dynsight.soap.timesoap¶

dynsight.soap.timesoap(soap, delay=1)[source]¶

Performs the ‘timeSOAP’ analysis on the given SOAP trajectory.

timeSOAP was developed by Cristina Caurso. See for reference the paper https://doi.org/10.1063/5.0147025.

Parameters:

soap (NDArray[np.float64]) – shape (n_particles, n_frames, n_comp) The SOAP spctra for the trajectory.
delay (int) – The delay between frames on which timeSOAP is computed. Default is 1.

Returns:

NDArray[np.float64]: Values of timesoap of each particle at each frame. Has shape (n_particles, n_frames - 1).

Return type:

NDArray[np.float64]

Example

import numpy as np
import MDAnalysis
from dynsight.soap import saponify_trajectory, timesoap

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

soap = saponify_trajectory(univ, cutoff, soap_respectpbc=False)
tsoap = timesoap(soap)