structuretoolkit.analyse.dscribe.soap_descriptor_per_atom

structuretoolkit.analyse.dscribe.soap_descriptor_per_atom#

structuretoolkit.analyse.dscribe.soap_descriptor_per_atom(structure: Atoms, r_cut: float | None = None, n_max: int | None = None, l_max: int | None = None, sigma: float | None = 1.0, rbf: str = 'gto', weighting: ndarray | None = None, average: str = 'off', compression: dict | None = None, species: list | None = None, periodic: bool = True, sparse: bool = False, dtype: str = 'float64', centers: ndarray | None = None, n_jobs: int = 1, only_physical_cores: bool = False, verbose: bool = False) → ndarray[source]#

Calculates the SOAP descriptor for each atom in the given structure.

Parameters:

  • structure (ase.atoms.Atoms) – The atomic structure.

  • r_cut (float, optional) – The cutoff radius. Defaults to None.

  • n_max (int, optional) – The maximum number of radial basis functions. Defaults to None.

  • l_max (int, optional) – The maximum degree of spherical harmonics. Defaults to None.

  • sigma (float, optional) – The width parameter for the Gaussian-type orbital. Defaults to 1.0.

  • rbf (str, optional) – The radial basis function. Defaults to “gto”.

  • weighting (np.ndarray, optional) – The weighting coefficients for the radial basis functions. Defaults to None.

  • average (str, optional) – The type of averaging. Defaults to “off”.

  • compression (dict, optional) – The compression settings. Defaults to {“mode”: “off”, “species_weighting”: None}.

  • species (list, optional) – The list of chemical symbols. Defaults to None.

  • periodic (bool, optional) – Whether the system is periodic. Defaults to True.

  • sparse (bool, optional) – Whether to use sparse matrices. Defaults to False.

  • dtype (str, optional) – The data type of the output. Defaults to “float64”.

  • centers (np.ndarray, optional) – The centers for the descriptor calculation. Defaults to None.

  • n_jobs (int, optional) – The number of parallel jobs. Defaults to 1.

  • only_physical_cores (bool, optional) – Whether to use only physical cores. Defaults to False.

  • verbose (bool, optional) – Whether to print verbose output. Defaults to False.

Returns:

The SOAP descriptor for each atom.

Return type:

np.ndarray