[ase-users] Pulling out data from NEB

[Jens Jørgen Mortensen]

Den 14-01-2013 11:29, Jesper Toft Rasmussen skrev:
>
> 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.
>

The energies in the two plots look similar, but the slopes of the small 
lines are wrong and those are calculated from the forces.  Try to print 
the forces from the fit0() function.  Are they the same when using the 
GUI and your script?

Are your atoms constrained in any way?

Jens Jørgen

> Thank you in advance,
>
> *Jesper Toft Rasmussen*
>
> PhD student
>
> DTU Nanotech
>
> *Technical University of Denmark*
>
> 	
>
> http://www.dtu.dk/images/DTU_email_logo_01.gif
>
> 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*
>
> 	
>
> http://www.dtu.dk/images/DTU_email_logo_01.gif
>
> 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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