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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API change, bug fix and new test file along with output.
Fixing a nasty bug in DMMoabSetGlobalFieldVector when using MoabVec.
Slight modification of the DMMoabSetFieldNames interface.
Bug was f

API change, bug fix and new test file along with output.
Fixing a nasty bug in DMMoabSetGlobalFieldVector when using MoabVec.
Slight modification of the DMMoabSetFieldNames interface.
Bug was found using the new test file ex2.c which does the following:
- Creates a mesh in memory or optionally from a user specified input file
- Propagates tags with variable names as specified by user or assumes a single variable by default
- The variables defined on the mesh are populated with random data
- User can optionally write out the resulting mesh database for visualization/analysis.
- Test output added for future reference.

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

Update the private header for DMMoab with documentation. Remove a public API function that was never used.

Changed the faulty interface that was reverted in previous commits for DMMoabSetFieldName.

Documentation and other updates for field handling in DMMoab.
- Adding detailed documentation for the DMMoabField* API functions.
- Renamed DMMoabSetFields to DMMoabSetFieldNames to be consistent.

Documentation and other updates for field handling in DMMoab.
- Adding detailed documentation for the DMMoabField* API functions.
- Renamed DMMoabSetFields to DMMoabSetFieldNames to be consistent.
- Added DMMoabGetFieldName.

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Making sure that the interface is const correct when dealing with MOAB objects on the getter methods.

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

Adding a public API method DMMoabGetOffset to get the local offset when dealing with global spaces for Vec/Mat.

Adding a new API function to set a field name. This is more of a utility function that follows the DMDA design.

Adding a variable to store ghosted elements. Change the public API to retrieve local and ghosted vertices/element sizes.

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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Adding the first draft capability to allow both MOAB and native Vec with DMMoab. Also setting the necessary Mapping data so that SetLocal and SetBlockedLocal can be used.

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.

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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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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Private interface changes in DMMoab.

d64c012: Adding storage for holding the boundary vertices and faces for easier traversal during FEM assembly calculations. Could move it somewhere else if need b

Private interface changes in DMMoab.

d64c012: Adding storage for holding the boundary vertices and faces for easier traversal during FEM assembly calculations. Could move it somewhere else if need be.
d7dd518: Adding more public interface methods to Output the mesh+solution fields, to set a Vec for a field handled by DMMoab and accessors for getting the boundary entities.
bdfc3ff: Fix a bug in checking whether a tag is valid.

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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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Add more verbose error checkers that gets the last error message from MOAB interface and prints along with user message.

Adding a first draft of utility functions for creating a structured mesh in memory using MOAB that can be used in applications directly in a dimension-independent fashion.

Add MOAB specific Vector array get/restore methods for both write and read-only operations to ease the use of MoabVec in FEM based computations. The arrays typically have a ghosted representation if

Add MOAB specific Vector array get/restore methods for both write and read-only operations to ease the use of MoabVec in FEM based computations. The arrays typically have a ghosted representation if the MOAB mesh is ghosted itself, else represents a truly distributed array.

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