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import pytest
from ase import Atoms
from ase.calculators.lj import LennardJones
from ase.mep import NEB, NEBTools, idpp_interpolate
from ase.optimize import BFGS, FIRE
@pytest.mark.optimize()
@pytest.mark.slow()
def test_neb_tr(testdir):
nimages = 3
fmax = 0.01
for remove_rotation_and_translation in [True, False]:
# Define coordinates for initial and final states
initial = Atoms('O4',
[(1.94366484, 2.24788196, 2.32204726),
(3.05353823, 2.08091038, 2.30712548),
(2.63770601, 3.05694348, 2.67368242),
(2.50579418, 2.12540646, 3.28585811)])
final = Atoms('O4',
[(1.95501370, 2.22270649, 2.33191017),
(3.07439495, 2.13662682, 2.31948449),
(2.44730550, 1.26930465, 2.65964947),
(2.52788189, 2.18990240, 3.29728667)])
final.set_cell((5, 5, 5))
initial.set_cell((5, 5, 5))
final.calc = LennardJones()
initial.calc = LennardJones()
images = [initial]
# Set calculator
for _ in range(nimages):
image = initial.copy()
image.calc = LennardJones()
images.append(image)
images.append(final)
# Define the NEB and make a linear interpolation
# with removing translational
# and rotational degrees of freedom
neb = NEB(
images,
remove_rotation_and_translation=remove_rotation_and_translation)
neb.interpolate()
# Test used these old defaults which are not optimial, but work
# in this particular system
idpp_interpolate(neb, fmax=0.1, optimizer=BFGS)
qn = FIRE(neb, dt=0.005, maxstep=0.05, dtmax=0.1)
qn.run(steps=20)
# Switch to CI-NEB, still removing the external degrees of freedom
# Also specify the linearly varying spring constants
neb = NEB(
images, climb=True,
remove_rotation_and_translation=remove_rotation_and_translation)
qn = FIRE(neb, dt=0.005, maxstep=0.05, dtmax=0.1)
qn.run(fmax=fmax)
images = neb.images
nebtools = NEBTools(images)
Ef_neb, _dE_neb = nebtools.get_barrier(fit=False)
nsteps_neb = qn.nsteps
if remove_rotation_and_translation:
Ef_neb_0 = Ef_neb
nsteps_neb_0 = nsteps_neb
assert abs(Ef_neb - Ef_neb_0) < 1e-2
assert nsteps_neb_0 < nsteps_neb * 0.7
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