Problem: Added class PetscProblem
- This is intended to encapsulate a set of discretizations and functions defining the physics
- It calculates total sizes and offsets

Merge branch 'master' into barry/saws-options

Merge branch 'knepley/feature-fv-class'

* knepley/feature-fv-class: (44 commits)
PetscFV: Another complex fix
DMPlex+TS: Fixing types
PetscFV: Straighten out complex types
TS ex11: Fix casts

Merge branch 'knepley/feature-fv-class'

* knepley/feature-fv-class: (44 commits)
PetscFV: Another complex fix
DMPlex+TS: Fixing types
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
PetscFV: Fix Fortran define
PetscFV: Complex fixes
SNES+DM: Added SNESMonitorFields() - Activated by -snes_monitor_fields
PetscFV: Add Fortran types
SNES ex62: Use new DMPlexAddBoundary() interface - Added declaration of DMPlexComputeL2FieldDiff() - Fixed cast
SNES ex12: Fixed Neumann boundary conditions, and moved to new DMPlexAddBoundary interface() - Now do not automatically mark boundary faces
PetscFV: Fixed Fortran bindings
PetscFV+Plex: Refactored to put reconstruction routines in PetscFV_LeastSquares - Added PetscFVComputeGradient() - Added PetscFVLeastSquaresSetMaxFaces() - Moved last squares fitting routines to PetscFV_LeastSquares, and all the work space
PetscLimiter: Add other implementations
TS ex11: Fixed parallel mesh creation - Distribute after physics - Add output for tests
DMPlex: Fixed bug when using refinement from options - Must copy over the point SF
DMPlex: Distribution should copy over BC info
TS ex11: Added refinement tests
TS ex11: Fix boundary conditions after refinement, set types from command line
DMPlex: Added DMPlexCopyBoundary() - Copy boundary conditions after DMRefine() and DMPlexConstructGhostCells()
TS ex11: Specify boundary label
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/plex.c
src/snes/examples/tutorials/ex62.c

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PetscFV: Initial checkin
- Added an Upwind implementation

Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into barry/xcode

Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

Merge branch 'master' into knepley/feature-dmda-section

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs

Merge branch 'master' into knepley/feature-dmda-section

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs
Increase patchlevel to 3.4.3
SNES: Now work vectors come from the DM
SNES ex62: Remove code generation
SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()
Compiler: Fix warnings from MPI impls which do not initialize outputs
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
PC: Removed support graph PC
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
...

Conflicts:
src/dm/impls/da/dalocal.c

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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 '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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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

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

Add discretization tools: Legendre polynomials and Gauss quadratures

Hg-commit: 784baf9728c4b138388b0998be51cc7f10a414ee