "Revert "Merge branch 'pr1451/hmorgan/fix-GLL-quadrature/master' [PR #1451]""

This reverts commit f8f0706ac36152a85c2163c77236a76f30185f56.

Merged in jmlarson/fixing_pounders_regression_test_plotting/maint (pull request #1504)

Was making too large of a matrix, which may result in incorrect profiling

Approved-by: Matthew Knepley <kneple

Merged in jmlarson/fixing_pounders_regression_test_plotting/maint (pull request #1504)

Was making too large of a matrix, which may result in incorrect profiling

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

show more ...

Was making too large of a matrix, which can result in incorrect profiling

documentation and manual fixes for least-squares codes

use petscdmnetwork was listed twice in defining petsc F90 module

Commit-type: bug-fix

Tao tutorial ex4: update tests for TAONM fix

TAONM: increment interation

Tao tutorial ex4: add iteration limits for more consistent tests

Tao tutorial ex4: fix flag from -mat_format to -matrix_format

Tao tutorials ex4: fixes for --with-clanguage=cxx

whitespace

tao ex4: clean

run uncrustify

tao ex4: clean up and test output files edit

tao ex4: notes and clean up

Tao ex4: update test for TAOLMVM, limiting interations

ex4: set up shell for soft thresholding

tao ex4: TAOSHELL softthresh

tao ex4: separable fix. wip

tao ex4: implemented separable obj in ADMM

Tao ex4: cleanup

wip: s_norm convergence issue

wip

T

ex4: set up shell for soft thresholding

tao ex4: TAOSHELL softthresh

tao ex4: separable fix. wip

tao ex4: implemented separable obj in ADMM

Tao ex4: cleanup

wip: s_norm convergence issue

wip

Tao ex4: fix signs

Consistently follow the scaled dual variable formulation of ADMM

Tao ex4: update TaoShell syntax

show more ...

tao ex4: implemented admm basis pursuit.

tao ex4: prem commit b4 merge

niceties

tao ex4: prem work for split obj

tao ex4 prem work b4 merge

tao ex4: admm implemented but not converging

tao ex4:

tao ex4: implemented admm basis pursuit.

tao ex4: prem commit b4 merge

niceties

tao ex4: prem work for split obj

tao ex4 prem work b4 merge

tao ex4: admm implemented but not converging

tao ex4: ADMM convergence check

Tao ex4: separable objective ADMM converging

Tao ex4: fix memory leak

ex4: suggestions for what next

tao ex4: Hessian implemented

Tao ex4: small fix to hessian computation, working now

Tao ex4: fix memory leak, hessian regression test

tao ex4: Hessian ADMM implemented

tao ex4: Primal and Dual stopping criteria

tao ex4: break check edit

tao ex4: MatCopy pattern to different for large mat

tao ex4: make tolerances configurable

show more ...