Merge branch 'knepley/fix-plex-examples' into knepley/feature-plex-refine-3d

* knepley/fix-plex-examples: (36 commits)
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff

Merge branch 'knepley/fix-plex-examples' into knepley/feature-plex-refine-3d

* knepley/fix-plex-examples: (36 commits)
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
SNES example: fix bad merge
config: only define DATAFILESPATH for non-null value
config: define lang-specific macros in petscconf.h, choose in petscsys.h
Mat: add MATOP_ values for missing functions
DMPlex: use VECSTANDARD for coordinates
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong. We have to use the largest thing in sf->mine[]
replaced ISCreateGeneral in CompositeDM with ISCreateStride. MatNest calls ISStrideGetInfo on these vectors, which was causing errors
DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets() - Non-broken example was in PetscSFDistributeSection()
...

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

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DMPlex: Fixed fortran binding for DMPlexCreateSubmesh()

Compiler: Fix warnings from MPI impls which do not initialize outputs

DMPlex ex4: Fixed test output

DMPlex ex7: Added missing test output

DMPlex ex8: Fixed leak

DMPlex ex7: Fixed test output
- Corrected orientations in interpolation

DMPlex ex1: Fixed test output
- Uniform refinement for quads changed

DMPlex: Fix overagressive checks

DMPlex: Fixed leak in submesh creation

DMPlex ex10: Fixed test output

DMPlex ex4: Added 3D simplicial hybrid test cases
- The testnum = 1 is still non-functional

DMPlex: Can now uniformly refine 3D simplicial hybrid meshes
- I know its a large number of changes, but I did not see a good way to break it up

DMPlex: Added DMPlexCreateHybridMesh()
- This was formerly done in a few steps by creating a submesh, making the label, and then constructing hybrid cells

DMPlex: Changed argument of DMPlexCreateSubmesh() to a DMLabel

DMPlex: Fixed determination of hybrid bounds

Merge branch 'jed/dmvecmattypes-stdcoords'

* jed/dmvecmattypes-stdcoords:
DMPlex: use VECSTANDARD for coordinates

Merge branch 'knepley/fix-plex-preallocation'

* knepley/fix-plex-preallocation:
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong.

Merge branch 'knepley/fix-plex-preallocation'

* knepley/fix-plex-preallocation:
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong. We have to use the largest thing in sf->mine[]
DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets() - Non-broken example was in PetscSFDistributeSection()
DMPlex: Fix leaks in preallocation debugging
DMPlex: Put in guard for preallocation sections which are smaller than the SF

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DMPlex ex4: Fixed 2D hybrid simplex tests

DMPlex ex5: Added checks and fixed output
- Fixes for supports

DMPlex: Fix for hybrid cell creation
- Adding hybrid face in support should not have been in loop

DMPlex: Fix distribution of hybrid cell information
- Fixed bizarre code intended for cell-vertex meshes

DMPlex: use VECSTANDARD for coordinates

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Ste

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Stefano
fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
MatSchurComplement: Must initialize KSP package
bib: fix inbook citation
Bib: Updated some refs
SNES: fix copy/paste in man page
fortran: fix KSPCONVERGEDDEFAULT and SNESCONVERGEDSKIP in fortran includes
Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used
PCGAMG: remove distracting comment
KSP ex49: restrict near-null space for elasticity example with sym BC
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
Fix accidental creation of the matrices in SNESNCG used for linear analogue LS.
PCGAMG: add man page for PCGAMGType
fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()
rm //
Sys: new_ir changed from PetscInt to PetscObjectState - so fix mallocs to use the new type
SNES: Fixed package init in SNESLineSearchCreate()
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex5.c
src/dm/impls/plex/plex.c
src/dm/interface/dm.c

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DMPlex ex5: Fixed tests for new hybrid cell formation
- Added in supports for cohesive edges, and cohesive faces