[ase-users] definition of path length?

[jensj at fysik.dtu.dk]

> Hi all,
>
> I was doing some NEB calculations and was curious as to how ASE
> defined 'path length' (reaction coordinate).
>
> It seems from line 168-183 of neb.py (below) that it is defined as the
> cumulative sum of the of the displacement magnitudes between each
> image. I assume this is done to ensure a monotonically growing
> reaction coordinate.
>
> Does that sound about right?

That is correct.

> def fit(images):
>      E = [i.get_potential_energy() for i in images]
>      F = [i.get_forces() for i in images]
>      R = [i.get_positions() for i in images]
>      return fit0(E, F, R)
>
> def fit0(E, F, R):
>      E = np.array(E) - E[0]
>      n = len(E)
>      Efit = np.empty((n - 1) * 20 + 1)
>      Sfit = np.empty((n - 1) * 20 + 1)
>
>      s = [0]
>      for i in range(n - 1):
>          s.append(s[-1] + sqrt(((R[i + 1] - R[i])**2).sum()))
>
>
>
> David E. Farrell
> Post-Doctoral Fellow
> Department of Materials Science and Engineering
> Northwestern University
> email: d-farrell2 at northwestern.edu
>
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