from ase import Atoms
from ase.constraints import FixAtoms
from ase.io import Trajectory
from ase.optimize import QuasiNewton
from ase.calculators.morse import MorsePotential

atoms = Atoms('H7',
              positions=[(0, 0, 0),
                         (1, 0, 0),
                         (0, 1, 0),
                         (1, 1, 0),
                         (0, 2, 0),
                         (1, 2, 0),
                         (0.5, 0.5, 1)],
              constraint=[FixAtoms(range(6))],
              calculator=MorsePotential())

traj = Trajectory('H.traj', 'w', atoms)
dyn = QuasiNewton(atoms, maxstep=0.2)
dyn.attach(traj.write)
dyn.run(fmax=0.01, steps=100)

print(atoms)
del atoms[-1]
print(atoms)
del atoms[5]
print(atoms)
assert len(atoms.constraints[0].index) == 5