DMPlex: Fixed markers on periodic boundary

completed some percentage of changes from %G format in prints

DMPlex: Reorganization of closure operations
- Rename DMPlexVecGetClosure_Static() —> DMPlexVecGetClosure_Depth1_Static()
- Added special cases with/out fields
- Removed the need for field offsets by

DMPlex: Reorganization of closure operations
- Rename DMPlexVecGetClosure_Static() —> DMPlexVecGetClosure_Depth1_Static()
- Added special cases with/out fields
- Removed the need for field offsets by interchanging loops over points and fields
- Fixed bug where field offsets were not calculated if an array was passed in
- Made all local functions static
- Using SNES ex62 to verify changes, and DMPlex ex9 to time them

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DMPlex: Fixed object check

DMPlex ex9: Now test VecClosure with index
- Made functions static

DM examples: include petscdm.h in examples that use DM_BOUNDARY_*

DMPlexMatSetClosure: allow NULL sections to use defaults

DMPlex Fortran: allow PETSC_NULL_OBJECT for sections

Reported-by: Dharmendar Reddy <dharmareddy84@gmail.com>

DMPlex F90: rename __ierr to ierr for use with macros

DMPlex: Optimization for Get/SetClosure
- Only need field offsets if there is more than one field

DMPlex: Now DMPlexCreateHexBox() can have a Mobius topology using DM_BOUNDARY_TWIST

DM: Moved DMDABoundaryTypes to DMBoundaryTypes
- Changed the enum values as well
- Changed docs and updated Changes
- Updated examples

DMPlex: DMPlexCreateHexBoxMesh() now allows periodicity
- Changed declaration and uses
- DMPlexCreateSquareMesh() now allows periodicity
- Works with refinement

DMPlex ex4: Added test for hybrid quads

DMPlex: Added in hybrid quad refinement
- Strange merge in the middle for some reason

DMPlex: Cleanup and fix for SF construction in refinement
- Had wrong numbering for vertices in quads

DMPlex: Bug fix for hybrid tet refinement
- The new edges for hybrid faces do not depend on the cap face orientation
- This happens because we are not attaching hybrid faces in an order dependent on

DMPlex: Bug fix for hybrid tet refinement
- The new edges for hybrid faces do not depend on the cap face orientation
- This happens because we are not attaching hybrid faces in an order dependent on the cap face orientation. Maybe we should.

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DMPlex: Bug fix for hybrid tet refinement
- The orientation that we get for hybrid faces depends on both the edge and face orientation
- This happens because we are not attaching hybrid faces in an o

DMPlex: Bug fix for hybrid tet refinement
- The orientation that we get for hybrid faces depends on both the edge and face orientation
- This happens because we are not attaching hybrid faces in an order dependent on the cap face orientation. Maybe we should.

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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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removed direct use of sin(), sqrt(), isnormal() etc from C source code and C examples

needed for __float128 precision

Merge branch 'knepley/fix-plex-comments'

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

Merge branch 'knepley/feature-dmda-section'

* knepley/feature-dmda-section: (29 commits)
DMPlex: fix stale docs about DMPlexGetCoordinateSection
DMDA: Fix compiler warnings
DMDA+DMPlex: Fixed

Merge branch 'knepley/feature-dmda-section'

* knepley/feature-dmda-section: (29 commits)
DMPlex: fix stale docs about DMPlexGetCoordinateSection
DMDA: Fix compiler warnings
DMDA+DMPlex: Fixed preallocation declarations
DMDA: c89 fix
DMDA: Forgot to add new source file
DMPlex: Fix merge from master
DMDA: Add a matrix preallocation routine that works with PetscSection
DMDA: Add transitive closure - Only working in 2D
DMDA: Add preallocation center dim for using PetscSection
DMDA: Added declaration for DMDAGetCellPoint()
DMDA: Added DMDAGetCellPoint()
DMPlex: Added documentation
DMDA: fix missing declarations and includes
DMPlex ex3: Fixed multicomponent functions - These were zero in all but the first component due to an earlier error
DMPlex: Cleaned up uses of DMPlexGet/SetCoordinateSection()
DMPlex: Cleaned up uses of DMPlexGet/SetCoordinateSection()
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests - Added -simplex argument - Uses DMDA for quad tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/dm/impls/plex/examples/tests/ex3.c
src/dm/impls/plex/examples/tests/output/ex3_2.out
src/dm/impls/plex/examples/tests/output/ex3_5.out

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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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Merge branch 'knepley/feature-fem-gradients'

* knepley/feature-fem-gradients:
DMPlex ex3: Fix derivative for quadratic test
DMPlex ex3: Fixed bug setting dimension (again) - Updated test output

Merge branch 'knepley/feature-fem-gradients'

* knepley/feature-fem-gradients:
DMPlex ex3: Fix derivative for quadratic test
DMPlex ex3: Fixed bug setting dimension (again) - Updated test output
DMPlex ex3: Put in gradient check - There seems to be a problem with tests 2 and 5
DMPlex: Added DMPlexComputeL2GradientDiff() - I was not sure what to do with BC
Test context passing in dm plex test ex3
Add a void *ctx argument to PetscDualSpaceApply and friends

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