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

[Eric Hermes]

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 
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