/usr/share/pyshared/ase/test/COCu111.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 | from math import sqrt
from ase import Atoms, Atom
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import BFGS, QuasiNewton
from ase.neb import NEB
# 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)
slab = fcc111 * (2, 2, 4)
slab.set_cell([2 * d, d * sqrt(3), 1])
slab.set_pbc((1, 1, 0))
slab.calc = EMT()
Z = slab.get_positions()[:, 2]
indices = [i for i, z in enumerate(Z) if z < Z.mean()]
constraint = FixAtoms(indices=indices)
slab.set_constraint(constraint)
dyn = QuasiNewton(slab)
dyn.run(fmax=0.05)
Z = slab.get_positions()[:, 2]
print Z[0] - Z[1]
print Z[1] - Z[2]
print Z[2] - Z[3]
b = 1.2
h = 1.5
slab += Atom('C', (d / 2, -b / 2, h))
slab += Atom('O', (d / 2, +b / 2, h))
s = slab.copy()
dyn = QuasiNewton(slab)
dyn.run(fmax=0.05)
#view(slab)
# Make band:
images = [slab]
for i in range(6):
image = slab.copy()
image.set_constraint(constraint)
image.calc = EMT()
images.append(image)
image[-2].position = image[-1].position
image[-1].x = d
image[-1].y = d / sqrt(3)
dyn = QuasiNewton(images[-1])
dyn.run(fmax=0.05)
neb = NEB(images, climb=not True)
# Set constraints and calculator:
# Displace last image:
# Relax height of Ag atom for initial and final states:
# Interpolate positions between initial and final states:
neb.interpolate()
for image in images:
print image.positions[-1], image.get_potential_energy()
#dyn = MDMin(neb, dt=0.4)
#dyn = FIRE(neb, dt=0.01)
dyn = BFGS(neb, maxstep=0.04, trajectory='mep.traj')
#from ase.optimize.oldqn import GoodOldQuasiNewton
#dyn = GoodOldQuasiNewton(neb)
dyn.run(fmax=0.05)
for image in images:
print image.positions[-1], image.get_potential_energy()
if locals().get('display'):
import os
error = os.system('ag mep.traj@-7:')
assert error == 0
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