dynsight.soap.fill_soap_vector_from_dscribe

dynsight.soap.fill_soap_vector_from_dscribe(soapfromdscribe, lmax=8, nmax=8)

Return the SOAP power spectrum from dscribe results.

• Author: Matteo Becchi

Parameters:

• soapfromdscribe (NDArray[np.float64]) – The result of the SOAP calculation from the dscribe utility.

• lmax (int) – The l_max specified in the calculation.

• nmax (int) – The n_max specified in the calculation.

Returns:

The full SOAP spectrum, with the symmetric part explicitly stored.

Return type:

NDArray[np.float64]

Example

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

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

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

full_soap = fill_soap_vector_from_dscribe(soap)