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.

Add the 2-D FEM example poisson solver in SS.

2d7ab24: Adding the first draft of MOAB based 2-D FEM computation using both DMDA and DMMoab
2b0793a: Updating some RW options for MOAB and enabling com

Add the 2-D FEM example poisson solver in SS.

2d7ab24: Adding the first draft of MOAB based 2-D FEM computation using both DMDA and DMMoab
2b0793a: Updating some RW options for MOAB and enabling command-line control of how the mesh gets loaded from file../../dmmbutil.cxx

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A first draft version of getting hte connectivity right. It still overpredicts in the current method based on edge adjacencies. Need to refine to do a second pass over local mesh to remove duplicates

A first draft version of getting hte connectivity right. It still overpredicts in the current method based on edge adjacencies. Need to refine to do a second pass over local mesh to remove duplicates in order to get the NNZ accurately.

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Several fixes for DMMoabCreateBoxMesh. Adding a fresh implementation of DMMoabLoadFromFile which works well. Both methods need testing in parallel but verified in serial.

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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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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Misc updates for examples.

1) Use DMMoabSetLocalVertices instead of DMMoabSetRange.
2) Move the MBRange typedef inside ifdef MOAB check.

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 a bug in matrix pre-allocation with nnz routine based on connectivity and a separate bug when calling get_connectivity on a structured mesh interface.

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.

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.

Rearrange the driver example for MOAB based Brusselator solver to use DMMoabVec GetArray/RestoreArray routines to simplify the assembly process.

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

Cosmetic renaming of functions to make driver clear.

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

Modifying Brusselator solver with various options to assemble the operators via Block routines, local/ghost forms etc that give various performance options. Needs further profiling, removal of commen

Modifying Brusselator solver with various options to assemble the operators via Block routines, local/ghost forms etc that give various performance options. Needs further profiling, removal of comments, and more documentation.

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Modify example to work with new DMMoab interface.

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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Update DMMoab interface functions and add a 1-D example to test/profile the implementation. (vijaysm:dmmoab/4937358..3f1b83c/)

replace all echo in test/tutorial makefiles with printf since echo behaves differently on different systems

Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,

Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,;()]+, *@PetscNewLog($1,@'

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dmmoab: fix compile error