IMPORTANT UPDATE! Changed how the cost function deals with the energy. It now takes ENERGY/ATOM rather that the Total Energy! This means you need to change alpha in the parameter file; see the revised way on how to calculate it or just go off of the 550 I have been using. Alpha=550 now becomes Alpha=0.44. This is based on the fact that the simulation seemed to work well with Alpha=550 for a 1250 atom model, and 550/1250=0.44. Now if we use Alpha=0.44, this will be a consistent way to calculate the cost function independent of the number of atoms in the model.
I also only write to the timing file if we are using the timing version of the code. This should speed things up a tiny bit.