Makefile modifications to compile dmmbfield and dmmbio.

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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Fix for the NNZ pattern computation when user asks for more layers of ghosted entities. The DMMoab itself does not care about these extra level of DOFs and only needs the interface(d837989). No need

Fix for the NNZ pattern computation when user asks for more layers of ghosted entities. The DMMoab itself does not care about these extra level of DOFs and only needs the interface(d837989). No need to override the user options from command line(b49477c4).

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Making the poisson driver stable along with modifications on how the local assembly is performed.

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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Some bug fixes for the ghosted exchange of tag data during Get/Restore Array for DMMoabVec

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.

Fix a bug in nonzero pattern when bs>1. Also remove the redundant gindices since we store this data in dmmoab.

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

Fully revamping the 1-D Brusselator solver based on DMMoab new API specification. Verified in serial.

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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A verified, parallel, debug version of the poisson solver based on DMMoab API and FEM assembly. Solution is consistent and gives verifiable results in serial and parallel. Can also use LOCAL_ASSEMBLY

A verified, parallel, debug version of the poisson solver based on DMMoab API and FEM assembly. Solution is consistent and gives verifiable results in serial and parallel. Can also use LOCAL_ASSEMBLY to do two different types of vector RHS assembly.

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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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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.

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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Fixed a possible bug when restoring array.

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.

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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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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