Merge branch 'knepley/fix-plex-hybrid-geometry' into 'main'

Plex: Fix hybrid integration

See merge request petsc/petsc!4048

Plex: Fix hybrid integration
- This will obviously go away after I figure out embedded integration
- Add hybrid tag to FEGeom
- Check tag when deciding what cell geometry we want

Merge branch 'barry/2021-05-16/fix-double-lines' into 'main'

Fix typos in source

See merge request petsc/petsc!3984

Remove all double blank lines from source

Commit-type: petsc-style
/2h

Merge branch 'knepley/feature-dm-aux-data-keys' into 'main'

Plex: Updates to declarative interface for FEM problems

See merge request petsc/petsc!3972

DT: Changed key and WeakForm internals
- Changed name to PetscFormKey
- Added part member
- Now maps are referred to by PetscWeakFormKind
- Added PetscWeakFormClearIndex() and PetscWeakFormClear()

DT: Changed key and WeakForm internals
- Changed name to PetscFormKey
- Added part member
- Now maps are referred to by PetscWeakFormKind
- Added PetscWeakFormClearIndex() and PetscWeakFormClear()
- Passing NULL to SetIndex is now ignored
- Added tests

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SNES+DM: Move Jacobian action to plexfem.c
- Create a MatShell for Jacobian action

Plex: DMPlexComputeJacobian_Hybrid_Internal() updated to uses keys
- Need to translate points from original DM to auxiliary DM for hybrid aux values

DM+Plex: Now auxliary data is retrieved by key

Merge branch 'knepley/feature-plex-ceed-integration' into 'main'

Plex: Initial CEED integration

See merge request petsc/petsc!3918

Plex: Now meshes can be created automatically from the command line, and some more fixes
- Changed internal mesh creation functions to operate on a DM instead of
creating a new one so that they can h

Plex: Now meshes can be created automatically from the command line, and some more fixes
- Changed internal mesh creation functions to operate on a DM instead of
creating a new one so that they can happen with options
- Fixed coordinates in CreateCubeBoundary_Internal()
- Added DMPlexShape for prebuilt meshes
- Added DMPlexIsSimplex()
- Added DMPlexCreateCoordinateSpace()
- DMPlexDistributeCoordinates() should copy the coordinate
discretization
- DMPlexInterpolateFaces_Internal() should be careful to preserve the
lower bound when resetting the chart
- PetscSectionSetChart() should ignore entries that match the current
ones
- Added DMPolytopeTypeSimpleShape()
- Do not require an EGADS model for TetGen
- Detail ASCII viewer shows all labels
- Default viewer shows periodicity

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Merge branch 'jacobf/2021-03-26/clang-static-linter' into 'main'

Feature: libClang PETSc Macro Static Analyzer

See merge request petsc/petsc!3773

Linter using libClang that checks PetscValidHeaderSpecifcType, PetscValidHeaderSpecific, PetscValidHeader, PetscValid[XXX]Pointer, PetscValidType, PetscCheckSameComm, PetscValidLogicalCollectiveXXX f

Linter using libClang that checks PetscValidHeaderSpecifcType, PetscValidHeaderSpecific, PetscValidHeader, PetscValid[XXX]Pointer, PetscValidType, PetscCheckSameComm, PetscValidLogicalCollectiveXXX for validity. Automatically generates diff files for problems with a known solution.

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Merge branch 'knepley/feature-ds-residualbd-key' into 'main'

DS+FE+Doc: Make BdResidual take a key

See merge request petsc/petsc!3761

Merge remote-tracking branch 'origin/release'

Merge branch 'jolivet/fix-documentation' into 'release'

Documentation fixes

See merge request petsc/petsc!3851

Documentation fixes

DM+Plex: Boundary integration functions are now stored in a PetscWeakForm held in the Boundary object
- Boundary residual/Jacobian functions now take a form key
- Now store DMLabel in DSBoundary
- Im

DM+Plex: Boundary integration functions are now stored in a PetscWeakForm held in the Boundary object
- Boundary residual/Jacobian functions now take a form key
- Now store DMLabel in DSBoundary
- Improved Boundary, Weak Form, and DS viewers
- Remove DMCopyBoundary(), DMCopyDisc() is sufficient
- Need DMTransferDS_Internal() to create new DS with label in the correct DM
- Correct all DMAddBoundary() in tests
- Allow DMBoundary to hold just a label name if necessary since p4est is missing labels in a lot of places
- Fix propagating coordinate dimension in DS

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DS+FE+Doc: Make BdResidual take a key
- Add documentation

Merge remote-tracking branch 'origin/barry/2021-03-28/fix-mpiu-allreduce-mpi-failure'

Fix capture of MPI error code in MPIU_Allreduce()

See merge request petsc/petsc!3777

All MPIU_ functions except MPIU_File return MPI error codes for checking

Update checkbadSource to find use of CHKERRQ with MPIU_ functions

Commit-type: i.e. error-checking, optimization, bug-fix, p

All MPIU_ functions except MPIU_File return MPI error codes for checking

Update checkbadSource to find use of CHKERRQ with MPIU_ functions

Commit-type: i.e. error-checking, optimization, 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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Merge branch 'knepley/feature-dm-aux-data' into 'main'

DM: Replace object composition with an API for auxiliary data

See merge request petsc/petsc!3798

DM: Replace object composition with an API for auxiliary data - Now allow data to be tagged with a label+value - Do not separately require a DM and Vec, get the DM from the Vec

Merge branch 'balay/fix-O3-warnings' into 'main'

CI: fix compile warnings when built with --with-debugging=0 COPTFLAGS=-O3

See merge request petsc/petsc!3784

CI: fix compile warnings when built with --with-debugging=0 COPTFLAGS=-O3