ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

import numpy as np
import ase.utils.geometry as geometry
import ase.io as io
ASE Manual, Release 3.6.1.2828
# Create a new atoms instance with Co at origo including all atoms on the
# surface of the unit cell
cosb3 = geometry.cut(skutterudite, origo=(0.25, 0.25, 0.25), extend=1.01)
# Define the atomic bonds to show
bondatoms = []
symbols = cosb3.get_chemical_symbols()
for i in xrange(len(cosb3)):
for j in xrange(i):
if (symbols[i] == symbols[j] == ’Co’ and
cosb3.get_distance(i, j) < 4.53):
bondatoms.append((i, j))
elif (symbols[i] == symbols[j] == ’Sb’ and
cosb3.get_distance(i, j) < 2.99):
bondatoms.append((i, j))
# Create nice-looking image using povray
io.write(’spacegroup-cosb3.pov’, cosb3,
transparent=False,
display=False,
run_povray=True,
camera_type=’perspective’,
canvas_width=320,
radii=0.4,
rotation=’90y’,
bondlinewidth=0.07,
bondatoms=bondatoms,
)
6.2. ASE 27