Renaming one of the cached variables for local ID storage and making it field dependent instead of just point dependent.

A very important fix for the ghosted vector updates.
The parallel bugs in incorrect residual evaluations in ex2.cxx were two-fold.

1) The ghost updates were incorrect.
2) The VecScatter context was

A very important fix for the ghosted vector updates.
The parallel bugs in incorrect residual evaluations in ex2.cxx were two-fold.

1) The ghost updates were incorrect.
2) The VecScatter context was wrongly formed. Perhaps a VecCopy might suffice for local Global-Local transfers. Optimize later.
3) The BC evaluation had a bug due to the way we were accessing the bit vector with EntityHandle static casts. This could be
a problem in evaluating field DOF data also. Currently not an issue but need to check if this can be optimized.
4) ex2.cxx runs correctly in serial and parallel. Preliminary profiling against ts/examples/tutorials/ex25.cxx shows that the FEM version against FD version is about 2-3 times slower in TSFunctionEval. This needs to be profiled further and corrected.
5) Now support both native PETSc and native MOAB-tag based Vec depending on whether mesh entities or contiguous.

Parallel bugs fixed. Optimizations upcoming to improve speedup.

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Fixing a bug in DMMoabSetLocalVertices and rearranging the DMSetUp method to allow for user setting the range of vertices separately where DM is explicitly defined on.

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.

Cleaning up DMMoab and splitting the monolithic implementation into smaller files for organization based on field-management and io. Adding several variables to core DMMoab data structure to cache th

Cleaning up DMMoab and splitting the monolithic implementation into smaller files for organization based on field-management and io. Adding several variables to core DMMoab data structure to cache the necessary IDs for FEM-type assembly and traversals. Removed all references to Section since profiling indicated that this was slow overall.

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A global field vector can optionally be passed to DM where the local field data are ripped out and serialized to file.

Fixing a MOAB output bug for parllel write.

Adding several important public API functions to DMMoab and few fixes.

611d6c0: Removing the storage of boundary nodes, vertices and faces. Leaning up DMMoab. Only store markers instead.
f68869f: Fi

Adding several important public API functions to DMMoab and few fixes.

611d6c0: Removing the storage of boundary nodes, vertices and faces. Leaning up DMMoab. Only store markers instead.
f68869f: Fix some segfaults due to incorrect memory allocation for boundary data.

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Initial modifications to allow vertex based traversals and miscellaneous bug-fixes.

1) Adding API functions for getting vertex-connectivity for FD type calculations and DOF-maps etc.
2) Fix bugs in

Initial modifications to allow vertex based traversals and miscellaneous bug-fixes.

1) Adding API functions for getting vertex-connectivity for FD type calculations and DOF-maps etc.
2) Fix bugs in memory allocations in most of the Field/Block/Local DOF calculation routines.
3) Add PetscBool arrays to store whether the entities are on the boundary. This makes the query for boundary vertices and elements a simple look-up during FEM/FD assembly.
4) Introducing DMMoabGetAllVertices to access both local+ghost vertices. This might not be entirely necessary for FD and can remove it in the future.

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Adding a GetDimension API method.

Make sure the nfields is initialized during creation. Added some error checks.

Adding several important public API functions to DMMoab and few fixes.

a3b7357: Add interface functions to get the global, local and ghosted vertex distributions of the DM.
7478aaf:
1) DMMoabSetGl

Adding several important public API functions to DMMoab and few fixes.

a3b7357: Add interface functions to get the global, local and ghosted vertex distributions of the DM.
7478aaf:
1) DMMoabSetGlobalFieldVector - Use when the number of fields > 1 and want to assign a single global solution vector to be split in terms of tag arrays.
2) DMMoabGetDofs - Local/Blocked variants to get the individual field-independent vertex GID numbering. This is useful for traversals based on nodes directly. Used in FD-type computations.
3) Some minor bug fixes.

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Adding an extra API functionality to use the local DOF to assemble vectors and matrices.

- This should generally be faster than using VecSetValues. Use DMMoabGetLocalFieldDofs for these operations.

Adding an extra API functionality to use the local DOF to assemble vectors and matrices.

- This should generally be faster than using VecSetValues. Use DMMoabGetLocalFieldDofs for these operations.
- Should work with MatSetValuesLocal, VecSetValuesLocal also (untested).

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Add boundary element storage for DM.

f1bd10d: Use skinner and filter to get the necessary data for boundary entities since the previous method of find_skin alone fails in parallel due to internal fa

Add boundary element storage for DM.

f1bd10d: Use skinner and filter to get the necessary data for boundary entities since the previous method of find_skin alone fails in parallel due to internal faces also being returned.
a1c8a3b: Adding a public interface to DMMoab to query if an entity lies on the boundary of the geometric domain. Essential during discrete physics assembly.

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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.

Bug fixes for deciphering leading dimension/DMCreateLocalVector_Moab and data output feature additions.

9cb894f: Adding some options for writing MOAB output files.
1e30170: Fixed a bug with leading

Bug fixes for deciphering leading dimension/DMCreateLocalVector_Moab and data output feature additions.

9cb894f: Adding some options for writing MOAB output files.
1e30170: Fixed a bug with leading dimension specification. MOAB->set_dimension should not be used. Miscellaneous fixes for DOF of fields: making global DOF index list as part of DM private data.
70830f3: Remove redundant use of gsindices and reuse global DOF list from DM. Fixed a bug in DMCreateLocalVector_Moab.

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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.

Several interface level changes to DMMoab implementation.

1) Compute the skin and store entities in DMMoab
2) Use PetscSection to propagate the DOF indices for various fields transparently through D

Several interface level changes to DMMoab implementation.

1) Compute the skin and store entities in DMMoab
2) Use PetscSection to propagate the DOF indices for various fields transparently through DM interface
3) Use filesets to perform local computations instead of always on the root set
4) Changing interface implementation of DMMoabGetLocalElements, DMMoabGetLocalVertices, DMMoabSetLocalElements
5) Adding interface implementation for DMMoabSetFields, DMMoabGetFieldDofs, DMMoabOutput, DMMoabSetFieldVector, DMMoabGetBoundaryEntities
6) Need to add better documentation for public interface functions

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Squashing multiple commits related to simplification of public interfaces and internal bug-fixes.

1b14864: Adding new public interface functions for DMMoab. Fixed a compiler error in MBERRVM. Interf

Squashing multiple commits related to simplification of public interfaces and internal bug-fixes.

1b14864: Adding new public interface functions for DMMoab. Fixed a compiler error in MBERRVM. Interface now supports the ability to create DM from a box-mesh in memory or load from file. Also, preliminary field manipulation interfaces in place.
994bad9: Adding variables to store Field data to make DMMoab little more whole.
d0a4170: Use a fileset to categorize DM entities. Useful when mutiple DMs are intiialized.
08af2fa: Renaming Set/Get Range routines to be more descriptive: Get/Set vertices. Also adding a getter for local elements.

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Fix additional bugs related to local to global ID tag. This argument can perhaps be removed since GLOBAL_ID_TAG_NAME handle can be obtained universally.

Fix a bug in DMCreateMOAB where the internal DMMoab object was not getting the right instances of Interface and PComm if user supplied NULL args.

Remove loops to get global_id and instead just use a single call with Range

Add important ltog and gtol routines apart from documentation and cleanup of code.

Several essential feature additions and internal modifications for DMMoab.

1) Petscify the DMMoab implementation and separate out the Mat and Vec handling parts to separate files.
2) Private data st

Several essential feature additions and internal modifications for DMMoab.

1) Petscify the DMMoab implementation and separate out the Mat and Vec handling parts to separate files.
2) Private data structure definitions moved to petsc-private.
3) Other feature additions include clean ways to perform local-global and global-local scatters.
4) Now there is a separate SetUp routine that handles consistency checks and initialization all necessary data for DMMoab.
5) The Matrix creation from DMMoab can handle AIJ and BAIJ type matrix creations based on how the user defined a tag. This assumes that
the primary solution is defined as a single tag in MOAB and hence block size is set in DMMoab globally. This should change in order
to allow more flexibility to create block matrices for single solution fields or combinations of them. Similar changes for Vec can
be provided based on tag structure. Perhaps taking in a MoabVec input can resolve this to maintain consistency.

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