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from math import radians, sin, cos
import pytest
from ase import Atoms
from ase.neb import NEB
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton, BFGS
# http://jcp.aip.org/resource/1/jcpsa6/v97/i10/p7507_s1
doo = 2.74
doht = 0.957
doh = 0.977
angle = radians(104.5)
@pytest.fixture
def initial():
return Atoms('HOHOH',
positions=[(-sin(angle) * doht, 0., cos(angle) * doht),
(0., 0., 0.),
(0., 0., doh),
(0., 0., doo),
(sin(angle) * doht, 0., doo - cos(angle) * doht)])
@pytest.fixture
def final(initial):
atoms = initial.copy()
atoms.positions[2, 2] = doo - doh
return atoms
def test_emt_h3o2m(initial, final):
# Make band:
images = [initial.copy()]
for i in range(3):
images.append(initial.copy())
images.append(final.copy())
neb = NEB(images, climb=True)
# Set constraints and calculator:
constraint = FixAtoms(indices=[1, 3]) # fix OO
for image in images:
image.calc = EMT()
image.set_constraint(constraint)
for image in images: # O-H(shared) distance
print(image.get_distance(1, 2), image.get_potential_energy())
# Relax initial and final states:
# One would have to optimize more tightly in order to get
# symmetric anion from both images[0] and [1], but
# if one optimizes tightly one gets rotated(H2O) ... OH- instead
dyn1 = QuasiNewton(images[0])
dyn1.run(fmax=0.01)
dyn2 = QuasiNewton(images[-1])
dyn2.run(fmax=0.01)
# Interpolate positions between initial and final states:
neb.interpolate()
for image in images:
print(image.get_distance(1, 2), image.get_potential_energy())
with BFGS(neb, trajectory='emt_h3o2m.traj') as dyn:
dyn.run(fmax=0.05)
for image in images:
print(image.get_distance(1, 2), image.get_potential_energy())
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