[gpaw-users] Restart NEB Calculation

[Jens Jørgen Mortensen]

On Wed, 2010-12-29 at 14:00 -0500, Hongliang Xin wrote:
> Dear gpaw users,
> 
> After following the tutorial, the NEB calculation with parallel images
> runs correctly. I have a little trouble with restarting the existing
> NEB calculations. 
> Can anyone give me suggestions what exactly needed to read in for this
> online example? 
> I tried something like below but it always fails because some .traj
> file will be overwritten and the script will complain about
> IOError('This is not a trajectory file!'). 
> 
>     if os.path.exists('neb'+str(i+1)+'.traj'):
>         image = read('neb'+str(i+1)+'.traj',index=-1,format='traj')
>     else:
>         image = initial.copy()
> 
> https://wiki.fysik.dtu.dk/gpaw/tutorials/neb/neb.html

You could use a new filename for the second round of optimizations (neb%
d.2.traj) or you could try to open the trajectories in append mode:

traj = PickleTrajectory('neb%d.traj' % j, 'a', images[j],
                        master=(rank % n == 0))

And don't forget to uncomment the 'neb.interpolate()' line!

Jens Jørgen

> Thanks,
> 
> Hongliang
> -- 
> Hongliang Xin
> Ph.D. Candidate
> Dept. of Chemical Engineering
> University of Michigan
> 3166 HH Dow
> 2300 Hayward
> Ann Arbor, MI 48109
> Phone: (734) 647-8051
> E-mail: hxin at umich.edu
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