DMPlex: Use closure index in DMPlexVecSetClosure() and DMPlexMatSetClosure()
- Moved depth 1 optimization to static function

DMPlex: Reorgnized closure index
- Now index stores points and orientations instead of offsets, so it can be used for updates as well
- Moved index creation to plexindices.c
- Moved optimization for

DMPlex: Reorgnized closure index
- Now index stores points and orientations instead of offsets, so it can be used for updates as well
- Moved index creation to plexindices.c
- Moved optimization for depth 1 mesh to a static function

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Merge branch 'knepley/fix-plex-comments'

* knepley/fix-plex-comments:
DMPlex: Fix comments

Merge branch 'knepley/feature-plex-refine-hex'

* knepley/feature-plex-refine-hex:
DMPlex: Fixes for ViewFromOptions - Passes regression
DM: Moved ViewFromOptions into DMSetUp_DA()
DMPlex: Inte

Merge branch 'knepley/feature-plex-refine-hex'

* knepley/feature-plex-refine-hex:
DMPlex: Fixes for ViewFromOptions - Passes regression
DM: Moved ViewFromOptions into DMSetUp_DA()
DMPlex: Interface fix in refinement
PetscFE: Fixed leak from bad merge
DMPlex: DMPlexCheckSkeleton() now handles hybrid cells
DMPlex ex4: All refinement tests passing
DMPlex: Added hybrid hex refinement
DMPlex: Bug fix for hybrid tet refinement - Wrong offset
DMPlex: Fixed errors in hybrid tet refinement - Use fMax instead of fStart for offset - Use p instead of fEnd for point value - 2 faces are created from each hybrid face, not 4
DMPlex: Corrected refinement coordinates for hybrid faces
DMPlex ex4: Hybrid tet refinement now working
DMPlex: Propagate fixes from tet refinement to hybrid tet refinement

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DMPlex: Fix comments

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

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed tes

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

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed test output
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dashboard.
ASCII printing of floating point numbers must cast to (double) to support quad precision
configure: check fortranDatatypes only when fortran is enabled [this fixes configure crash with --with-fc=0]
don't use non-portable and also dependent on floating point precision system level math constants
picky compilers
fix a couple compiler warnings/errors (depending on compiler) for Matlab engine code
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()
Fuckup: Fix for merge that is still untangling bad rebase from Oct. 17th 2013 - Fixed const in declarations - Fixed merge from PetscFE - Fixed 2 mallocs
replace all echo in test/tutorial makefiles with printf since echo behaves differently on different systems
DMDA: Missing header - Damn rebase
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
DMDA: Make closure operations also return the size
DMDA: Changed DMDACreateSection() to emulate DMPlexCreateSection()
...

Conflicts:
config/builder.py
include/petscdmda.h
src/dm/dt/interface/dtfe.c
src/dm/impls/da/dageometry.c
src/dm/impls/da/dalocal.c
src/dm/impls/plex/plexgeometry.c

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Merge branch 'knepley/fix-fem-opencl'

* knepley/fix-fem-opencl:
PetscFe+OpenCL: Removed N_c variable
PetscFE+OpenCL: Removed redundant numQuadraturePoints, numBasisFunctions, and numBasisCompone

Merge branch 'knepley/fix-fem-opencl'

* knepley/fix-fem-opencl:
PetscFe+OpenCL: Removed N_c variable
PetscFE+OpenCL: Removed redundant numQuadraturePoints, numBasisFunctions, and numBasisComponents
SNES ex12: Added uniform refinement
PetscFE: Fixed syntax bug
PetscFE: Removed offset members that were used once
PetscFE: Use correct flags for code inclusion for auxiliary fields in OpenCL
SNES ex12: Fix run type options
DMPlex: Fix section creation when depth == 1
DMPlex: Fixed flop calculation for OpenCL evaluator - The old version had (2+2)*dim*N_comp, but I think this should only be 2*dim, which is a 5% effect
DMPlex: Fix FEM bug with initialization of auxiliary coefficient array

Conflicts:
src/snes/examples/tutorials/ex12.c

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Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-plex-gmsh

* master: (163 commits)
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dash

Merge branch 'master' into knepley/feature-plex-gmsh

* master: (163 commits)
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dashboard.
ASCII printing of floating point numbers must cast to (double) to support quad precision
configure: check fortranDatatypes only when fortran is enabled [this fixes configure crash with --with-fc=0]
don't use non-portable and also dependent on floating point precision system level math constants
picky compilers
fix a couple compiler warnings/errors (depending on compiler) for Matlab engine code
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()
Fuckup: Fix for merge that is still untangling bad rebase from Oct. 17th 2013 - Fixed const in declarations - Fixed merge from PetscFE - Fixed 2 mallocs
replace all echo in test/tutorial makefiles with printf since echo behaves differently on different systems
DMDA: Missing header - Damn rebase
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
DMDA: Make closure operations also return the size
DMDA: Changed DMDACreateSection() to emulate DMPlexCreateSection()
DMDA: Added functions which emulate DMPlex functionality
DMDA: Now DMDAGetNumCells() returns the cells in each direction as well
...

Conflicts:
config/builder.py

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Merge branch 'madams/gamg-destroy' into prbrune/pcgamg-classicalinterpolationstrategies

Merge branch 'master' into madams/gamg-destroy

Conflicts:
src/ksp/pc/impls/gamg/gamg.c

Merge branch 'master' into knepley/feature-plex-refine-hex

* master: (68 commits)
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()

Merge branch 'master' into knepley/feature-plex-refine-hex

* master: (68 commits)
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()
Fuckup: Fix for merge that is still untangling bad rebase from Oct. 17th 2013 - Fixed const in declarations - Fixed merge from PetscFE - Fixed 2 mallocs
DMDA: Missing header - Damn rebase
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
DMDA: Make closure operations also return the size
DMDA: Changed DMDACreateSection() to emulate DMPlexCreateSection()
DMDA: Added functions which emulate DMPlex functionality
DMDA: Now DMDAGetNumCells() returns the cells in each direction as well
PetscFE: Added support for tensor product cells in PetscDualSpace_Lagrange
PetscFE: Added tensor product polynomial spaces
example fix /sandbox/petsc/petsc.clone-3/include/petscmath.h(260): error: identifier "PETSC_CXX_STATIC_INLINE" is undefined PETSC_STATIC_INLINE PetscReal PetscAbsScalar(PetscScalar a) {return a < 0.0 ? -a : a;} ^
remove warning in fun3d example "user.F", line 1256: warning: In-place macro substitution leaves line truncated "user.F", line 1259: warning: In-place macro substitution leaves line truncated "user.F", line 1262: warning: In-place macro substitution leaves line truncated
/Users/petsc/petsc.clone-2/src/ksp/ksp/examples/tutorials/ex56.c:59: warning: comparison between signed and unsigned integer expressions
fix examples for portability
fixed to example outputs
fix output for a few examples changed due to changes to -mat_view and not using -snes_monitor_short
...

Conflicts:
src/dm/impls/plex/plexrefine.c

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DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()

DM: Added DMGet/SetCoordinateSection()

Merge branch 'barry/update-xxxviewfromoptions'

Merge branch 'master' into barry/reduce-dmsetup-da-memoryusage

Conflicts:
src/dm/examples/tests/ex15.c
src/dm/examples/tutorials/ex3.c
src/dm/impls/da/da2.c
src/dm/impls/da/da3.c

Merged master into barry/update-xxxviewfromoptions

Merge branch 'master' into barry/xcode

DMPlex: DMPlexCheckSkeleton() now handles hybrid cells

Merge branch 'barry/saws-push-header-body' into barry/saws-options

Merge branch 'knepley/feature-plex-hybrid-3d'

* knepley/feature-plex-hybrid-3d: (45 commits)
DMPlex ex5: Check faces on all meshes
DMPlex ex5: Fix consistency of original meshes - Fix orientatio

Merge branch 'knepley/feature-plex-hybrid-3d'

* knepley/feature-plex-hybrid-3d: (45 commits)
DMPlex ex5: Check faces on all meshes
DMPlex ex5: Fix consistency of original meshes - Fix orientations of tet meshes - Redo hex test to automatically interpolate - Replaced output
DMPlex ex5: Check original meshes for consistency
DMPlex: make non-namespaced CellRefiner functions static
DMPlex: Fix hybrid bounds in DMPlexCheckFaces()
DMPlex ex5: Now all test working - Two faults working correctly
DMPlex: Fix for hybrid meshes with multiple surfaces - Move the original hybrid cells to the end of the numbering, so that split+hybrid points are inserted as a block - Use DMPlexShiftPoint_Internal() uniformly
SNES ex4: Fix for DMCheckSkeleton()
DMPlex ex4: All non-hybrid refinement test pass (Fuck Yeah)
DMPlex: In tet refinement, fixed edge orientation in internal face
DMPlex ex4: Correct output after cross-tet edge orientation fix
DMPlex: In tet refinement, correct internal tet face orientations
DMPlex: In tet refinement, correct internal face cones
DMPlex: In tet refinement, correct check for cross-tet edge
DMPlex: Now DMPlexCheckFaces() also checks all subfaces
DMPlex: Added 1D stuff to DMPlexGetRawFaces_Internal()
DMPlex ex4: hex refinement now fixed
DMPlex: Fixed split face supports for tet refinement
DMPlex: Multiple refinement for hex now working - Fixed face orientations for hexes - Fixed split face orientations - Fixed split face supports - Fixed internal face orientations - Fixed internal edge supports
DMPlex: Added GetQuadEdgeInverse_Static() and GetQuadSubfaceInverse_Static() for refinement
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plexsubmesh.c

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Fix use of MPI_Type_size versus MPI_Type_get_extent

This affects use of non-contiguous types.

Merge branch 'jed/malloc-array'

Type arguments dropped from PetscMalloc[2-7], PetscNew, and PetscNewLog,
added PetscMalloc1 for allocating typed arrays, add PetscCalloc[1-7] for
allocating cleared (

Merge branch 'jed/malloc-array'

Type arguments dropped from PetscMalloc[2-7], PetscNew, and PetscNewLog,
added PetscMalloc1 for allocating typed arrays, add PetscCalloc[1-7] for
allocating cleared (zeroed) memory.

* jed/malloc-array:
Sys: Add pointer casts from (void **) in calls to PetscMalloc1()
Sys: drop explicit type arguments from PetscNew() and PetscNewLog()
Sys: add PetscCalloc[1-7]
Sys: add PetscMalloc1 macro, array allocation without redundant types
PetscMalloc[2-7]: remove type arguments, infer from pointer type
SNESComputeJacobianDefaultColor: fix uninitialized variable

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DMPlex: Fix hybrid bounds in DMPlexCheckFaces()

Merge commit '58723a9' into knepley/feature-plex-hybrid-3d

* commit '58723a9':
DMPlex: Fix DMPlexCheckSkeleton() for submeshes
DMPlex ex5: Added second fault for quad test
DMPlex: Fix setting

Merge commit '58723a9' into knepley/feature-plex-hybrid-3d

* commit '58723a9':
DMPlex: Fix DMPlexCheckSkeleton() for submeshes
DMPlex ex5: Added second fault for quad test
DMPlex: Fix setting of hybrid bounds for multiple faults
DMPlex ex5: Turn on second fault in quad test
DMPlex: Removed compiler warnings
DMPlex ex5: Cleaned up 2D tensor tests to rely on interpolation
DMPlex ex5: Cleaned up 2D simplex tests to rely on interpolation

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plexrefine.c

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