/usr/share/python-ase/doc/gallery/o2pt100.py is in python-ase-doc 3.12.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | # creates: o2pt100.png
import numpy as np
from ase.io import write
from ase.build import fcc100, add_adsorbate
# the metal slab
atoms = fcc100('Pt', size=[4, 10, 3], vacuum=10)
transmittances = [0 for a in atoms]
bonded_atoms = []
upper_layer_idx = [a.index for a in atoms if a.tag == 1]
middle = atoms.positions[upper_layer_idx, :2].max(axis=0) / 2
# the dissociating oxygen... fake some dissociation curve
gas_dist = 1.1
max_height = 8.
min_height = 1.
max_dist = 6
# running index for the bonds
index = len(atoms)
for i, x in enumerate(np.linspace(0, 1.5, 6)):
height = (max_height - min_height) * np.exp(-2 * x) + min_height
d = np.exp(1.5 * x) / np.exp(1.5**2) * max_dist + gas_dist
pos = middle + [0, d / 2]
add_adsorbate(atoms, 'O', height=height, position=pos)
pos = middle - [0, d / 2]
add_adsorbate(atoms, 'O', height=height, position=pos)
transmittances += [x / 2] * 2
# we want bonds for the first two molecules
if i < 2:
bonded_atoms.append([len(atoms) - 1, len(atoms) - 2])
textures = ['ase3' for a in atoms]
# add some semi-transparent bath (only in x/y direction for this example)
cell = atoms.cell
idx = [a.index for a in atoms if a.symbol == 'Pt']
Nbulk = len(idx)
multiples = [0, 1, -1]
for i in multiples:
for j in multiples:
if i == j == 0:
continue
chunk = atoms[idx]
chunk.translate(i * cell[0] + j * cell[1])
atoms += chunk
transmittances += [0.8] * Nbulk
textures += ['pale'] * Nbulk
bbox = [-30, 10, 5, 25]
write('o2pt100.pov', atoms,
rotation='90z,-75x',
show_unit_cell=0,
run_povray=True,
display=False,
pause=False,
canvas_width=1024,
bondatoms=bonded_atoms,
camera_type='perspective',
transmittances=transmittances,
textures=textures,
bbox=bbox)
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