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
|
from ase import Atoms
from ase.build import add_adsorbate, fcc111
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
h = 1.85
d = 1.10
slab = fcc111('Cu', size=(4, 4, 2), vacuum=10.0)
slab.calc = EMT()
e_slab = slab.get_potential_energy()
molecule = Atoms('2N', positions=[(0., 0., 0.), (0., 0., d)])
molecule.calc = EMT()
e_N2 = molecule.get_potential_energy()
add_adsorbate(slab, molecule, h, 'ontop')
constraint = FixAtoms(mask=[a.symbol != 'N' for a in slab])
slab.set_constraint(constraint)
dyn = QuasiNewton(slab, trajectory='N2Cu.traj')
dyn.run(fmax=0.05)
print('Adsorption energy:', e_slab + e_N2 - slab.get_potential_energy())
|
