bugfix for '--with-mpi=0'

Merge branch 'knepley/feature-plex-cv-input'

Begin refactorization of MatShell to make the code more straightforward and extensible

Introduce MatSetOperation() for changing operations on non-MATSHELLs
Introduce two modes for MATSHELL
1) MAT

Begin refactorization of MatShell to make the code more straightforward and extensible

Introduce MatSetOperation() for changing operations on non-MATSHELLs
Introduce two modes for MATSHELL
1) MATSHELL manages scalings and shifts automatically
2) Creator of MATSHELL can provide their own code for managing scaling and shifts
This is used by MatCreateADA() and MatCreateSubMatrixFree()

The extensibility is so that a MatShell can be easily used in as many places as possible as other matrices,
for example,

/* A = diag(u) G */
ierr = MatCopy(appctx->SEMop.grad,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatDiagonalScale(A,globalin,NULL);CHKERRQ(ierr);
/* A = A + diag(Gu) */
ierr = VecDuplicate(globalin,&Gglobalin);CHKERRQ(ierr);
ierr = MatMult(appctx->SEMop.grad,globalin,Gglobalin);CHKERRQ(ierr);
ierr = MatDiagonalSet(A,Gglobalin,ADD_VALUES);CHKERRQ(ierr);
ierr = VecDestroy(&Gglobalin);CHKERRQ(ierr);
/* A = K - A */
ierr = MatScale(A,-1.0);CHKERRQ(ierr);
ierr = MatAXPY(A,1.0,appctx->SEMop.keptstiff,SAME_NONZERO_PATTERN);

Commit-type: feature

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More minor fixes for spectral burgers examples

Commit-type: bug-fix, portability-fix, testing-fix, example
Reported-by: nightly tests

Missing CHKERRQ() in examples

Commit-type: testing-fix,style-fix
Reported-by: nightly

add (const*) to DMDAVecGet/RestoreArrayRead() calls to prevent compiler warning about const

Commit-type: style-fix

add forgotten output file

Commit-type: i.e. bug-fix, portability-fix, testing-fix,style-fix, feature, documentation, example
Funded-by:
Project:
Time: hours
Reported-by:
Thanks-to:
Development T

add forgotten output file

Commit-type: i.e. bug-fix, portability-fix, testing-fix,style-fix, feature, documentation, example
Funded-by:
Project:
Time: hours
Reported-by:
Thanks-to:
Development Tools: Vim, Emacs, Eclipse

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Start to add 1d matrix free version of burgers spectral ODE example

Commit-type: feature, example

remove memory leaks from burgers examples and fix for parallel runs

Commit-type: bug-fix

Cleanup dead code from burgers_spectral

Commit-type: testing-fix,style-fix, example

Update output for burgers_spectral to match new Jacobian

Commit-type: bug-fix, testing-fix

use correct Jacobian for Burgers equation

Commit-type: bug-fix, portability-fix, testing-fix,style-fix, feature, example
Thanks-to: Oana Marin <omarin@anl.gov>

add reference to paper

Minor cleanup of burgers_spectral code

Commit-type: style-fix

add Burger's spectral test case

Improve PetscMkdir() if directory already exists

Commit-type: testing-fix, feature

Change Fortran SETERRA and SETERRQ to be simple statements

Also fix for --with-errorchecking=0 and repair shashi.F90 (which was
invalid for a variety of reasons) so that it compiles. Fortran is not

Change Fortran SETERRA and SETERRQ to be simple statements

Also fix for --with-errorchecking=0 and repair shashi.F90 (which was
invalid for a variety of reasons) so that it compiles. Fortran is not
my favorite language.

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Fix name MatSolverPackage since it is better to be consistent and use the terminology Type.

Commit-type: style-fix, documentation

TODO for examples that produce very different output

Commit-type: portability-fix, testing-fix

Merge branch 'barry/fortran-initialize-objects'

Merge branch 'tmunson/tao-pounders-fix-code'

Merge branch 'tmunson/tao-pounders-add-tests'

Merge branch 'barry/ksp/tests-to-new-harness'

Plex: Now DMPlexMarkBoundaryFaces() can determine the marker from associated vertices

turn off testing of three chwirut cases since results very inconsistent across machines

Commit-type: portability-fix, testing-fix
Reported-by: nightly tests

remove example from tests because of inconsistent results

Commit-type: portability-fix, testing-fix
Reported-by: nightly