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

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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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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DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection
- Has not been tested with moment dofs
- Accommodates vector functions

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

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fort

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

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran interface
PetscSection: Added docs for Fortran binding for VecSetValuesSection()
Vec: Removed old F90 binding for PetscSection
bgq: fix deadlock on bgq due to inconsistant values returned by getpwuid(getuid()) on runs with 256nodes [or 4096 cores]. This fix removes the reliance on PetscGetHomeDirectory() returning 'same' value across nodes. [using the fact that PetscOptionsInsertFile() uses HOMEDIR from node-0 only]
DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1)
DMPlex: Fix 64-bit int problem in VTK
Mat: Fix for PetscSparseDenseMaxDot() for complex
Vec: Correct VecUniqueEntries() for 64-bit indices
MatSeqAIJGetArrayF90: add man pages and fix typo in MatDense version
SF docs: add link to summary page and fix title
Doc: Fixed DM code in manual
metis/parmetis: update to metis-5.1.0/parmetis-4.0.3 Also update the test output as the partitioning appears to have changed.
DMPlex: remove unused variables
blaslapack: update f,f2c tarballs to 3.4.2 version
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
...

Conflicts:
include/petscdmplex.h

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Merge branch 'knepley/fix-plex-matclosure'

* knepley/fix-plex-matclosure:
DMPlex: Update calls to DMPlexMatSetClosure() to eliminate default arguments
DMPlex: Do not allow default sections in DM

Merge branch 'knepley/fix-plex-matclosure'

* knepley/fix-plex-matclosure:
DMPlex: Update calls to DMPlexMatSetClosure() to eliminate default arguments
DMPlex: Do not allow default sections in DMPlexMatSetClosure() - This makes the call collective

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Merge branch 'knepley/plex-speed-tests'

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if arr

Merge branch 'knepley/plex-speed-tests'

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if array is passed in
DMPlex: Added special case for DMPlexVecSetClosure() - Could add more modes
DMPlex: Optimizations for DMPlexVecGetClosure() - Removed branch (seems to have little effect) - Removed calculation of size when array is provided (profiled for 20% effect)
DMPlex: Forgot one init for DMPlexVecGetClosure()
DMPlex: Must initialize argument to DMPlexVecGetClosure()
DMPlex ex9: Added ability to reuse array in VecGetClosure()
DMPlex: Allow DMPlexVecGetClosure() to take an input array
DMPlex: Fix bug in specialization of DMPlexVecGetClosure()
DMPlex: Bug fix for special case in DMPlexVecGetClosure()
DMPlex: Added optimization for depth 1 DMPlexVecGetClosure()
DMPlex ex9: Does not fail by default - Will turn back on failure once we calculate variance
SNES ex12: Cleaning up in preparation for speed testing
DMPlex: Added ex9 to test performance, put in depth 1 special case for TransitiveClosure

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c
src/snes/examples/tutorials/output/ex12_5.out

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

DMPlex+PetscFE: Fix compile errors for complex
- LAPACK calls still broken

Merge branch 'knepley/plex-speed-tests' into knepley/feature-dt-fem

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need

Merge branch 'knepley/plex-speed-tests' into knepley/feature-dt-fem

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if array is passed in
DMPlex: Added special case for DMPlexVecSetClosure() - Could add more modes
DMPlex: Optimizations for DMPlexVecGetClosure() - Removed branch (seems to have little effect) - Removed calculation of size when array is provided (profiled for 20% effect)
DMPlex: Forgot one init for DMPlexVecGetClosure()
DMPlex: Must initialize argument to DMPlexVecGetClosure()
DMPlex ex9: Added ability to reuse array in VecGetClosure()
DMPlex: Allow DMPlexVecGetClosure() to take an input array
DMPlex: Fix bug in specialization of DMPlexVecGetClosure()
DMPlex: Bug fix for special case in DMPlexVecGetClosure()
DMPlex: Added optimization for depth 1 DMPlexVecGetClosure()
DMPlex ex9: Does not fail by default - Will turn back on failure once we calculate variance
SNES ex12: Cleaning up in preparation for speed testing
DMPlex: Added ex9 to test performance, put in depth 1 special case for TransitiveClosure

Conflicts:
config/builder.py
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/output/ex12_10.out
src/snes/examples/tutorials/output/ex12_11.out
src/snes/examples/tutorials/output/ex12_5.out
src/snes/examples/tutorials/output/ex12_6.out
src/snes/examples/tutorials/output/ex12_8.out
src/snes/examples/tutorials/output/ex12_9.out

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

DM: Added a tolerance to DMPrintLocalVec()
- Also added member to DMPlex to store tolerance, use -dm_plex_print_tol to set

PetscFE: Now cell blocks are settable from options
- Fixed bad merge in 8residual integration

DMPlex: Fix DMPlexComputeL2Diff() to take PetscFE

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

DMPlex: Remove some dead code

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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DMPlex: Must initialize argument to DMPlexVecGetClosure()