Merge branch 'ksagiyam/dmplex_path_change' into 'main'

Ksagiyam/dmplex path change

Closes #956 and #896

See merge request petsc/petsc!4441

plex: add LogEvents

plexhdf5: Introduce storage versioning and version 2.0.0;

* introduce DMPlexStorageVersion x.y.z
* if no version specified in file => 1.0.0
[original version before the project - that in petsc rel

plexhdf5: Introduce storage versioning and version 2.0.0;

* introduce DMPlexStorageVersion x.y.z
* if no version specified in file => 1.0.0
[original version before the project - that in petsc release 3.16.0]
* check version in both file and option -dm_plex_view_hdf5_storage_version
* version 2.0.0 changes paths to topology, labels, coordinates
* support both versions 1.0.0 and 2.0.0 for writing
* use sizeof in PetscSNPrintf() calls

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Merge branch 'knepley/feature-plex-1d-amr' into 'main'

Plex: Added 1D adaptive refinement - Plex ex46 tests it

See merge request petsc/petsc!4524

Plex: Added 1D adaptive refinement - Plex ex46 tests it

Merge branch 'barry/2021-06-10/fix-chkerrq' into 'main'

Fix missing ierr =, removed incorrect CHKERRQ(), change CHKStringError

See merge request petsc/petsc!4078

bug-fixes

style-fixes

Merge branch 'jwallwork23/metric-utils-api' into 'main'

Public API for Riemannian metric

See merge request petsc/petsc!4408

plex metric: set metric options

Merge branch 'knepley/feature-plex-extrude-symmetric' into 'main'

Plex: DMPlexExtrude() can now symmetrically extrude

See merge request petsc/petsc!4367

DM: Now extrusion is like DMRefine() and implemented through DMPlexTransform - DMExtrude() replaces DMPlexExtrude() - Added an extrusion transformation - Added DMPlexTransformSetDimensions() and setd

DM: Now extrusion is like DMRefine() and implemented through DMPlexTransform - DMExtrude() replaces DMPlexExtrude() - Added an extrusion transformation - Added DMPlexTransformSetDimensions() and setdimensions function - DMPlexTransformMapCoordinates() and DMPlexSnapToGeomModel() now take the coordinate dimension - -dm_extrude replaces -dm_plex_extrude_layers

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Plex: Allow viewing coordinates in other coordinate systems

Merge branch 'psanan-release-patch-82973' into 'main'

Developer docs, style: remove rule about using "if (!rank)" and replace all "!rank" usage with "rank == 0"

See merge request petsc/petsc!4146

Style: replace "!rank" with "rank == 0"

In SF tutorial ex1 (src/vec/is/sf/tutorials/ex1.c), add parentheses around "rank == 0". This is relevant because ! binds more tightly than +, but == binds les

Style: replace "!rank" with "rank == 0"

In SF tutorial ex1 (src/vec/is/sf/tutorials/ex1.c), add parentheses around "rank == 0". This is relevant because ! binds more tightly than +, but == binds less
tightly, so the result of the computation would otherwise change.

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Merge remote-tracking branch 'origin/jose/fix-manpages'

Fix manpages to avoid errors reported by doctext

See merge request petsc/petsc!4309

Fix manpages: more errors reported by doctext

Fix manpages: mismatching number of parameters

Fix manpages: Input/Output Parameters --> Parameter

Fix manpages: Input/Output Parameter --> Parameters

Merge branch 'jose/spelling-errors' into 'main'

Fix many spelling errors in manpages and comments

See merge request petsc/petsc!4283

Fix spelling errors in manpages and comments

Merge branch 'knepley/feature-orientation-rethink' into 'main'

Plex: Rethink Plex orientation

See merge request petsc/petsc!4218

Plex: DMPlexTransform is now the way to manipulate a Plex
- Replace DMPlexCellRefiner with DMPlexTransform
- Replace CellRefinerInCellTest_Internal() with DMPolytopeInCellTest()
- Replace DMPlexCe

Plex: DMPlexTransform is now the way to manipulate a Plex
- Replace DMPlexCellRefiner with DMPlexTransform
- Replace CellRefinerInCellTest_Internal() with DMPolytopeInCellTest()
- Replace DMPlexCellRefinerGetAffineTransforms() with
DMPlexRefineRegularGetAffineTransforms()

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DM: New idea for cell orientations
- Add DMPolytopeTypeGetNumArrangments()
- Add DMPolytopeTypeGetArrangment()
- Add DMPolytopeTypeGetVertexArrangment()
- Add DMPolytopeTypeComposeOrientation()
- Add

DM: New idea for cell orientations
- Add DMPolytopeTypeGetNumArrangments()
- Add DMPolytopeTypeGetArrangment()
- Add DMPolytopeTypeGetVertexArrangment()
- Add DMPolytopeTypeComposeOrientation()
- Add DMPolytopeTypeComposeOrientationInv()
- Add DMPolytopeGetOrientation()
- Add DMPolytopeGetVertexOrientation()
- Inversion now uses just negation instead of face size
- Remove DMPlexOrientCell(), DMPlexReverseCell(), DMPlexCompareOrientations()
- Add DMPlexOrientPoint()
- Add MPIU_4INT and MPI_4INT
- Rewrote transitive closure
- DMPlexGetTransitiveClosure_Depth1_Static() now correctly handles ornt
- PetscDualSpaceLagrange and PetscSection use the number of arragnements and not the cone size
- Update examples

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