DMPlex: Fix 1D face geometry in DMPlexComputeProjection2Dto1D_Internal()
- Used inverse rotation by mistake

Merge branch 'knepley/fix-plex-geometry-hex'

* knepley/fix-plex-geometry-hex:
DMPlex: If “vtk” label has no cells, do not use it
DMPlex: DMPlexCreateCohesiveSubmesh() must also extract orientati

Merge branch 'knepley/fix-plex-geometry-hex'

* knepley/fix-plex-geometry-hex:
DMPlex: If “vtk” label has no cells, do not use it
DMPlex: DMPlexCreateCohesiveSubmesh() must also extract orientations
DMPlex: Add 1D code for DMPlexCheckSkeleton()
DMPlex: Cleanup code for VTK output - Removed diagnostic print - Use DMLabel interface
DMPlex: Change geometry check to support interpolated meshes - This all has to be replaced anyway

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DMPlex: Change geometry check to support interpolated meshes
- This all has to be replaced anyway

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

DMPlex: Cleaned up uses of DMPlexGet/SetCoordinateSection()

DMPlex: Cleaned up uses of DMPlexGet/SetCoordinateSection()

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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Wrapped math.h and quadmath.h functions used in petsc source exempting examples

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

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries

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

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

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

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

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib

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

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
include/petscdmplex.h

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

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib e

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

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

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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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Merge branch 'knepley/fix-3d-orientation'

* knepley/fix-3d-orientation:
DMPlex: Fix initialization for DMPlexVecGetClosure()
DMPlex: fix argument to DMPlexVecRestoreClosure
DMPlex: Fix orienta

Merge branch 'knepley/fix-3d-orientation'

* knepley/fix-3d-orientation:
DMPlex: Fix initialization for DMPlexVecGetClosure()
DMPlex: fix argument to DMPlexVecRestoreClosure
DMPlex: Fix orientation for VTU output
plex: remove unused variable
DMPlex: Fixed orientation conversion for VTK
DMPlex: Fixed field interpolation in tetrahedra and hexahedra for new orientation
DMPlex: Fixed face definition in tetrahedra and hexahedra for new orientation
DMPlex: Fixed point location in hexahedrons for new orientation
DMPlex: Added generic DMPlexInvertCell() to aid in changing orientation to the internal convention

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Merge branch 'knepley/fix-plex-geometry'

* knepley/fix-plex-geometry:
DMPlex: Now geometry tests can take an input mesh - Use Exodus format - Input all mesh data in options - Made builder runs for

Merge branch 'knepley/fix-plex-geometry'

* knepley/fix-plex-geometry:
DMPlex: Now geometry tests can take an input mesh - Use Exodus format - Input all mesh data in options - Made builder runs for 3 hexes
DMPlex: Test ex8 now runs interpolated tests separately - Added new builder runs
DMPlex: Added FVM geometry to interpolation test
DMPlex: FVM geometry was ignoring face orientation

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DMPlex: Forgot one init for DMPlexVecGetClosure()