Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'stefano_zampini/pcbddc-maint' into stefano_zampini/pcbddc_deluxe

Merge branch 'barry/feature-dmmoab-hdf5-tests'

Conflicts:
src/dm/interface/dmregall.c
src/ts/examples/tutorials/makefile

Fix some unitialized variable warnings

Fix a memory crash with options related string handling

Fix a memory crash with options related string handling

Refactor code for simplex connectivity.

Modifying the BoxMesh creation function to also generate simplices (triangles and tets) in a structured fashion. This complements the quad, hex generation. Now the createmesh function takes an option

Modifying the BoxMesh creation function to also generate simplices (triangles and tets) in a structured fashion. This complements the quad, hex generation. Now the createmesh function takes an optional isSimplex argument.

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Fixing a bug in options for read/write where there was garbage in newly initialize char arrays.

Updating DMMoab interface to the latest PETSc changes related to PetscNew. Removing occurrences of stringstream and replacing with PetscSNPrintf for manipulating IO options.

Adding DMSetFromOptions_Moab to unify all options database retrieval from command line. Added appropriate storage fields in data-structures and made sure that they are universally used, consistently.

Adding DMSetFromOptions_Moab to unify all options database retrieval from command line. Added appropriate storage fields in data-structures and made sure that they are universally used, consistently. Still need to figure out: how to propagate read options to DM before DMSetFromOptions is called.

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Adding more documentation to all main source files and making sure the documentation is generated according to PETSc standards.

Rename some private function and add documentation to public API functions.

Fixing errors due to bad merge after cherry-picking earlier in the branch.

Adding an extra argument to box mesh creation in order to specify the domain bounds. Modifying examples accordingly.

Updating mbutil to the new moab interface change.

Feature additions and fixes. 1) Making the fileset by default represent root set. Useful when user handles the creation of mesh etc. 2) Renumber all entities after resolving shared nodes.

Getting the parallel mesh generation to work correctly. Generate extra sets to categories different dimensional entities so that we can apply some useful tags onto them in future.

Fix the NNZ computation by removing the old methods and implemented a more rigorous traversal to find nnz and onz. Other minor cleanups in DMMoab - remove prints, debug statements etc.

Fixing the parallel mesh generation using slices. The in-memory mesh has contiguous local and then ghosted entities. Tests successful.

Parallel mesh generation.

2b2088d: Ghost layer creation needs to be addressed for in-memory structured meshgen.
c5fa303: Owned vertex ranges might not always be contiguous when reading from files. N

Parallel mesh generation.

2b2088d: Ghost layer creation needs to be addressed for in-memory structured meshgen.
c5fa303: Owned vertex ranges might not always be contiguous when reading from files. Need alternate way to handle MOAB Vec.

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Updates to the 2-D example and additional options for reading mesh from file.

51ee65e: Adding new public interface functions to simplify user assembly code. Added methods to get connectivity of an e

Updates to the 2-D example and additional options for reading mesh from file.

51ee65e: Adding new public interface functions to simplify user assembly code. Added methods to get connectivity of an element, coordinates of vertices, and to check if given vertices lie on the boundary.
866cea9: Updating some RW options for MOAB and enabling command-line control.
fd2859a: Remove the DA related routines and references in 2-D example.

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Make sure that all Global ids are 1-based. There is an internal call in DMMoab_SetUp to correct this to zero-based indices for suitable use in PETSc and other array related usage.