fixed the makefile
fixing some compile time bugs
I have implemeted Molecules everywhere I could remember to. will now attempt to compile.
finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
bug fixes many bug fixes
still working on the SimSetup routine. also fixed some things in Exclude.hpp
I'm overhauling the molecule class to contain it's own bonds, bends, and torsions. may god have mercy on my soul.
This commit was generated by cvs2svn to compensate for changes in r377, which included commits to RCS files with non-trunk default branches.
New OOPSE Tree
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