from ase_ext.optimize.mdmin import MDMin
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
initial = Atoms('Cu4',
positions=[(0, 0, 0), (0, b, b), (b, 0, b), (b, b, 0)],
cell=(a, a, a),
pbc=True)
initial *= (4, 4, 4)
del initial[0]
images = [initial] + [initial.copy() for i in range(6)]
images[-1].positions[0] = (0, 0, 0)
for image in images:
image.set_calculator(EMT())
#image.set_calculator(ASAP())
for image in [images[0], images[-1]]:
QuasiNewton(image).run(fmax=0.01)
neb = NEB(images)
neb.interpolate()
for a in images:
print(a.positions[0], a.get_potential_energy())
dyn = MDMin(neb, dt=0.1, trajectory='mep1.traj')
#dyn = QuasiNewton(neb)
import numpy as np
from ase_ext import Atoms
from ase_ext.io import write, read
a = 5.0
d = 1.9
c = a / 2
atoms = Atoms('AuH',
positions=[(c, c, 0), (c, c, d)],
cell=(a, a, 2 * d),
pbc=(0, 0, 1))
extra = np.array([2.3, 4.2])
atoms.set_array("extra", extra)
atoms *= (1, 1, 2)
images = [atoms.copy(), atoms.copy()]
r = ['xyz', 'traj', 'cube', 'pdb', 'cfg', 'struct']
w = r + ['xsf']
try:
import matplotlib
except ImportError:
pass
else:
w += ['png', 'eps']
for format in w:
print(format, 'O', end=' ')
fname1 = 'io-test.1.' + format
fname2 = 'io-test.2.' + format
write(fname1, atoms, format=format)
if format not in ['cube', 'png', 'eps', 'cfg', 'struct']:
write(fname2, images, format=format)
#initial.set_pbc((True,True,False))
# Approximate height of Ag atom on Cu(100) surfece:
h0 = 2.2373
initial += Atom('Pt', (10.96, 11.074, h0))
initial += Atom('Pt', (13.7, 11.074, h0))
initial += Atom('Pt', (9.59, 8.701, h0))
initial += Atom('Pt', (12.33, 8.701, h0))
initial += Atom('Pt', (15.07, 8.701, h0))
initial += Atom('Pt', (10.96, 6.328, h0))
initial += Atom('Pt', (13.7, 6.328, h0))
if 0:
view(initial)
# Make band:
images = [initial.copy() for i in range(7)]
neb = NEB(images)
# Set constraints and calculator:
indices = np.compress(initial.positions[:, 2] < -5.0,
list(range(len(initial))))
constraint = FixAtoms(indices)
for image in images:
image.set_calculator(ASAP())
image.constraints.append(constraint)
# Displace last image:
for i in range(1, 8, 1):
images[-1].positions[-i] += (d / 2, -h1 / 3, 0)
write('initial.traj', images[0])
