IMPORTANT UPDATE:

--- Fixed critical error incured in last version, where forces were not being applied because Nbatches was not defined

--- Fixed frequency scaling system, so CMD is now fully implemented
	(MassScaleFactor is now calculated for the mass of the normal modes. This is factored in by the thermostats to calculate kinetic energy of the jth normal mode)

--- Fixed the way initial velocities are generated for the beads to correctly sample the canonical distribution for a free ring