ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
z = 1.8
d = 1.10 # N2 bond length
# Molecular state parallel to the surface:
slab += Atoms(’2N’, [(x, y, z), (x + sqrt3 * d / 2, y + d / 2, z)])
# Use the EMT calculator for the forces and energies:
slab.set_calculator(EMT())
# We don’t want to worry about the Cu degrees of freedom:
mask = [atom.symbol == ’Cu’ for atom in slab]
slab.set_constraint(FixAtoms(mask=mask))
relax = QuasiNewton(slab)
relax.run(fmax=0.05)
print ’initial state:’, slab.get_potential_energy()
write(’N2.traj’, slab)
# Now the final state.
# Move the second N atom to a neighboring hollow site:
slab[-1].set_position((x + a, y, z))
relax.run()
print ’final state: ’, slab.get_potential_energy()
write(’2N.traj’, slab)
import numpy as np
from ase.io import read
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.neb import NEB
from ase.optimize import QuasiNewton
initial = read(’N2.traj’)
final = read(’2N.traj’)
configs = [initial.copy() for i in range(8)] + [final]
constraint = FixAtoms(mask=[atom.symbol != ’N’ for atom in initial])
for config in configs:
config.set_calculator(EMT())
config.set_constraint(constraint)
band = NEB(configs)
band.interpolate()
# Create a quickmin object:
relax = QuasiNewton(band)
relax.run(steps=20)
e0 = initial.get_potential_energy()
for config in configs:
d = config[-2].position - config[-1].position
print np.linalg.norm(d), config.get_potential_energy() - e0
6.2.8 Dissociation using ANEB
from ase import *
# XXX This cannot be converted to ase 3, since we lack ANEB
raise NotImplementedError
32 Chapter 6. Tutorials