Surface adsorption

In this tutorial we will adsorb a CO molecule on Au(111) surface.

>>> import numpy as np
>>> from ase.build import fcc111, molecule
>>> from batoms import Batoms
>>> atoms = fcc111("Au", size = (4, 4, 4), vacuum=0)
>>> au111 = Batoms(label = "au111", from_ase = atoms)
>>> au111.cell[2, 2] += 10
>>> co = Batoms(label = "co", from_ase = molecule("CO"))
>>> # In Edit mode, you can see the index of gold atoms.
>>> t = au111.positions[58] - co.positions[0] + np.array([0, 0, 2.5])
>>> co.translate(t)
>>> au111 = au111 + co

Save structure to file, POSCAR, xyz and so on.

>>> au111.write("POSCAR")

Save image, as show bellow:

>>> au111.get_image(viewport = [1, 0.1, 0.1])