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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
def test_example():
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())
with Trajectory('H.traj', 'w', atoms) as traj:
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
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