amp_test_atoms, amp_test_traj, n_test, save_interval, timestep=timestep, convert=True, ) anl = Analyzer() r, rdf = anl.calculate_rdf(test_traj, r_max=6.0) r_amp, rdf_amp = anl.calculate_rdf(amp_test_traj, r_max=6.0) rdf_plot = system + "_" + "rdf.png" plter.plot_rdf(rdf_plot, legend, r, rdf, rdf_amp) steps, energy_exact, energy_amp = anl.calculate_pot_energy_diff( test_traj, amp_test_traj, save_interval=save_interval ) pot_plot = system + "_" + "pot.png" plter.plot_pot_energy_diff(pot_plot, legend, steps, energy_exact, energy_amp) steps, energy_exact, energy_amp = anl.calculate_energy_diff( test_traj, amp_test_traj, save_interval=save_interval ) energy_plot = system + "_" + "energy.png" plter.plot_energy_diff(energy_plot, legend, steps, energy_exact, energy_amp) steps, msd = anl.calculate_msd(test_traj, save_interval=save_interval) steps, amp_msd = anl.calculate_msd(amp_test_traj, save_interval=save_interval) msd_plot = system + "_" + "msd.png" plter.plot_msd(msd_plot, legend, steps, msd, amp_msd)