Chimie Théorique » QMX

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)