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import numpy as np
from ase import Atoms
from ase.calculators.acn import (ACN, m_me, r_cn, r_mec,
sigma_me, sigma_c, sigma_n,
epsilon_me, epsilon_c, epsilon_n)
from ase.calculators.qmmm import SimpleQMMM, EIQMMM, LJInteractionsGeneral
from ase.md.verlet import VelocityVerlet
from ase.constraints import FixLinearTriatomic
import ase.units as units
def test_rattle_linear():
"""Test RATTLE and QM/MM for rigid linear acetonitrile."""
sigma = np.array([sigma_me, sigma_c, sigma_n])
epsilon = np.array([epsilon_me, epsilon_c, epsilon_n])
i = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3)
for calc in [ACN(),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()),
EIQMMM([0, 1, 2], ACN(), ACN(), i)]:
dimer = Atoms('CCNCCN',
[(-r_mec, 0, 0),
(0, 0, 0),
(r_cn, 0, 0),
(r_mec, 3.7, 0),
(0, 3.7, 0),
(-r_cn, 3.7, 0)])
masses = dimer.get_masses()
masses[::3] = m_me
dimer.set_masses(masses)
fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)])
dimer.set_constraint(fixd)
dimer.calc = calc
d1 = dimer[:3].get_all_distances()
d2 = dimer[3:].get_all_distances()
e = dimer.get_potential_energy()
with VelocityVerlet(dimer, 2.0 * units.fs,
trajectory=calc.name + '.traj',
logfile=calc.name + '.log',
loginterval=20) as md:
md.run(100)
de = dimer.get_potential_energy() - e
assert np.all(abs(dimer[:3].get_all_distances()-d1) < 1e-10)
assert np.all(abs(dimer[3:].get_all_distances()-d2) < 1e-10)
assert abs(de - -0.005) < 0.001
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