[ase-users] NEB Calculation

[Abid Channa]

Hey Ask Hjorth,     (Repeated : Diffusion of Pt from fcc to hcp via top)
I got your point. But problem is that , if I am fixing a point at top site for doing one NEB calculation from fcc to top. I have to relax both stages . It is ok in fcc site case , while problem is occurring at ontop site (If I am keeping this fixed, How I relax my top system before doing NEB).
If I am not wrong, you are saying that I  do first NEB from fcc (relaxed) site to top (fixed/unrelaxed) and then second NEB from top (fixed) to hcp (relaxed) ? .
Best,
___________________________________
           
                 ABID  ALI 

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

 

    On Sunday, January 14, 2018, 3:18:12 PM GMT, Ask Hjorth Larsen <asklarsen at gmail.com> wrote:  
 
 Hi.

2018-01-11 1:03 GMT+01:00 Abid Channa <abid_channa04 at yahoo.com>:
> Hey Ask Hjorth,
>
> Bundle of thanks for your replies. this script was reaction pathway from fcc
> to hcp site via bridge.
> Now I want to get my reaction pathway from fcc to hcp via top not bridge
> (Diffusion of Pt adatom from fcc to hcp via top).  For doing this, How I
> modify my script ?

Since you have a fixed point in the middle now, I'd do two NEBs: One
from fcc to top, and one from top to hcp.

Best regards
Ask

>
> Best,
>
>
> ___________________________________
>
>                  ABID  ALI
>
> PhD (Marie Curie-ITN) Fellow
> Theoretical Chemistry
> Science Institute, University of Iceland
>
>
>
> On Wednesday, January 10, 2018, 10:59:47 PM GMT+5, Ask Hjorth Larsen
> <asklarsen at gmail.com> wrote:
>
>
> Hi,
>
> 2018-01-10 17:59 GMT+01:00 Abid Channa <abid_channa04 at yahoo.com>:
>> My target is " Diffusion of Pt adatom from fcc to hcp via Bridge" , system
>> is fcc, Pt 111
>>
>> Script is
>>
>> 1- for fcc site in which I have described my initial.traj
>>
>> 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())
>>
>> # Initial state:
>> qn = QuasiNewton(slab, trajectory='initial.traj')
>> qn.run(fmax=0.05)
>>
>> 2-for hcp site in which I have described my final.traj
>>
>>
>>
>> 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, 'hcp')
>> 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())
>>
>> # Final state:
>> qn = QuasiNewton(slab, trajectory='final.traj')
>> qn.run(fmax=0.05)
>>
>>  3-Script for NEB calculation in which I have defined initial.traj fcc
>> site
>> and final.traj hcp site.
>>
>>
>> from ase.io import read
>> from ase.constraints import FixAtoms
>> from ase.calculators.emt import EMT
>> from ase.neb import NEB
>> from ase.optimize import BFGS
>>
>> initial = read('initial.traj')
>> final = read('final.traj')
>>
>> constraint = FixAtoms(mask=[atom.tag > 1 for atom in initial])
>>
>> images = [initial]
>> for i in range(3):
>>    image = initial.copy()
>>    image.set_calculator(EMT())
>>    image.set_constraint(constraint)
>>    images.append(image)
>>
>> images.append(final)
>>
>> neb = NEB(images)
>> neb.interpolate()
>> qn = BFGS(neb, trajectory='neb.traj')
>> qn.run(fmax=0.05)
>>
>>
>> Best,
>
> Okay, that is clear.
>
> As far as I can see it works correctly though: The final five images
> of the output trajectory describe the reaction path from the fcc site
> to an adjacent hcp site.  What was the exact source of trouble?
>
> Best regards
> Ask
  
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