[ase-users] definition of path length?

[David Farrell]

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?

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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