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/fix-plex-hybrid-assembly' into 'master'

Knepley/fix plex hybrid assembly

See merge request petsc/petsc!2793

Plex: More hybrid fixes
- Converted hybrid assembly to use PetscTabulation
- Protect for NULL discretizations, which happen with no dofs for a field
- Added PetscDiscType enum
- Changed PetscDSIsFE_I

Plex: More hybrid fixes
- Converted hybrid assembly to use PetscTabulation
- Protect for NULL discretizations, which happen with no dofs for a field
- Added PetscDiscType enum
- Changed PetscDSIsFE_Internal() to PetscDSGetDiscType_Internal()
- Must inject coordinates from hybrid cells into the ambient space

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Plex+FE: Updates for hybrid integration
- Added support for hybrid Jacobians
- Added PetscDSHasBdJacobian()
- Added boundary Jacobian preconditioner
- Needed a path to integrate the hybrid Jacobian p

Plex+FE: Updates for hybrid integration
- Added support for hybrid Jacobians
- Added PetscDSHasBdJacobian()
- Added boundary Jacobian preconditioner
- Needed a path to integrate the hybrid Jacobian preconditioner
- Fixed indexing in hybrid element mat update
- Be careful about the difference between intrinsic dimension and embedding dimension for hybrid integration
- Need to use rectangular transformation of gradient in case they are different
- Fix use of embedding dimension
- Make sure FEGeom struct has the dimensions set
- Pointwise function derivatives are in the embedding space
- Use PetscArrayzero()
- Change TransitiveClosure() for hybrid cells
- We get the closures of the endcaps, and then the hybrid faces, this allows degenerate cells that we need in PyLith

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Merge branch 'knepley/feature-project-different-spaces' into 'master'

Knepley/feature project different spaces

See merge request petsc/petsc!2153

FE+DS: Introduce PetscTabulation to hold tabulated function data
- This was created to prevent mismatches in sizes I was getting by just
passing around arrays
- FE+FV+DS now hold tabulations
- GetTab

FE+DS: Introduce PetscTabulation to hold tabulated function data
- This was created to prevent mismatches in sizes I was getting by just
passing around arrays
- FE+FV+DS now hold tabulations
- GetTabulation() --> CreateTabulation() and it creates an object rather
than using DMGetWorkArray(). I put in ComputeTabulation() to reuse
space, but there still may be performance regression.
- Default tabulations are now "cell tabulations"
- The replicas in the tabulation are used to index faces in a face
tabulation

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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 'maint'

Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Merged in knepley/feature-plex-pullback (pull request #1632)

Plex: Implemented pullback/pushforward

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

Plex: Implemented pullback/pushforward - Added k to PetscDualSpace. It indicates what kind of transformation we use. - DualSpace does pullback and FE integration routines do pushforward - All integra

Plex: Implemented pullback/pushforward - Added k to PetscDualSpace. It indicates what kind of transformation we use. - DualSpace does pullback and FE integration routines do pushforward - All integration now takes a PetscFEGeom argument and pushes forward correctly - Added PetscDualSpaceTransformType - Removed TransformF() because we now transform the basis function instead - Chaged workspace management in DS - Updated L2 diff functions - Updated interpolation functions - Added way to output exact solution in DMSNESCheck()

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Merged in knepley/feature-poiseuille-example (pull request #1446)

Knepley/feature poiseuille example

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

DM+DS: Exact solution functions should also carry contexts

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-snes-patch

Merge branch 'knepley/feature-ds-hybrid'

Merge remote-tracking branch 'origin/knepley/feature-ds-hybrid' into knepley/feature-multiple-ds

* origin/knepley/feature-ds-hybrid:
PetscDS+Doc: More discussion
PetscDS: Need more space for hyb

Merge remote-tracking branch 'origin/knepley/feature-ds-hybrid' into knepley/feature-multiple-ds

* origin/knepley/feature-ds-hybrid:
PetscDS+Doc: More discussion
PetscDS: Need more space for hybrid systems
PetscDS: Unnecessary guard
PetscDS: Improved viewer
PetscDS: Added hybrid flag for cohesive cell systems - Cleaned up members - Added Get/SetHybrid()

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PetscDS: Added hybrid flag for cohesive cell systems
- Cleaned up members
- Added Get/SetHybrid()

Merged petsc/petsc into master

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master