[ase-users] Pulling out data from NEB

[Jesper Toft Rasmussen]

Hi Jens Jørgen,

Of course - stupid mistake to forget a minimal working example.
I have a small script that reads as follows:

from ase.io import read,write
from ase.neb import fit
slice = read('neb.traj at -11:')
write('neb_last_step.traj',slice)
print [i.get_potential_energy() for i in slice]
s, E, Sfit, Efit, lines = fit(slice)

Where neb.traj is obtained from another run,

neb = NEB(images)
neb.interpolate()
qn = FIRE(neb,logfile='optimize.log',trajectory='neb.traj')
qn.run(fmax=0.01)

After all calculations I plot s,E,Sfit,Efit, and lines in MatLAB to get the previously included figures.
>From what I can see from the source code, this is also the way the GUI works,
which is why I have spent a long time scratching my head..

I have made a local workaround by modifying the gui/neb.py file to output s,E,Sfit,Efit and lines to txt files,
which I then use In my further analysis. But an actual solution would be nice.

Thank you in advance,


Jesper Toft Rasmussen

PhD student

DTU Nanotech



Technical University of Denmark

[cid:image001.gif at 01CDF24A.5EFBBBB0]

Department of Micro- and Nanotechnology

Ørsteds Plads

Building 344

DK - 2800 Kgs. Lyngby

Denmark

Direct +45 45255694

jestr at nanotech.dtu.dk<mailto:jestr at nanotech.dtu.dk>

www.nanotech.dtu.dk<http://www.nanotech.dtu.dk/>





From: Jens Jørgen Mortensen
Sent: 10. januar 2013 16:50
To: Jesper Toft Rasmussen
Cc: 'ase-users at listserv.fysik.dtu.dk'
Subject: Re: [ase-users] Pulling out data from NEB

Den 02-01-2013 14:29, Jesper Toft Rasmussen skrev:
Dear all ASE users,

I have set up a system, where I want to perform nudged elastic band calculations using the ASE interface. After having created the initial/final images and interpolating, I come to the task of analyzing the data.

By using the ASE GUI, I have tested the NEB tool, but since I need to further fiddle with the data, I need some way of extracting these data sets. One way is to use the fit/fit0 routines (found from the source code). However, when I do this I clearly don't get the same result as the GUI provides. I have added images as proof. It is clear that the tangents are completely off.

Can anyone tell me why this is the case? And what I should do to get out the correct data?

Can you show us how you used fit/fit0 ?

Jens Jørgen


 Best regards,


Jesper Toft Rasmussen

PhD student

DTU Nanotech



Technical University of Denmark

[cid:image001.gif at 01CDF24A.5EFBBBB0]

Department of Micro- and Nanotechnology

Ørsteds Plads

Building 344

DK - 2800 Kgs. Lyngby

Denmark

Direct +45 45255694

jestr at nanotech.dtu.dk<mailto:jestr at nanotech.dtu.dk>

www.nanotech.dtu.dk<http://www.nanotech.dtu.dk/>









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