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)