Sys: add PetscCalloc[1-7]

Replace lots of places where PetscMemzero is called immediately after
allocation.

Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(

Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(.*sizeof' src | xargs perl -pi -e 's@PetscMalloc\(([^,;]*[^,; ]) *\* *sizeof\([^,;()]+\),@PetscMalloc1($1,@'

This commit contains an additional bug-fix in csrperm.c, fixing pointer
arity. The code was introduced in 2006, but the allocation could not
have been correct at any time. This probably means that
MatDuplicate_SeqAIJPERM has never been tested.

a54129beb540034ba105796c682d589e7e1111f2
Richard Tran Mills <rmills@ornl.gov>

Added MATSEQCSRPERM support for MatDuplicate() and conversion to/from
MATSEQAIJ. Note that these changes are not quite debugged.

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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()

PetscMalloc[2-7]: remove type arguments, infer from pointer type

This change can be performed almost entirely by this script:

git grep -l PetscMalloc[2-7] $1 | xargs perl -pi \
-e '
s@PetscMalloc

PetscMalloc[2-7]: remove type arguments, infer from pointer type

This change can be performed almost entirely by this script:

git grep -l PetscMalloc[2-7] $1 | xargs perl -pi \
-e '
s@PetscMalloc2\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc2($1,$3,$4,$6)@;
s@PetscMalloc3\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc3($1,$3,$4,$6,$7,$9)@;
s@PetscMalloc4\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc4($1,$3,$4,$6,$7,$9,$10,$12)@;
s@PetscMalloc5\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc5($1,$3,$4,$6,$7,$9,$10,$12,$13,$15)@;
s@PetscMalloc6\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc6($1,$3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18)@;
s@PetscMalloc7\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc7($1,$3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18,$19,$21)@;
'

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DMPlex ex4: hex refinement now fixed

DMPlex: Fixed leak in SF creation for submesh
- Changed name of subpointIS to avoid confusion

DMPlex: Fixed SF creation in hybrid tet refinement, added better check

DMPlex: Guard for empty submesh in parallel during subSF creation

DMPlex ex1: Added test for Gmsh

DMPlex: Added Gmsh input

Merge branch 'knepley/fix-fem-bd-integrate'

* knepley/fix-fem-bd-integrate:
SNES ex12: Fix Neumann tests - Now using normal from f0, f1 - Turned on 3D test
DMPlex: DMPlex: Fix 1D face geometry i

Merge branch 'knepley/fix-fem-bd-integrate'

* knepley/fix-fem-bd-integrate:
SNES ex12: Fix Neumann tests - Now using normal from f0, f1 - Turned on 3D test
DMPlex: DMPlex: Fix 1D face geometry in DMPlexComputeGeometryFVM_1D_Internal() - Normalize vector
DMPlex: DMPlex: Fix 1D face geometry in DMPlexComputeGeometryFVM_1D_Internal() - Used inward pointing normal
DMPlex: Fix 1D face geometry in DMPlexComputeProjection2Dto1D_Internal() - Used inverse rotation by mistake
SNES ex12: Fixed bug in 3D P2 test cases - I was not marking boundary edges, so these variables were unconstrained
SNES ex12: Fixed newline at the end of test output
SNES ex12: Now complete the boundary label in all circumstances - The boundary integration ignores non-faces
DMPlex: Added determination of the normal for boundary faces
DMPlex: Only allow boundary integration on faces

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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 edg

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

show more ...

DMPlex: Added GetQuadEdgeInverse_Static() and GetQuadSubfaceInverse_Static() for refinement

DMPlex: Improved error message for DMPlexCheckFaces()

DMPlex: Better docs for DMPlexGetRawFaces_Internal()

DMPlex: Make DMPlexCreateCohesiveSubmesh_Interpolated() also create PetscSF

DMPlex ex4: Tet tests with single refinement now passing again
- Hex still broken