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)
