Merge branch 'dalcinl/feature-plex-gmsh' into 'master'

Gmsh: Support for high-order geometries

See merge request petsc/petsc!3081

DM: Add DMProjectCoordinates()

Merge branch 'knepley/feature-plex-stokes-tutorial' into 'master'

Knepley/feature plex stokes tutorial

See merge request petsc/petsc!3038

DM: Nullspace constructor should report old and new field numbers

Merge branch 'rlwalker/feature-plex-example-poroelasticity-cryer' into 'master'

Rlwalker/feature plex example poroelasticity cryer

See merge request petsc/petsc!3013

Plex: Need to add BC for the solution time derivative in TS problems
- Added DMPlexInsertTimeDerivativeBoundaryValues()
- Added time derivative of the solution argument to DMAddBoundary(),
DMGetBou

Plex: Need to add BC for the solution time derivative in TS problems
- Added DMPlexInsertTimeDerivativeBoundaryValues()
- Added time derivative of the solution argument to DMAddBoundary(),
DMGetBoundary(), PetscDSAddBoundary(), PetscDSUpdateBoundary(),
PetscDSGetBoundary()

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Merge branch 'knepley/feature-plex-ts-checks' into 'master'

TS+Plex: Convergence estimation now working of time dependent PDEs

See merge request petsc/petsc!2985

TS+Plex: Convergence estimation now working of time dependent PDEs
- Add exact solution time derivative to DS
- Put monitor in ConvEst for TS
- Fixed error determination in ConvEst for TS

Co-Authore

TS+Plex: Convergence estimation now working of time dependent PDEs
- Add exact solution time derivative to DS
- Put monitor in ConvEst for TS
- Fixed error determination in ConvEst for TS

Co-Authored-By: Brad Aagaard <baagaard@usgs.gov>

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Merge branch 'knepley/feature-dm-exact-solution' into 'master'

Knepley/feature dm exact solution

See merge request petsc/petsc!2940

DM: Now DS stores exact solution functions for everything
- Added DMComputeExactSolution()
- DMSNES/TSCheck*() now use DS for functions

Merge branch 'jed/plex-tensor-closure-depth' into 'master'

Jed/plex tensor closure depth

See merge request petsc/petsc!2802

DM: Add DMFindRegionNum()

Merge branch 'knepley/feature-plex-check-multiple-ds' into 'master'

Knepley/feature plex check multiple ds

See merge request petsc/petsc!2806

Plex+SNES: Large update to support multiple DSes
- Now allow simple divisions of the domain with DMSetField()
- DMPlexComputeResidual_Internal() supports multiple DSes
- DMPlexComputeJacobian_Interna

Plex+SNES: Large update to support multiple DSes
- Now allow simple divisions of the domain with DMSetField()
- DMPlexComputeResidual_Internal() supports multiple DSes
- DMPlexComputeJacobian_Internal() supports multiple DSes
- DMSNESCheckDisretization() supports multiple DSes
- DMSNESCheckResidual() supports multiple DSes
- DMSNESCheckJacoiban() supports multiple DSes
- DMComputeL2FieldDiff() supports multiple DSes
- PetscConveEst supports multiple DSes
- Fixed bug refering to cStart from a cellIS
- Added PetscDSGetQuadrature()
- Added DMSetField_Internal()
- Added DMSetRegionNumDS()
- Protect PetscSectionView() from empty bcIndices
- ISDifference now allows a NULL second argument

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Merge branch 'knepley/feature-dm-boundary-function-projection' into 'master'

DM: Added DMProjectBdFieldLabelLocal()

See merge request petsc/petsc!2667

DM: Added DMProjectBdFieldLabelLocal()
- Called from DMPlexInsertBoundaryValuesEssentialBdFIeld()
- Added projectbdfieldlabelLocal() to DM
- Added Plex impl
- Added more documentation of the InsertBo

DM: Added DMProjectBdFieldLabelLocal()
- Called from DMPlexInsertBoundaryValuesEssentialBdFIeld()
- Added projectbdfieldlabelLocal() to DM
- Added Plex impl
- Added more documentation of the InsertBoundaryValues*() methods

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Merge branch 'knepley/feature-dm-remove-hybrid' into 'master'

Knepley/feature dm remove hybrid

See merge request petsc/petsc!2614

DMPlex: Fixed cell reordering and namespaced cell type names
- Namespaced DMPlexCellRefinerType enum items
- Added DMPlexReorderCell() and refactored DMPlexInvertCell()
- Update Gmsh reader to han

DMPlex: Fixed cell reordering and namespaced cell type names
- Namespaced DMPlexCellRefinerType enum items
- Added DMPlexReorderCell() and refactored DMPlexInvertCell()
- Update Gmsh reader to handle tet+tri-prism meshes

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DM+Plex: Removed the idea of hybrid and ghost cells, in favor of cell type
- Improved Plex tests to work for other cell types
- Plex creation, interpolation, submesh, and refinement routines now set

DM+Plex: Removed the idea of hybrid and ghost cells, in favor of cell type
- Improved Plex tests to work for other cell types
- Plex creation, interpolation, submesh, and refinement routines now set the cell type
- Distribution sorts strata by cell type
- Fixed orientation of prisms from input formats
- Added Plex ex40 to test regular refinement
- CellRefiner is a PetscObject
- dm_plex_cell_refiner chooses the refinement strategy
- Removed SimplexToTensor stuff in favor of ToHex refiner
- Most functions take DMPolytopeType instead of CellRefiner
- CellRefinerInCellTest_Internal()
- CellRefinerGetAffineTransforms_Internal()
- CellRefinerGetAffineFaceTransforms_Internal()
- DMForest now responds to DMPlexGetOverlap() and propagates its overlap to the underlying Plex
- Use DMPlexComputeCellType_Internal() to classify a cell based only on topology
- Added DMPlexGetSimplexOrBoxCells() to replace DMPlexGetInteriorCellStratum()
- Added DM_POLYTOPE_POINT_PRISM_TENSOR
- Added DMPolytopTypeGetDim() and DMPolyTopeTypeGetConeSize()
- Added DMLabelSetStratumBounds()
- Added DMPlexSetCellType()
- Added celltypes to DMView()
- Added DMPolytopeTypeGetNumVertices()
- Added DMPlexCreateReferenceCellByType()
- Added DMPolytopeTypeFromGmsh()
- Made DMPlexRefineUniform() public

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Merge branch 'knepley/feature-dm-monitor' into 'master'

Knepley/feature dm monitor

See merge request petsc/petsc!2369

DM: Added monitors - Added DMMonitorSet(), DMMonitorCancel(), DMMonitorSetFromOptions(), DMMonitor() - Added DMPlexMonitorThroughput() and -dm_plex_monitor_throughput - SNES calls DMMonitor()

Merge branch 'mark/fix-viewfromoptions' into 'master'

prototype for ViewFromOptions macro-->functions

See merge request petsc/petsc!2083

prototype for ViewFromOptions macro-->functions

Merge branch 'haplav/simplify-dm-label-list' into 'master'

improvements of DMLabel linked list in DM

Closes #386

See merge request petsc/petsc!2108

Improve DM label list. Generalize DMCopyLabels().

* DMAddLabel:
- Add label to the end of list so DMGetLabelByNum() keeps the numbering of old ones.
- Assign depth label right away.
* Get rid of

Improve DM label list. Generalize DMCopyLabels().

* DMAddLabel:
- Add label to the end of list so DMGetLabelByNum() keeps the numbering of old ones.
- Assign depth label right away.
* Get rid of DMLabelLinkList.
* Make use of PetscObject reference count of individual labels.
* DMCopyLabels: add input args PetscCopyMode mode and PetscBool all.
* Update PetscCopyMode manpage for use with objects.

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