[ase-users] NEB Calculation

[Abid Channa]

Hey Ask Hjorth,
Thanks for reply. But still I have unclear. I am trying determine MEP by performing NEB calculation from fcc to hcp site Via bridge.If I am taking system with adding adatom on fcc , it gives diffusion results from fcc to fcc , but I am trying from fcc to hcpand if I am adding adatom on hcp site, it gives results with hcp to hcp .
I think there is some mis understanding in script ?
Best, 
___________________________________
           
                 ABID  ALI 

PhD (Marie Curie-ITN) FellowTheoretical ChemistryScience Institute, University of Iceland

      From: Ask Hjorth Larsen <asklarsen at gmail.com>
 To: Abid Channa <abid_channa04 at yahoo.com> 
Cc: Ase-users <ase-users at listserv.fysik.dtu.dk>
 Sent: Tuesday, January 9, 2018 12:17 PM
 Subject: Re: [ase-users] NEB Calculation
   
Hi,

2018-01-09 12:50 GMT+01:00 Abid Channa via ase-users
<ase-users at listserv.fysik.dtu.dk>:
> Hello users,
>
> I am doing NEB calculations . My system is Pt (fcc111) unit cell 4,4 with 7
> layers.
>
> My target is to determine MEP by performing NEB calculations of " Pt adatom
> diffusion from fcc-hcp sites via bridge. I am running following script . it
> gives diffusion from fcc to fcc not hcp . Is there any problem in my script
> or I am not defining correct final stage in script ? . Kindly help me in
> order to make script or How I define my initial stage as fcc site and final
> stage as hcp site in my script.
>
> from ase.build import fcc111, add_adsorbate
> from ase.constraints import FixAtoms
> from ase.calculators.emt import EMT
> from ase.optimize import QuasiNewton
>
> slab = fcc111('Pt', size=(4, 4, 7))
> add_adsorbate(slab, 'Pt', 1.7, 'fcc')
> slab.center(axis=2, vacuum=4.0)
>
> mask = [atom.tag > 5 for atom in slab]
>
> slab.set_constraint(FixAtoms(mask=mask))
>
> slab.set_calculator(EMT())
>
> qn = QuasiNewton(slab, trajectory='initial.traj')
> qn.run(fmax=0.05)
>
> # Final state:
> slab[-1].x += slab.get_cell()[0, 0] / 2

Is that an hcp site?

Try add_adsorbate(..., 'hcp') when generating the second image.

Best regards
Ask

> qn = QuasiNewton(slab, trajectory='final.traj')
>
> qn.run(fmax=0.05)
>
> Best,
>
> ___________________________________
>
>                  ABID  ALI
>
> PhD (Marie Curie-ITN) Fellow
> Theoretical Chemistry
> Science Institute, University of Iceland
>
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
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