#3 Restart functionality

[Glen Hocky]

Tools for allowing "restart" functionality should be included. Given the nature of our current simulations, we need a way to dump all "core" common data structures (atomic positions, mask, etc) as well as a string and or array of simulation variables (e.g. temperature) to a file (or simply back to a python object where it can be "pickled"), and a way of reloading this information