Chimie Théorique » QMX

"""

IO support for the Gaussian cube format.

See the format specifications on:

http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/

"""

import numpy as np

from ase.atoms import Atoms

from ase.units import Bohr

from ase.parallel import paropen

def write_cube(fileobj, atoms, data=None):

    if isinstance(fileobj, str):

        fileobj = paropen(fileobj, 'w')

    if isinstance(atoms, list):

        if len(atoms) > 1:

            raise ValueError('Can only write one configuration '

                             'to a cube file!')

        atoms = atoms[0]

    if data is None:

        data = np.ones((2, 2, 2))

    data = np.asarray(data)

    if data.dtype == complex:

        data = np.abs(data)

    fileobj.write('cube file from ase\n')

    fileobj.write('OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n')

    cell = atoms.get_cell()

    shape = np.array(data.shape)

    corner = np.zeros(3)

    for i in range(3):

        if shape[i] % 2 == 1:

            shape[i] += 1

            corner += cell[i] / shape[i] / Bohr

    fileobj.write('%5d%12.6f%12.6f%12.6f\n' % (len(atoms), corner[0],

                                               corner[1], corner[2]))

    for i in range(3):

        n = data.shape[i]

        d = cell[i] / shape[i] / Bohr

        fileobj.write('%5d%12.6f%12.6f%12.6f\n' % (n, d[0], d[1], d[2]))

    positions = atoms.get_positions() / Bohr

    numbers = atoms.get_atomic_numbers()

    for Z, (x, y, z) in zip(numbers, positions):

        fileobj.write('%5d%12.6f%12.6f%12.6f%12.6f\n' % (Z, 0.0, x, y, z))

    data.tofile(fileobj, sep='\n', format='%e')

def read_cube(fileobj, index=-1, read_data=False):

    if isinstance(fileobj, str):

        fileobj = open(fileobj)

    readline = fileobj.readline

    readline()

    axes = ['XYZ'.index(s[0]) for s in readline().split()[2::3]]

    if axes == []:

        axes = [0, 1, 2]

    line = readline().split()

    natoms = int(line[0])

    corner = [Bohr * float(x) for x in line[1:]]

    cell = np.empty((3, 3))

    shape = []

    for i in range(3):

        n, x, y, z = [float(s) for s in readline().split()]

        shape.append(n)

        if n % 2 == 1:

            n += 1

        cell[i] = n * Bohr * np.array([x, y, z])

    numbers = np.empty(natoms, int)

    positions = np.empty((natoms, 3))

    for i in range(natoms):

        line = readline().split()

        numbers[i] = int(line[0])

        positions[i] = [float(s) for s in line[2:]]

    positions *= Bohr

    atoms = Atoms(numbers=numbers, positions=positions, cell=cell)

    if read_data:

        data = np.array([float(s)

                         for s in fileobj.read().split()]).reshape(shape)

        if axes != [0, 1, 2]:

            data = data.transpose(axes).copy()

        return data, atoms

    return atoms

def read_cube_data(fileobj):

    return read_cube(fileobj, read_data=True)