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# creates: o2pt100.png
import numpy as np
from ase.build import add_adsorbate, fcc100
from ase.io import write
# 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]
renderer = write('o2pt100.pov', atoms,
rotation='90z,-75x',
bbox=bbox,
show_unit_cell=0,
povray_settings=dict(
pause=False,
canvas_width=1024,
bondatoms=bonded_atoms,
camera_type='perspective',
transmittances=transmittances,
textures=textures))
renderer.render()
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