dynsight.soap.normalize_soap¶

dynsight.soap.normalize_soap(soap)[source]¶

Returns the SOAP spectra normalized to unitary length.

Parameters:

soap (NDArray[np.float64]) – shape (n_particles, n_frames, n_comp) The SOAP spctra for the trajectory.

Returns:

np.ndarray of shape (n_particles, n_frames, n_components): The normalized SOAP spectra.

Return type:

NDArray[np.float64]

Example

import numpy as np
import MDAnalysis
from dynsight.soap import (
    saponify_trajectory,
    normalize_soap,
)

univ = MDAnalysis.Universe(path / "trajectory.xyz")
cutoff = 2.0

soap = saponify_trajectory(univ, cutoff, soap_respectpbc=False)
unitary_soap = normalize_soap(soap)