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import pytest
from math import sqrt
from ase import Atoms, Atom, io
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.neb import NEB
from ase.optimize import BFGS
# XXXXXXXX this is mostly a copy of COCu111 !!! Grrrr!
@pytest.mark.slow
def test_COCu111_2():
logfile = "-" # supresses
Optimizer = BFGS
# Distance between Cu atoms on a (111) surface:
a = 3.6
d = a / sqrt(2)
fcc111 = Atoms(symbols='Cu',
cell=[(d, 0, 0),
(d / 2, d * sqrt(3) / 2, 0),
(d / 2, d * sqrt(3) / 6, -a / sqrt(3))],
pbc=True)
initial = fcc111 * (2, 2, 4)
initial.set_cell([2 * d, d * sqrt(3), 1])
initial.set_pbc((1, 1, 0))
initial.calc = EMT()
Z = initial.get_positions()[:, 2]
indices = [i for i, z in enumerate(Z) if z < Z.mean()]
constraint = FixAtoms(indices=indices)
initial.set_constraint(constraint)
dyn = Optimizer(initial, logfile=logfile)
dyn.run(fmax=0.05)
# relax initial image
b = 1.2
h = 1.5
initial += Atom('C', (d / 2, -b / 2, h))
initial += Atom('O', (d / 2, +b / 2, h))
dyn = Optimizer(initial, logfile=logfile)
dyn.run(fmax=0.05)
# relax final image
final = initial.copy()
final.calc = EMT()
final.set_constraint(constraint)
final[-2].position = final[-1].position
final[-1].x = d
final[-1].y = d / sqrt(3)
dyn = Optimizer(final, logfile=logfile)
dyn.run(fmax=0.1)
# view(final)
# Create neb with 2 intermediate steps
neb = NEB([initial, initial.copy(), initial.copy(), final],
allow_shared_calculator=True)
# refine() removed, not implemented any more
neb.interpolate()
# Optimize neb using a single calculator
neb.set_calculators(EMT())
# refine() removed, not implemented any more
dyn = Optimizer(neb, maxstep=0.04, trajectory='mep_2coarse.traj',
logfile=logfile)
dyn.run(fmax=0.1)
# Optimize neb using a many calculators
neb = NEB([initial, initial.copy(), initial.copy(), final])
neb.interpolate()
neb.set_calculators([EMT() for _ in range(neb.nimages)])
dyn = Optimizer(neb, maxstep=0.04, trajectory='mep_2coarse.traj',
logfile=logfile)
dyn.run(fmax=0.1)
# read from the trajectory
neb = NEB(io.read('mep_2coarse.traj', index='-4:'),
allow_shared_calculator=True)
# refine() removed, not implemented any more
neb.set_calculators(EMT())
# Optimize refined neb using a single calculator
dyn = Optimizer(neb, maxstep=0.04, trajectory='mep_2fine.traj',
logfile=logfile)
dyn.run(fmax=0.1)
assert len(neb.images) == 4
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