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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.optimize import QuasiNewton, BFGS
from ase.visualize import view
@pytest.mark.calculator('nwchem')
def test_h3o2m(factory):
# http://jcp.aip.org/resource/1/jcpsa6/v97/i10/p7507_s1
doo = 2.74
doht = 0.957
doh = 0.977
angle = radians(104.5)
initial = 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)])
if 0:
view(initial)
final = Atoms('HOHOH',
positions=[(- sin(angle) * doht, 0., cos(angle) * doht),
(0., 0., 0.),
(0., 0., doo - doh),
(0., 0., doo),
(sin(angle) * doht, 0., doo - cos(angle) * doht)])
if 0:
view(final)
# Make band:
images = [initial.copy()]
for i in range(3):
images.append(initial.copy())
images.append(final.copy())
neb = NEB(images, climb=True)
def calculator():
return factory.calc(
task='gradient',
theory='scf',
charge=-1
)
# Set constraints and calculator:
constraint = FixAtoms(indices=[1, 3]) # fix OO
for image in images:
image.calc = calculator()
image.set_constraint(constraint)
# Relax initial and final states:
if 1:
dyn1 = QuasiNewton(images[0])
dyn1.run(fmax=0.10)
dyn2 = QuasiNewton(images[-1])
dyn2.run(fmax=0.10)
# Interpolate positions between initial and final states:
neb.interpolate()
if 1:
for image in images:
print(image.get_distance(1, 2), image.get_potential_energy())
dyn = BFGS(neb)
dyn.run(fmax=0.10) # use better basis (e.g. aug-cc-pvdz) for NEB to converge
for image in images:
print(image.get_distance(1, 2), image.get_potential_energy())
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