/usr/share/pyshared/ase/examples/neb1.py is in python-ase 3.6.0.2515-1.1.
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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 | from ase import *
from math import sqrt
a = 4.0614
b = a / sqrt(2)
h = b / 2
initial = Atoms([Atom('Al', (0, 0, 0)),
Atom('Al', (a / 2, b / 2, -h))],
pbc=(1, 1, 0),
cell=(a, b, 2 * h))
initial *= (2, 2, 2)
initial.append(Atom('Al', (a / 2, b / 2, 3 * h)))
#view(initial)
#initial.set_cell((2*2,2*b,)
final = initial.copy()
final.positions[-1, 1] += b
# Construct a list of images:
images = [initial]
for i in range(5):
images.append(initial.copy())
images.append(final)
# Make a mask of zeros and ones that select the dynamic atoms (the
# three topmost layers):
mask = initial.positions[:, 2] < 0.5 * h
constraint = FixAtoms(mask=mask)
print mask
print 'Fixed atoms:', constraint.fixed
for image in images:
# Let all images use an EMT calculator:
image.set_calculator(EMT())
image.set_constraint(constraint)
# Relax the initial and final states:
QuasiNewton(initial).run(fmax=0.05)
QuasiNewton(final).run(fmax=0.05)
# Create a Nudged Elastic Band:
neb = NEB(images)
# Mak a starting guess for the minimum energy path (a straight line
# from the initial to the final state):
neb.interpolate()
# Use MDMin to relax the path:
minimizer = QuasiNewton(neb)
minimizer.run(fmax=0.05)
# Write the path to a trajectory:
traj = PickleTrajectory('jump1.traj', 'w')
neb.write(traj)
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