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outdated example that doesn't match coding style removed and buggy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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PetscSection: Better check when creating global section

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

IS+HDF5: Corrected code for new block size interface where it is never negative

Merge branch 'knepley/feature-plex-hdf5'

* knepley/feature-plex-hdf5: (63 commits)
DMPlex ex2: Added an example that checks a mesh
DMPlex: #ifdef support functions for HDF5
TS: Fix output sequ

Merge branch 'knepley/feature-plex-hdf5'

* knepley/feature-plex-hdf5: (63 commits)
DMPlex ex2: Added an example that checks a mesh
DMPlex: #ifdef support functions for HDF5
TS: Fix output sequence
DMPlex: Check for HDF5 attributes before writing them
DMPlex: Label with timestep number since we do not have times
Viewer+HDF5: Added PetscViewerHDF5HasAttribute()
TS: Set output sequence for timesteps
DMPlex: Handle output sequences - Added static to some functions
DM: Add idea of an output sequence - Added DMGet/SetOutputSequenceNumber() - Added doc for outputDM
REVERT TS: Timestep gets set into DMTS
DMPlex: Fix up HDF5 segregation
DMPlex: Replace MAXPATHLEN with PETSC_MAX_PATH_LEN
DMPlex: Fix HDF5 timestep handling
DMPlex: Set correct block size on HDF5 field vectors
TS: Timestep gets set into DMTS
DMTS: Added timestep
DMPlex: Fix output of fields - Corrected name - Fixed vector type
DMPlex: Return errors from HDF5 function
DMPlex+Viewer: Now output separate fields for viz - Added the PETSC_VIEWER_HDF5_VIZ format for creating viz fields - Added field type determination
Sys+HDF5: Added PetscDataType string and HDF5 support for it
...

Conflicts:
config/BuildSystem/config/packages/__init__.py
src/ts/interface/ts.c

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Insure that all ASCII viewers for PETSc objects call PetscObjectPrintClassNamePrefixType()

IS: Forgot to protect HDF5

IS: Added ISLoad() and an HDF5 implementation
- I know this only works for general now

PetscSection: Added an optional permutation for the chart
- Removed the unnecessary atlasLayout
- This permutation will allow people to segregate ghost unknowns at the end of their numbering,
and

PetscSection: Added an optional permutation for the chart
- Removed the unnecessary atlasLayout
- This permutation will allow people to segregate ghost unknowns at the end of their numbering,
and also to get around the stratification of point numbering in Plex

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PetscSection: Added PetscSectionHasConstraints()

Merge branch 'knepley/fix-fem-multifield'

* knepley/fix-fem-multifield:
DMDT: Fixed Fortran PetscQuadrature definition
DMPlex ex3: Added Q2 tests - Made DA tests only 2x2 - Changed output format

Merge branch 'knepley/fix-fem-multifield'

* knepley/fix-fem-multifield:
DMDT: Fixed Fortran PetscQuadrature definition
DMPlex ex3: Added Q2 tests - Made DA tests only 2x2 - Changed output format - Quad tests now actually work
DMDA: Added DMDAComputeL2GradientDiff()
PetscSpace: Fixed polynomial derivative evaluation for quads
DMDA: Fix closure operations in 2D
DMPlex: Interpolation cleanup - Remove unused PetscSpace - Fix uninitialized variable
PetscFE: Fix PetscBool handling
SNES ex62: Updated output
DMPlex ex3: Use PetscFECreateDefault() and correct tensor tests
PetscFE: Fix PetscFECreateDefault() - The space should default to tensor on a non-simplex - The quadrature should be tensor Gauss on a non-simplex
DT: Added PetscDTGaussTensorQuadrature()
DT: Added citation for Gloub+Welsch method
PetscSection: Now global section can also be viewed
DMPlex: Allow NULL function for ProjectFunction()
PetscDualSpace: Added doc for PetscDualSpaceApply() - Cherry-picked from df2d8bb
PetscFE: Fixed PetscFECreateDefault() - Setup FE - Minimum quad order - Destroy quad after setting
PetscFE: PetscFECreateDefault() now takes a number of components and a reference cell type - Cherry-picked from a255314
PetscFE: Added PetscFECreateDefault() - Cherry-picked from 8919f5a
PetscFE: Allow lowest order cell Lagrange dual basis functions
DMPlex: Fix preallocation with cell variables - I had an incorrect loop optimization

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

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PetscSection: Fixed PetscSFDistributeSection() for the case of an empty partition

PetscSection: Now global section can also be viewed

IS: Fix comm for ISLocalToGlobalMappingApplyIS()
Reported-by: Vincent Frans Maria De Groof <Vincent.De-Groof@uibk.ac.at>

Mat & Vec: make block sizes lazy

In the past, MatSetUp eagerly set the block sizes (to 1) if not already
set. This prevents use of the "convenience" constructors because they
call MatSetUp before r

Mat & Vec: make block sizes lazy

In the past, MatSetUp eagerly set the block sizes (to 1) if not already
set. This prevents use of the "convenience" constructors because they
call MatSetUp before returning. We could add bs as an explicit argument
to those constructors, but block size is an extraneous concept for most
users. The default value of the block size is -1, so now we use
PetscAbs(map->bs) anywhere it is not known in advance that bs has been
explicitly set. This allows block sizes to be lazy, and they can be set
arbitrarily late, so long as the new size is compatible with the
existing distribution. For (S)BAIJ matrices, the block size is
structural so it gets set explicitly and can thus be referenced directly
rather than via MatGetBlockSize or wrapped in PetscAbs.

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PetscLayoutSetBlockSize: allow PETSC_DECIDE for use when block size has already been set

This slightly simplifies logic in some places, where otherwise we would
have to MatGetBlockSize() and pass it

PetscLayoutSetBlockSize: allow PETSC_DECIDE for use when block size has already been set

This slightly simplifies logic in some places, where otherwise we would
have to MatGetBlockSize() and pass it back in.

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Section: Small doc fix

Merge branch 'knepley/fix-plex-closure-index'

* knepley/fix-plex-closure-index:
DMPlex: work around -Wmaybe-uninitialized
DMPlex: Small fix
PetscSection: Added PetscSectionGetField()
DMPlex:

Merge branch 'knepley/fix-plex-closure-index'

* knepley/fix-plex-closure-index:
DMPlex: work around -Wmaybe-uninitialized
DMPlex: Small fix
PetscSection: Added PetscSectionGetField()
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
DMPlex: Fixed object check
DMPlex ex9: Now test VecClosure with index - Made functions static
DMPlex: Optimization for Get/SetClosure - Only need field offsets if there is more than one field
PetscSection: Change clIndices member to clPoints - Added some docs
SNES ex12: Use ViewFromOptions correctly
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 depth 1 mesh to a static function
DMPlex: Fixed two bugs with DMPlexCreateClosureIndex() - Must make index for entire DM chart - Need to update cloff when no fields are present

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

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DMPlex: Small fix

PetscSection: Added PetscSectionGetField()

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

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