Chimie Théorique » QMX

from math import sqrt

from ase import Atoms, Atom

from ase.constraints import FixAtoms

from ase.calculators.emt import EMT

from ase.optimize import QuasiNewton

from ase.io import read

from ase.vibrations import Vibrations

# Distance between Cu atoms on a (100) surface:

d = 3.6 / sqrt(2)

a = Atoms('Cu',

          positions=[(0, 0, 0)],

          cell=(d, d, 1.0),

          pbc=(True, True, False))

a *= (2, 2, 1)  # 2x2 (100) surface-cell

# Approximate height of Ag atom on Cu(100) surfece:

h0 = 2.0

a += Atom('Ag', (d / 2, d / 2, h0))

if 0:

    view(a)

constraint = FixAtoms(range(len(a) - 1))

a.set_calculator(EMT())

a.set_constraint(constraint)

dyn1 = QuasiNewton(a, trajectory='AgCu1.traj', logfile='AgCu1.log')

dyn1.run(fmax=0.1)

a = read('AgCu1.traj')

a.set_calculator(EMT())

print a.constraints

dyn2 = QuasiNewton(a, trajectory='AgCu2.traj', logfile='AgCu2.log')

dyn2.replay_trajectory('AgCu1.traj')

dyn2.run(fmax=0.01)