Visualizing in jmol

Vasp transition state theory tools

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anirudhnk
Posts: 18
Joined: Thu Dec 09, 2021 5:49 pm

Visualizing in jmol

Post by anirudhnk »

Dear Prof. Henkelman,

Sometimes when I view the movie of a system in jmol, why do some of the atoms jump to the other end even though they are not involved in the migration path of study? I see that their coordinate changes by the lattice constant i.e 0.9 becomes -0.1 if the lattice constant was 1. But can the fact that there is a shift in these atoms also contribute to the migration barrier?
as68397
Posts: 2
Joined: Mon Aug 16, 2021 3:11 pm

Re: Visualizing in jmol

Post by as68397 »

So it sounds like that is the periodic image of the system (in the -x direction), i.e the atom with coordinate 0.9 becomes -0.1. If it is only the periodic representation (which it sounds like), it won't affect the NEB barrier at all.

Thanks,
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