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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PetscQuadrature: Add a 0d corner case

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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PetscQuadrature: Revamped
- Removed basis tabulation
- Shortened names
- Added PetscQuadratureView()

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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DMDT: move FEM space support to own file dtfe.c

DMDT: use PetscClassId for class ids [needed for 64-bit-indices]

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

PetscFE: Fix bug in PetscDualSpaceSetUp_Lagrange()

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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DT: Changed PetscDTGaussJacobiQuadrature() to take a PetscQuadrature object

PetscFE: Fix use of typename

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

PetscFE: Added derivative tabulation

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

PetscDualSpace: Fix destructor

PetscSpace: Removed unnecessary A matrix

PetscFE: Added field components
- Right now, element is just duplicated for each component, we need to experiment with vector elements to see how to really do it

PetscDualSpace: Added support for 3D and 2nd order Lagrange

PetscDualSpace: Reference count DM