Merge branch 'knepley/feature-plex-adaptive-interpolation' into 'master'

Knepley/feature plex adaptive interpolation

See merge request petsc/petsc!3018

Merge branch 'barry/2020-08-16/fix-source-formatting' into 'master'

Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

See merge request petsc/petsc

Merge branch 'barry/2020-08-16/fix-source-formatting' into 'master'

Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

See merge request petsc/petsc!3064

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Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

Commit-type: portability-fix, testing-fix, style-fix, feature, maintainability
/spend 1.5h

DM+SNES: Preliminary adaptive interpolation
- Using the scheme from BootstrapAMG with some modifications to apply to GMG
- Moved adaptive interpolation into DM from Plex
- Added event for adaptation

DM+SNES: Preliminary adaptive interpolation
- Using the scheme from BootstrapAMG with some modifications to apply to GMG
- Moved adaptive interpolation into DM from Plex
- Added event for adaptation
- Added routine to check an interpolator
- Added viewer for coarse and fine vectors used for interpolation optimization
- Add coarse space determined by eigenvectors
- Right now adaptive interpolation is unweighted

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PCMG: Added adaptive interpolation
- Added coarse vectors to resolve at each level
- Added adaptation flag and API
- Added option -pc_mg_adapt_interp to turn on adaptation
- Use -dm_interpolator_ada

PCMG: Added adaptive interpolation
- Added coarse vectors to resolve at each level
- Added adaptation flag and API
- Added option -pc_mg_adapt_interp to turn on adaptation
- Use -dm_interpolator_adapt_k to set subspace size and -dm_interpolator_adapt_use_poly to select type of functions
- Doc fixes for functions
- Fix options for construction of a vanilla coarse space
- Require Galerkin matrices for adaptive interpolation
- Fixed problem with composed eigenvalue
- Normalize eigenvector in smoothing loop
- Added option to use generalized eigenvector basis (For some reason, this is worse on test problems)
- Make adaptive allocation happen only initially, protect adaptive functions from invalid levels

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Merge branch 'dalcinl/fix-null' into 'master'

KSP/PC: Fix 0 ->NULL for pointers

See merge request petsc/petsc!2794

KSP/PC: Fix 0 ->NULL for pointers

Merge branch 'stefanozampini/fix-dm-composition' into 'master'

Fix DM composition with work vectors and matrices

See merge request petsc/petsc!2551

Remove dead function DMSetVec and dm->x

This function is not even declared in the public header and not used by PETSc codebase or any of the tests

Merge remote-tracking branch 'origin/maint'

Merge remote-tracking branch 'origin/barry/2020-02-13/fix-separate-spelling' into maint

git grep -l "seperate" | xargs sed -i '' -e 's/seperate/separate/g'

See merge request petsc/petsc!2522

git grep -l "seperate" | xargs sed -i '' -e 's/seperate/separate/g'

Commit-type: spelling-fix
Reported-by: Pierre JOLIVET <Pierre.Jolivet@enseeiht.fr>

Merge branch 'gropp/doc-fixes-1' [PR #1838]

Merge from doc-fixes branch

Fixes for doctext update

Merged in Fande-Kong/feature_hmg (pull request #1682)

Hybrid of PETSc preconditioners (such as ASM, BJacobi, SOR, etc.) and Hypre BoomerAMG

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

Merge remote-tracking branch 'origin/psanan/docs-remove-manconcepts' [PR #1733]

HMG: Added tests for reuse interpolation and interface functions

Also addressed comments from Barry

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

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Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but not from examples).

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 -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find src -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/d' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/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

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Merged in psanan/man-pages-remove-keywords (pull request #1717)

Man pages: Remove .keywords fields

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

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 ...

Merged in pefarrell/mg-smoothu-dm (pull request #1486)

Set the DM on the up-smoother KSP in multigrid also

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

MG: If smoothu is not the same as smoothd, give it the DM also

Merge branch 'master' of bitbucket.org:petsc/petsc