Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreat

Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreate.c
src/dm/impls/mesh/section.c
src/snes/examples/tutorials/ex10.c
src/snes/examples/tutorials/ex12.c
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/ex62.c
src/snes/utils/mesh/dmmeshsnes.c

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Merge branch 'knepley/feature-fem-dgspace' into knepley/fix-fem-0d

* knepley/feature-fem-dgspace:
PetscFE: Fixed quadrature names for OpenCL
PetscSpace: Added a DG space - Defined on a set of qu

Merge branch 'knepley/feature-fem-dgspace' into knepley/fix-fem-0d

* knepley/feature-fem-dgspace:
PetscFE: Fixed quadrature names for OpenCL
PetscSpace: Added a DG space - Defined on a set of quadrature points - Need tests
PetscQuadrature: Revamped - Removed basis tabulation - Shortened names - Added PetscQuadratureView()

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Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (124 commits)
SNES ex12: Fix buggy checkin
add missing output file src/snes/examples/tutorials/output/ex14_3.out
fixed bunch

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (124 commits)
SNES ex12: Fix buggy checkin
add missing output file src/snes/examples/tutorials/output/ex14_3.out
fixed bunch of bibtex items that should ahve used abbreviations only
PetscDualSpace: Pointer check barfs for function pointer
Sys: Add ability to turn off CUBLAS initialization - This continually SEGVs on my Air
SNES ex62: Updated test output - Matrix now prints attached nullspace indicator - 3D tests are wierdly different, they need to be verified by hand
SNES ex12: Updated test output - Mostly for completed labels
SNES ex12/62: Changed to new DMPlexProjectFunction() interface - Took DM out of main struct
SNES ex12/62: Complete boundary label - Puts in edges in 3D - Perhaps should be moved to the creation routine
PetscDualSpace: Fixed orientation of reference tetrahedron - Now this does not match FIAT
PetscDualSpace: Fixed numDof for P0
PetscDualSpace: Added PetscDualSpaceApply() for the action of a functional - Declared PetscDualSpaceGetFunctional()
DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection - Has not been tested with moment dofs - Accommodates vector functions
DMPlex: Added support for INSERT_BC_VALUES in VecSetClosure()
DMPlex: Fixed missing RestoreTransitiveClosure()
DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array
DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
DMPlex: Fix VecGetClosure() when the array is input
PetscFE: OpenCL is hardcoded for P0 coefficients right now
SNES ex12: Added test cases for variable coefficient Laplace - The P1 tests reproduce the analytic linear coefficient
...

Conflicts:
config/builder.py
src/dm/impls/plex/plex.c

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Merge branch 'knepley/feature-dt-fem'

* knepley/feature-dt-fem: (122 commits)
SNES ex12: Fix buggy checkin
PetscDualSpace: Pointer check barfs for function pointer
Sys: Add ability to turn off

Merge branch 'knepley/feature-dt-fem'

* knepley/feature-dt-fem: (122 commits)
SNES ex12: Fix buggy checkin
PetscDualSpace: Pointer check barfs for function pointer
Sys: Add ability to turn off CUBLAS initialization - This continually SEGVs on my Air
SNES ex62: Updated test output - Matrix now prints attached nullspace indicator - 3D tests are wierdly different, they need to be verified by hand
SNES ex12: Updated test output - Mostly for completed labels
SNES ex12/62: Changed to new DMPlexProjectFunction() interface - Took DM out of main struct
SNES ex12/62: Complete boundary label - Puts in edges in 3D - Perhaps should be moved to the creation routine
PetscDualSpace: Fixed orientation of reference tetrahedron - Now this does not match FIAT
PetscDualSpace: Fixed numDof for P0
PetscDualSpace: Added PetscDualSpaceApply() for the action of a functional - Declared PetscDualSpaceGetFunctional()
DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection - Has not been tested with moment dofs - Accommodates vector functions
DMPlex: Added support for INSERT_BC_VALUES in VecSetClosure()
DMPlex: Fixed missing RestoreTransitiveClosure()
DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array
DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
DMPlex: Fix VecGetClosure() when the array is input
PetscFE: OpenCL is hardcoded for P0 coefficients right now
SNES ex12: Added test cases for variable coefficient Laplace - The P1 tests reproduce the analytic linear coefficient
PetscFE: Added auxiliary fields to PetscFEIntegrateJacobian() - Hooked it up to DMPlexComputeJacobian()
SNES ex12: Removed code generation
...

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PetscSpace: Added a DG space
- Defined on a set of quadrature points
- Need tests

Merge branch 'knepley/feature-dt-fem' into knepley/feature-fem-dgspace

* knepley/feature-dt-fem: (123 commits)
SNES ex12: Fix buggy checkin
Builder: strip test output before comparing
PetscDua

Merge branch 'knepley/feature-dt-fem' into knepley/feature-fem-dgspace

* knepley/feature-dt-fem: (123 commits)
SNES ex12: Fix buggy checkin
Builder: strip test output before comparing
PetscDualSpace: Pointer check barfs for function pointer
Sys: Add ability to turn off CUBLAS initialization - This continually SEGVs on my Air
SNES ex62: Updated test output - Matrix now prints attached nullspace indicator - 3D tests are wierdly different, they need to be verified by hand
SNES ex12: Updated test output - Mostly for completed labels
SNES ex12/62: Changed to new DMPlexProjectFunction() interface - Took DM out of main struct
SNES ex12/62: Complete boundary label - Puts in edges in 3D - Perhaps should be moved to the creation routine
PetscDualSpace: Fixed orientation of reference tetrahedron - Now this does not match FIAT
PetscDualSpace: Fixed numDof for P0
PetscDualSpace: Added PetscDualSpaceApply() for the action of a functional - Declared PetscDualSpaceGetFunctional()
DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection - Has not been tested with moment dofs - Accommodates vector functions
DMPlex: Added support for INSERT_BC_VALUES in VecSetClosure()
DMPlex: Fixed missing RestoreTransitiveClosure()
DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array
DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
DMPlex: Fix VecGetClosure() when the array is input
PetscFE: OpenCL is hardcoded for P0 coefficients right now
SNES ex12: Added test cases for variable coefficient Laplace - The P1 tests reproduce the analytic linear coefficient
PetscFE: Added auxiliary fields to PetscFEIntegrateJacobian() - Hooked it up to DMPlexComputeJacobian()
...

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PetscDualSpace: Added PetscDualSpaceApply() for the action of a functional
- Declared PetscDualSpaceGetFunctional()

PetscFE: Added auxiliary fields to PetscFEIntegrateJacobian()
- Hooked it up to DMPlexComputeJacobian()

DMPlex+PetscFE: Looks like boundary integration is working
- DMComputeResidualFEM() checks for feBd, and does bd integral if present
- Normals are still not being calculated
- Added PetscFEIntegrateB

DMPlex+PetscFE: Looks like boundary integration is working
- DMComputeResidualFEM() checks for feBd, and does bd integral if present
- Normals are still not being calculated
- Added PetscFEIntegrateBdResidual() and a basic implementation
- Added normals to PetscCellGeometry
- Auxiliary fields not turned on in bd integrals

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PetscFE: Remove Quadrature from PetscFEM, added boundary elements

PetscFE: Changed PetscFEIntegrateResidual() to take auxiliary fields
- Also changed the PetscFEM struct to take auxiliary elements
- Added P_0 Lagrange element

PetscFE: Added a real number type to the OpenCL implementation

PetscFE: Fixed missing declarations

DMPlex+PetscFE: Moved integration functions from DMPlex to PetscFE
- Now PetscFE type indicates the integration method
- Added all machinery for PetscFE types

PetscFE: FEM Jacobian computation working, and now cache default tabulation
- Added PetscFEIntegratJacobianChunk()
- Changed interface in DMPlexComputeJacobianFEM()
- Changed signature of integrateJa

PetscFE: FEM Jacobian computation working, and now cache default tabulation
- Added PetscFEIntegratJacobianChunk()
- Changed interface in DMPlexComputeJacobianFEM()
- Changed signature of integrateJacobianFEM in DMPlex
- Added DMPLEX_JacobianFEM event
- Now PetscFE caches default tabulation

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PetscFE: Large reorganization of FEM dispatch
- WARNING: Now DMPlex and PetscFE have a circular dependence. We need to move the FEM methods to PetscFE
- Changed FEMIntegrateResidualBatch() from to Pe

PetscFE: Large reorganization of FEM dispatch
- WARNING: Now DMPlex and PetscFE have a circular dependence. We need to move the FEM methods to PetscFE
- Changed FEMIntegrateResidualBatch() from to PetscFEIntegrateResidualChunk()
- Changed DMPlexComputeResidualFEM() to use new interface
- Changed signature of f_k and g_kl functions
- Added DMPlexResidualFEM event
- Put PetscQuadrature and PetscCellGeometry
- Moved and changed PetscFEM structure

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PetscFE: Added PetscDualSpaceCreateReferenceCell(), PetscDualSpaceGetNumDof(), PetscFEGetSpatialDimension() and PetscFEGetNumDof()

PetscFE: Added quadrature
- Added PetscFEGet/SetQuadrature()
- Changed signature for PetscFEGet/RestoreTabulation()
- Added PetscQuadratureDestroy()
- Fixed PetscDualSpaceDestroy()

PetscFE: More declarations

PetscFE: Added declarations

PetscFE: This begins explicit FEM support in PETSc
- PetscSpace: A linear space, like P_1, the P from Ciarlet
- PetscDualSpace: The dual space to a PetscSpace, P' and K from Ciarlet, so it takes a re

PetscFE: This begins explicit FEM support in PETSc
- PetscSpace: A linear space, like P_1, the P from Ciarlet
- PetscDualSpace: The dual space to a PetscSpace, P' and K from Ciarlet, so it takes a reference element DM, uses PetscQuadrature for functionals
- PetscFE: Combines PetscSpace, PetscDualSpace, PetscQuadrature to define an element, no implementations yet

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