Chimie Théorique » QMX

from math import sin, cos, pi, sqrt

import numpy as np

from ase.atoms import Atoms, Atom

from ase.parallel import paropen

"""Module to read and write atoms in cif file format"""

def read_cif(fileobj, index=-1):

    if isinstance(fileobj, str):

        fileobj = open(fileobj)

    def search_key(fobj, key):

        for line in fobj:

            if key in line:

                return line

        return None

    def get_key(fobj, key, pos=1):

        line = search_key(fobj, key)

        if line:

            return float(line.split()[pos].split('(')[0])

        return None

    a = get_key(fileobj, '_cell_length_a')

    b = get_key(fileobj, '_cell_length_b')

    c = get_key(fileobj, '_cell_length_c')

    alpha =  pi * get_key(fileobj, '_cell_angle_alpha') / 180

    beta = pi * get_key(fileobj, '_cell_angle_beta') / 180

    gamma =  pi * get_key(fileobj, '_cell_angle_gamma') / 180

    va = a * np.array([1, 0, 0])

    vb = b * np.array([cos(gamma), sin(gamma), 0])

    cx = cos(beta)

    cy = (cos(alpha) - cos(beta) * cos(gamma)) / sin(gamma)

    cz = sqrt(1. - cx*cx - cy*cy)

    vc = c * np.array([cx, cy, cz])

    cell = np.array([va, vb, vc])

    atoms = Atoms(cell=cell)

    read = False

    for line in fileobj:

        if not read:

            if '_atom_site_disorder_group' in line:

                read = True

        else:

            word = line.split()

            if len(word) < 5:

                break

            symbol = word[1]

            pos = (float(word[2].split('(')[0]) * va +

                   float(word[3].split('(')[0]) * vb +

                   float(word[4].split('(')[0]) * vc   )

            atoms.append(Atom(symbol, pos))

    return atoms