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import numpy as np
from ase import Atoms, io
from ase.calculators.lj import LennardJones
from ase.optimize.basin import BasinHopping
from ase.io import read
from ase.units import kB
# Global minima from
# Wales and Doye, J. Phys. Chem. A, vol 101 (1997) 5111-5116
E_global = {
4: -6.000000,
5: -9.103852,
6: -12.712062,
7: -16.505384}
N = 7
R = N**(1. / 3.)
np.random.seed(42)
pos = np.random.uniform(-R, R, (N, 3))
s = Atoms('He' + str(N),
positions=pos)
s.set_calculator(LennardJones())
original_positions = 1. * s.get_positions()
ftraj = 'lowest.traj'
for GlobalOptimizer in [BasinHopping(s,
temperature=100 * kB,
dr=0.5,
trajectory=ftraj,
optimizer_logfile=None)]:
if isinstance(GlobalOptimizer, BasinHopping):
GlobalOptimizer.run(10)
Emin, smin = GlobalOptimizer.get_minimum()
else:
GlobalOptimizer(totalsteps=10)
Emin = s.get_potential_energy()
smin = s
print("N=", N, 'minimal energy found', Emin,
' global minimum:', E_global[N])
# recalc energy
smin.set_calculator(LennardJones())
E = smin.get_potential_energy()
assert abs(E - Emin) < 1e-15
smim = read(ftraj)
E = smin.get_potential_energy()
assert abs(E - Emin) < 1e-15
# check that only minima were written
last_energy = None
for im in io.read(ftraj + '@:'):
energy = im.get_potential_energy()
if last_energy is not None:
assert energy < last_energy
last_energy = energy
# reset positions
s.set_positions(original_positions)
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