little bug fixes here and there.
Fixes to fileio for MPI
bug fixes many bug fixes
Making DumpWriter less dependent on sequence of atoms on the other processors. Node 0 now fires potatoes at other processors to get them to send french fries back.
the skeleton for making the molecules is in place. ForceField needs to be updated next.
fixed a couple of the "static" bugs in Atom and Exclude
still working on the SimSetup routine. also fixed some things in Exclude.hpp
Added Atom.cpp and Exclude.cpp
Fixes in Atom and Exclude list
Make Atom.cpp able to add and delete ranges of atoms
added an Exclude class with static arrays similar to the Atom class
I'm overhauling the molecule class to contain it's own bonds, bends, and torsions. may god have mercy on my soul.
Finished globalIndex.
MPI stuff for passing out molecules
working on load balancing
Fixes for Parallel thermalization
fixed an mpi include bug in THermo.cpp
Fixed bugs with calculation of potential energy and temperature.
*** empty log message ***
electrostatic changes for dipole / RF separation
little bug fixes here and there
fixed bug where short range interactions were not being calculated. removed some debug print statements
various write statements for debugging
Fixed F_MACH_DEP bug
Makefile fixes, directory re-org, autoconf fixes
Makefile fixes for depends
This commit was generated by cvs2svn to compensate for changes in r377, which included commits to RCS files with non-trunk default branches.