Changes for RigidBody dynamics (Somewhat extensive)
Add some lines into global.cpp to make it work with energy minimization
added routines for the sysbuilder to work with simSetup
added harmonical potential to z-constraint method
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
add index range checking into ZConstraint
working on the props code
*** empty log message ***
cleaned up simSetup
fixed some bugs, Changed entry_plug to info where appropriate
working on the system builder
fixing some compile time bugs
finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
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.
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