[ase-users] no energies in .traj file when running neb calculations with siesta calculator

[Eric Hermes]

There was a typo in my previous script. I've attached the fixed version
(name -> fname).

Eric

On Mon, 2017-04-10 at 15:41 +0000, Eric Hermes via ase-users wrote:
> On Mon, 2017-04-10 at 14:56 +0000, Louwerse,	M.J. (Manuel) via
> ase-
> users wrote:
> > Dear All,
> >  
> > When I am running nudged elastic band (neb) calculations with
> > Siesta
> > as calculator, my trajectory files do not contain any energies.
> > When I run neb calculations with the simple EMT calculator I do get
> > energies written to my trajectory file, and when I do a simple
> > minimization with the siesta calculator also. But when using the
> > combination of neb and siesta no energies are written.
> > Does anyone have any idea what may cause this and how it can be
> > solved?
> >  
> > Thanks,
> > Manuel
> 
> Manuel,
> 
> I thought I had replied to your previous email, but I don't see my
> reply, so it looks like I didn't.
> 
> Please see the attached script, which is modified from the example
> you
> sent in your previous email. I have made some changes which are
> merely
> semantic (i.e. we would normally say that your example has 8 images,
> not 10, since we do not perform calculations on either the initial or
> final images), but others are functional.
> 
> For example, each image should get its *own* calculator object. While
> your code may work as written for serial calculations, it is very
> strange to move a calculator from Atoms object to Atoms object. If
> each
> image gets its own calculator, you will also be able to run the NEB
> in
> parallel (that is, with each image running simultaneously on
> different
> processors by calling NEB with parallel=True).
> 
> I also am not sure what the final few lines of your script was trying
> to do. As written, your script will run the NEB and create a
> trajectory
> file where each group of 10 sequential images is a single iteration
> of
> the NEB, but then you appear to overwrite it with an empty file. I
> think what you are trying to do is read the trajectory file written
> by
> NEB, but you need to do that with ase.io.read, not
> ase.io.trajectory. 
> 
> Let me know if this doesn't work with your system. I do not have
> experience with Siesta or the Siesta calculator in ASE, so there
> might
> be issues I am unaware of.
> 
> Eric 
> > _______________________________________________
> > ase-users mailing list
> > ase-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> 
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