adrizhong/dF-protocol-optimization: New release

iPython notebooks for dF protocol optimization

dF-protocol-optimization.ipynb is the main notebook. For the worm-like chain, generate-init-conditions-WLC.ipynb is needed to generate initial condition files. We have included two of these init condition arrays for n_beads = 15, k = 6, sigma_LJ = 4, epsilon_LJ = 8, k_ext = 100; and lambda_i = sig_LJ(2**(1./6)), lambda_f = 0.9n_beads.