Source code for aim2dat.strct.ext_analysis.prdf

"""Calculate partial radial distribution function."""

# Standard library imports
from typing import Tuple

# Internal library imports
from aim2dat.strct.strct import Structure
from aim2dat.strct.ext_analysis.decorator import external_analysis_method
from aim2dat.strct.strct_prdf import _calculate_prdf



[docs]
@external_analysis_method
def calculate_prdf(
    structure: Structure,
    r_max: float = 20.0,
    delta_bin: float = 0.005,
    distinguish_kinds: bool = False,
) -> Tuple[dict, dict]:
    """
    Calculate the partial radial distribution function. The calculation is based on:
    :doi:`10.1103/PhysRevB.89.205118`.

    Parameters
    ----------
    structure : aim2dat.strct.Structure
        Structure object.
    r_max : float (optional)
        Cut-off value for the maximum distance between two atoms in angstrom.
    delta_bin : float (optional)
        Bin size to descritize the function in angstrom.
    distinguish_kinds: bool (optional)
        Whether different kinds should be distinguished e.g. Ni0 and Ni1 would be considered as
        different elements if ``True``.

    Returns
    -------
    element_prdf : dict
        Dictionary containing all partial radial distribution functions of the structure
        summed over all atoms of the same element.
    atomic_prdf : dict
        Dictionary containing all individual partial radial distribution functions for each
        atomic site.
    """
    bins, element_prdf, atomic_prdf = _calculate_prdf(
        structure, r_max, delta_bin, distinguish_kinds, "prdf"
    )
    for el_pair, prdf in element_prdf.items():
        element_prdf[el_pair] = prdf.tolist()
    for idx, prdfs in enumerate(atomic_prdf):
        for el_pair, prdf in prdfs.items():
            atomic_prdf[idx][el_pair] = prdf.tolist()
    return None, (element_prdf, atomic_prdf)