Plex+HDF5: Ignore negative sequence numbers

DMPlex: When creating a section, we should only complete a label once

DMPlex: Now DMPlexProjectFieldLocal() correctly masks out fields with no function

DMPlex: Added DMPlexVecSetFieldClosure_Internal()
- Allows fields to be masked

DMPlex: Fixes preallocation checks

DMPlex: Fix error in 3D-to-2D projection

Merge branch 'knepley/feature-plex-neumann-bc'

* knepley/feature-plex-neumann-bc:
SNES ex12: Added support for boundary Jacobian
DMPlex: Added boundary Jacobian to DMPlexComputeJacobianFEM()
D

Merge branch 'knepley/feature-plex-neumann-bc'

* knepley/feature-plex-neumann-bc:
SNES ex12: Added support for boundary Jacobian
DMPlex: Added boundary Jacobian to DMPlexComputeJacobianFEM()
DMPlex: Removed defunct interpolator function
PetscFE: Added PetscFEIntegrateBdJacobian() - Added pointwise functions to PetscFEM - Added an implementation for Basic
DMPlex: Correct boundary iteration for Neumann conditions in residual assembly

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Merge branch 'knepley/feature-fe-derivatives'

* knepley/feature-fe-derivatives:
Doc+Plex: Small fix for distribution
PetscFE: Correct type for reference space derivatives
SNES ex62: Updated to

Merge branch 'knepley/feature-fe-derivatives'

* knepley/feature-fe-derivatives:
Doc+Plex: Small fix for distribution
PetscFE: Correct type for reference space derivatives
SNES ex62: Updated to new derivative mapping
SNES ex12: Updated to new derivative mapping
PetscFE: Changed mapping of derivatives - Now they are transformed only pointwise, instead of transforming the whole tabulation
SNES ex62: Works with new derivative mapping
SNES ex12: Works with new derivative mapping
PetscFE: Changed PetscFEIntegrateResidual_Basic() derivative mapping - Instead of mapping the basis derivatives, we only map the pointwise derivatives gradU and f_1 Suggested-by: Jed Brown <jedbrown@mcs.anl.gov>
PetscFE: Removed PetscGenerateFEMQuadrature*.py

Conflicts:
config/builder.py

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DMPlex: Now Plex output is parallel
- We now write visualization specific topology in /viz/topology
- We output a point reordering, coneSizes, cones, and orientations
- Now longer need to interpolate

DMPlex: Now Plex output is parallel
- We now write visualization specific topology in /viz/topology
- We output a point reordering, coneSizes, cones, and orientations
- Now longer need to interpolate on load

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DMPlex: Use the presence of faceGeometry in the DM to signal we are using FVM
- This will become a PetscFVM object soon

DMPlex: Preserve the block size of the coordinate vector after distribution

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this wa

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad)
outdated example that doesn't match coding style removed and buggy
petscversion.h: workaround ifort -cpp lack of referential transparency
configure: ignore AR, MAKEFLAGS [if set in env]
incorrect first entry in array being zeroed in example
sizeof.c: remove dependence on petsc [and fix syntax error]
nightlybuilds: use consistant PETSC_ARCH, machine names
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
change MPIVersion streams to use MPI_Wtime() to be portable to Windows do not use scalar square root on real number; it upsets Microsoft
cannot use I in PETSc code because in complex it sometimes represents imaginary number cannot pass PetscScalar * to VecNorm()
in dashboard don't warn about SSL and BOI deprecated
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
streams: translate code from 'bash' to 'sh' [fix freebsd]
barry is an idiot who doesn't have a clue as to what he is doing (and git's unfriendlyness doesn't help matters)
don't list examples under C that don't work with complex!
forgotten output file
removed valgrind warning about sending uninitialized data
nightly builds ignore unrecognized pragma and .c file as C++ code
...

Conflicts:
include/petsc-private/dmpleximpl.h

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Plex+HDF5: Moved all HDF5 to a separate file, and mapped 2D periodic mesh to the cylinder
- Now visualization specific things are in /viz

Merge branch 'knepley/fix-plex-bc'

* knepley/fix-plex-bc:
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
TS ex11: Must separate reconst

Merge branch 'knepley/fix-plex-bc'

* knepley/fix-plex-bc:
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
TS ex11: Must separate reconstruction setup from geometry setup
DMPlex: DMPlexConstructGhostCells() should not be calling DMSetFromOptions()
DMPlex: FVM BC should only be applied to faces - Refinement adds in vertices/edges on refined faces
DMPlex: Must decide what kind of BC to apply for output

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Merge branch 'knepley/feature-plex-periodic'

* knepley/feature-plex-periodic:
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
Draw: Fixed bad check
SNES ex62: Enhance ex

Merge branch 'knepley/feature-plex-periodic'

* knepley/feature-plex-periodic:
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
Draw: Fixed bad check
SNES ex62: Enhance ex62 to use tensor-product cells
DMPlex: Now we are correctly creating the Mobius band - Coordinates for uniform refinement are still broken
DMPlex: If domain is periodic, uniform refinement of coordinates will respect this
DMPlex: Allow geometry routines to recognize periodic quads
DMPlex: Added DMPlexLocalizeCoordinates() - This pulls coordinates from vertices to the cell, which allows discontinuities - We use this for periodic problems
DM: Added preliminary support for periodic coordinates - Added DMGet/SetPeriodicity() which is for clipping coordinates to a periodic box
DMPlex: Needed a custom Fortran wrapper for DMPlexInterpolate() because now we require that the incoming mesh be NULL
DMPlex: Fix handling of Fortran NULLs
DMPlex: Updated test output - The DMView was changed
SNES ex12: Cleanup structure - Use PetscFECreateDefault()
PetscFE: Added a view for Basic
SNES ex12: Starting to cleanup test names
SNES ex62: Marked MF tests as broken

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Doc+Plex: Small fix for distribution

DMPlex: Added boundary Jacobian to DMPlexComputeJacobianFEM()

DMPlex: Removed defunct interpolator function

DMPlex: Fix comparison for complex

Doc+DMPlex: Added function documentation for some refinement functions

Merge branch 'barry/add-names-for-all-ascii-viewers'

DMPlex: DMPlexConstructGhostCells() should not be calling DMSetFromOptions()

DMPlex: FVM BC should only be applied to faces
- Refinement adds in vertices/edges on refined faces

DMPlex: Must decide what kind of BC to apply for output

DMPlex: Now we are correctly creating the Mobius band
- Coordinates for uniform refinement are still broken