Source code for

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


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

[docs]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)) yield from images[index]
[docs]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