init commit

Merge from doc-fixes branch

Fixes for doctext update

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Improve interfaces and make HMG more general

Now HMG can take any PC as an inner PC as long as the PC
provides PCGetInterpolations and PCGetCoarseOperators

If hypre is available, it will be used b

Improve interfaces and make HMG more general

Now HMG can take any PC as an inner PC as long as the PC
provides PCGetInterpolations and PCGetCoarseOperators

If hypre is available, it will be used by default, otherwise use GAMG.
Users can override the setting using -hmg_inner_pc_type

show more ...

HMG should work without hypre as well.

Implemented an AMG that uses Hypre to coarsen matrix

and generate a sequence of coarse matrices. These coarse
matrices are used to setup a PETSc PCMG.

There are two benefits:

(1) We can use any PE

Implemented an AMG that uses Hypre to coarsen matrix

and generate a sequence of coarse matrices. These coarse
matrices are used to setup a PETSc PCMG.

There are two benefits:

(1) We can use any PETSc preconditioners such as ASM, BJacobi as
level smoothers (solvers). For some applicaitons, the combination
of ASM and AMG works great while only AMG or AMS does not work at all.

(2) For multicomponent problems, we could just coarsen one submatrix
associated with one particular component. In this way, the setup of the
preconditioner is significantly improved. One typical use case is
neutron transport equations. There are many variables on each mesh
vertex due to the discretization of angle and energy. Each variable,
in fact, corresponds to the same PDEs but with different material
properties.

show more ...

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

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 -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/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

show more ...

Work on PetscViewerString. Fix use of PetscInt -> size_t, add new functionality, add usage by basic solver objects, add test case

Commit-type: style-fix, feature, documentation, example

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

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