Updated depends
Added OpenSpeedShop ignores
Implemented SparseMatrix with STL containers
Clean up
Clean up and use STL containers
Removed no longer used code
Use STL containers
Cleaned up warnings
Switch to STL containers
Clean up
Clean up warnings
Clean up
Clean up and removed density calculations that do not help core purpose.
Clean up
Clean up and removed no longer used code
Use STL containers, clean up, and remove code no longer used
Moved more global variables to arguments, clean up, use STL containers
Rmeoved no longer used code, use STL containers, clean up, moved more global variables to arguments
Logic simplification
Moved some globals to args, use STL containers