steps, test_traj = trjbd.integrate_atoms(
test_atoms, test_traj, n_test, save_interval, timestep=timestep, convert=True
)
amp_test_traj = "amp_test.traj"
steps, amp_test_traj = trjbd.integrate_atoms(
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)
import matplotlib.pyplot as plt
import seaborn as sns
sys.path.insert(1, "../tools")
from analysis import Analyzer
from plotting import Plotter
from training import Trainer
if __name__ == "__main__":
sns.set()
plot_dir = "plots"
plot_file = os.path.join(plot_dir, "rdf.png")
if not os.path.exists(plot_dir):
os.mkdir(plot_dir)
anl = Analyzer()
plter = Plotter()
r_cut = 6.0
r, rdf = anl.calculate_rdf("trajs/training.traj", r_max=r_cut)
rdf[np.nonzero(rdf)] /= max(rdf)
cutoff = plter.polynomial(r, r_cut, gamma=5.0)
plt.plot(r, rdf, label="Radial distribution function")
plt.plot(r, cutoff, label="Polynomial cutoff, gamma=5.0")
plt.legend()
plt.title("Copper radial distribution function")
plt.xlabel("Radial distance [Angstrom]")
plt.ylabel("Radial distribution function (normalized to 1)")
plt.savefig(plot_file)
trn.create_Gs(elements, num_radial_etas, num_angular_etas, num_zetas,
angular_type)
symm_funcs["Selected"] = trn.Gs
G2 = make_symmetry_functions(elements=elements,
type="G2",
etas=[0.05, 0.23, 1.0, 5.0],
centers=np.zeros(4))
G4 = make_symmetry_functions(
elements=elements,
type="G4",
etas=0.005 * np.ones(1),
zetas=[1.0, 4.0],
gammas=[1.0, -1.0],
)
symm_funcs["Default"] = G2 + G4
anl = Analyzer()
plter = Plotter()
r, rdf = anl.calculate_rdf(train_traj, r_max=cutoff.Rc)
for label, symm_func in symm_funcs.items():
plter.plot_symmetry_functions(
label + "_rad.png",
label + "_ang.png",
symm_func,
rij=r,
rdf=rdf,
cutoff=cutoff,
)
