Merge branch 'jed/plex-tensor-periodic' into 'main'

DMPlex: support tensor closure permutations with periodic

See merge request petsc/petsc!2178

Merge branch 'stefanozampini/matis-negative-indices' into 'main'

matis negative indices

See merge request petsc/petsc!4923

DMGetLocalToGlobalMapping: fix bug

DM: add bias to anchor/constraint system

DM constraints: move defaultConstraints into sub-struct for grouping

DMPlex: minor doc updates/cross-references

Merge branch 'knepley/fix-doc-errors' into 'main'

Doc: Trying to remove all reported errors

See merge request petsc/petsc!4930

Doc: Trying to remove all reported errors - Since it reports as an error, and only occurs a very few times, I have removed the Imput/Output Parameters sections and replaced them by Output Parameters

Doc: Trying to remove all reported errors - Since it reports as an error, and only occurs a very few times, I have removed the Imput/Output Parameters sections and replaced them by Output Parameters with documentation

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Merge branch 'knepley/feature-fe-wxy-again' into 'main'

FE on triangular prisms

See merge request petsc/petsc!4826

DM+FE+DT: Added correct geometry and quadrature for triangular prism
- Added affine geometry for triangular prism
- Added PetscDTTensorQuadratureCreate()
- Added PetscFECreateByCell()
- Added PetscFE

DM+FE+DT: Added correct geometry and quadrature for triangular prism
- Added affine geometry for triangular prism
- Added PetscDTTensorQuadratureCreate()
- Added PetscFECreateByCell()
- Added PetscFECreateLagrangeByCell()
- Added DMCreateFEDefault()
- Now DMField uses PetscFECreateLagrange()
- Refactored FE creation
- If the degree is prescribed on a prism, do not create a tensor space
- Use new interface in DMField_DS
- Fix default creation when number of components is changed by command line

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Merge branch 'jed/plex-schwarz-p' into 'main'

DMPlexCreateTPSMesh: triply-periodic surface meshing

See merge request petsc/petsc!2709

DMPlexCreateTPSMesh: triply-periodic surface meshing

Mesh the surface of the Schwarz P surface with an arbitrary number of
refinements. Thanks to Nikita Simonian and Matthias Messner for
bringing t

DMPlexCreateTPSMesh: triply-periodic surface meshing

Mesh the surface of the Schwarz P surface with an arbitrary number of
refinements. Thanks to Nikita Simonian and Matthias Messner for
bringing these surfaces to my attention and for meshing discussion.

This commit squashes a line of development started in April 2020, with
some merges and conflict resolution with bug fixes and features needed
from upstream.

Add DMPlexCreateGyroidMesh(): will be folded into DMPlexCreateTPSMesh()

https://en.wikipedia.org/wiki/Gyroid

DMPlexCreateTPSMesh: add Face Sets and better output checking

DMPlexCreateTPSMesh: add edge sets for gyroid

DMPlexCreateTPSMesh: fix precision issues

DMPlexCreateTPSMesh: support extrusion to 3D mesh (broken because Face Sets are missing)

DMSetCoordinatesLocal: allow NULL to clear any prior coordinates

DMPlex: add -dm_plex_shape [schwarz_p|gyroid]

Skip distribution before extrusion due to parallel bug #1114.

Co-authored-by: Toby Isaac <tisaac@cc.gatech.edu>

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Merge remote-tracking branch 'origin/release'

Merge branch 'jed/fix-plex-local-to-global/maint' into 'release'

DM: fix constrained dofs in local to global mapping

See merge request petsc/petsc!4894

DM: fix constrained dofs in local to global mapping

Merge branch 'jacobf/2022-01-05/c99' into 'main'

Feature: C99 and C++11

See merge request petsc/petsc!4700

rename PetscAssert() -> PetscCheck() and PetscAssertDebug() -> PetscAssert()

add PetscAssert() and PetscAssertFalse()

SETERRQ[1-9]+ begone

Merge branch 'knepley/feature-plex-explicit-timestepping' into 'main'

DM+TS: Add support for mass matrices

See merge request petsc/petsc!4683

DM+TS: Add support for mass matrices
- Added a lumped mass matrix for explicit timestepping
- Add functions for DMTS to manage the mass matrix
- Fix Plex mass matrix creation

Merge branch 'jed/plex-first-point-at-height' into 'main'

DMPlexGetLocalOffsets: fix obtaining DS when labels not completed

See merge request petsc/petsc!4786

DMGetRegionDS: return the unlabeled region if no labeled region exists

This is consistent with the existing behavior in DMGetCellDS().

Merge branch 'jczhang/feature-kokkos-coo' into 'main'

Support MatSetValuesCOO() for AIJKOKKOS matrices

See merge request petsc/petsc!4726

DMGetLocalToGlobalMapping: fix logic regarding constrained dofs

Constrained dofs appear in the local vector, but not in the global
vector. MatSetValues and friends will ignore entries with negative

DMGetLocalToGlobalMapping: fix logic regarding constrained dofs

Constrained dofs appear in the local vector, but not in the global
vector. MatSetValues and friends will ignore entries with negative
indices. This fixes a bug in which `cind` was always equal to 0 and
constrained dofs were added to positive offsets.

Commit-type: bug-fix

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