index | modules | gitlab

# Source code for ase.io.xyz

    """Reference implementation of reader and writer for standard XYZ files.

    See https://en.wikipedia.org/wiki/XYZ_file_format

    Note that the .xyz files are handled by the extxyz module by default.
    """
    from ase.atoms import Atoms

    def read_xyz(fileobj, index):
        # This function reads first all atoms and then yields based on the index.
        # Perfomance could be improved, but this serves as a simple reference.
        # It'd require more code to estimate the total number of images
        # without reading through the whole file (note: the number of atoms
        # can differ for every image).
        lines = fileobj.readlines()
        images = []
        while len(lines) > 0:
            symbols = []
            positions = []
            natoms = int(lines.pop(0))
            lines.pop(0)  # Comment line; ignored
            for _ in range(natoms):
                line = lines.pop(0)
                symbol, x, y, z = line.split()[:4]
                symbol = symbol.lower().capitalize()
                symbols.append(symbol)
                positions.append([float(x), float(y), float(z)])
            images.append(Atoms(symbols=symbols, positions=positions))
        for atoms in images[index]:
            yield atoms

    def write_xyz(fileobj, images, comment='', fmt='%22.15f'):
        comment = comment.rstrip()
        if '\n' in comment:
            raise ValueError('Comment line should not have line breaks.')
        for atoms in images:
            natoms = len(atoms)
            fileobj.write('%d\n%s\n' % (natoms, comment))
            for s, (x, y, z) in zip(atoms.symbols, atoms.positions):
                fileobj.write('%-2s %s %s %s\n' % (s, fmt % x, fmt % y, fmt % z))

    # Compatibility with older releases
    simple_read_xyz = read_xyz
    simple_write_xyz = write_xyz