Chimie Théorique » QMX

from math import pi, cos, sin, sqrt, acos

import numpy as np

from ase.data import chemical_symbols

from ase.atoms import Atoms

from ase.parallel import paropen

iwm_symbols = {'1' : 'C',

               '2' : 'Au',

               '5' : 'Ag'}

def read_iwm(fileobj, index=-1):

    if isinstance(fileobj, str):

        fileobj = open(fileobj)

    lines = fileobj.readlines()

    L1 = lines[1].split()

    if len(L1) == 1:

        del lines[:3]

        natoms = int(L1[0])

    else:

        natoms = len(lines)

    images = []

    positions = []

    symbols = []

    for line in lines[:natoms]:

        symbol, mass, x, y, z = line.split()[:5]

        if symbol in iwm_symbols:

            symbols.append(iwm_symbols[symbol])

        else:

            symbols.append(chemical_symbols[int(symbol)])

        positions.append([float(x), float(y), float(z)])

    del(lines[natoms:3 * natoms + 3])

    cell = []

    for line in lines[natoms:natoms+3]:

        x, y, z = line.split()[:3]

        cell.append(np.array([float(x), float(y), float(z)]))

    images.append(Atoms(symbols=symbols, positions=positions, cell=cell))

    return images[index]