[ase-users] Restarting NEB

[Roberto Schimmenti]

Dear ASE-users

I'm encountering some problem for restarting NEB calculations using
ASE+SIESTA; I know that there are several topic concerning this in the
mailing list but I would like a more detailed explanation unpon setting up
a NEB calculation using old trajectory file.


This is one of my typical input file:

initial = read('initial.traj')
final = read('final.traj')
constraint = FixAtoms(mask=[atom.tag > 1 for atom in initial])


calc = Siesta(label='systemxx',
              xc='KBM',
              ....)

images = [initial]
for i in range(4):
    image = initial.copy()
    image.set_calculator(calc)
    image.set_constraint(constraint)
    images.append(image)
images.append(final)

neb = NEB(images,k=[0.15,0.15,0.25,0.15,0.15],climb=True)
neb.interpolate()
qn = BFGS(neb, trajectory='neb.traj')
qn.run(fmax=0.04)


With this I can obtain a neb.traj file in wich all the path optimization
are included.

I know from the manual that it's possible to use images=
io.read('neb.traj'@-5) but I don't understand how this can be used for
taking into account only the last iterations of the trajectory file. Could
you provide me more complete example?

Thank you

Roberto Schimmenti
Ph.D. student
Università degli Studi di Palermo
Dipartimento di Fisica e Chimica
Viale delle Scienze, Ed. 17
90128 PALERMO (PA)