1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
"""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))
yield from images[index]
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
|
