# creates: C2H4.png
from ase.build.molecule import molecule
from ase.io import write
from ase.io.pov import get_bondpairs, set_high_bondorder_pairs
C2H4 = molecule('C2H4')
r = [{'C': 0.4, 'H': 0.2}[at.symbol] for at in C2H4]
bondpairs = get_bondpairs(C2H4, radius=1.1)
high_bondorder_pairs = {}
high_bondorder_pairs[(0, 1)] = (
(0, 0, 0), 2, (0.17, 0.17, 0)
) #This defines offset, bond order, and bond_offset of the bond between 0 and 1
bondpairs = set_high_bondorder_pairs(bondpairs, high_bondorder_pairs)
write('C2H4.pov',
C2H4,
format='pov',
run_povray=True,
canvas_width=200,
radii=r,
bondatoms=bondpairs,
rotation="90y")
from ase.build.molecule import molecule
from ase.io import write
import numpy as np
benzene = molecule('C6H6')
# Instead of using default value for radius of each atom, which is covalent radius, here we manually set radius for each atom.
# Default values come from ase.data import covalent_radii
r_C = 0.4
r_H = 0.2
r = np.zeros([benzene.get_number_of_atoms()])
for i, at in enumerate(benzene):
if at.symbol == 'C':
r[i] = r_C
else:
r[i] = r_H
# Determine bonds between atoms. get_bondpairs will search all pairs with distance smaller than radius * sum of covalent bonds of the pair.
from ase.io.pov import get_bondpairs
bond_pairs = get_bondpairs(benzene, radius=1.1)
# manually set color for each atom. Default colors are good, but sometime, we need to set our own colors.
# Colors can be defined using RGB format, and they are saved in a tuple or a list
colors = []
for i, at in enumerate(benzene):
if at.symbol == 'C':
# Set color for C: from black to gray then to white
colors.append((0. + i * 1 / 6., 0. + i * 1 / 6., 0. + i * 1 / 6.))