[ase-users] energies are lost when switch on remove_rotation_and_translation in NEB

[GENG SUN]

Dear Ask

Thanks for your replying. I understand the rotation and translation move
the coordinates, hence the energies are lost.
Because it is a normal procedure to monitor the status of NEB calculations
(such as whether there exists an intermediate structure by inspecting the
shape of  MEP), the recalculations are too expensive for monitoring
purposes. Recalculation is only reasonable when NEB is converged, and in
that case we only need the final result.

I thought there should be a more efficient way to do this. Such as saving
the energies and forces during rotation and translation by
SinglePointCalculator.
But I am not very sure whether it conflicts with some parts in the NEB
method.

Best Wishes,

Geng




On Thu, Jan 23, 2020 at 9:40 AM Ask Hjorth Larsen <asklarsen at gmail.com>
wrote:

> Dear Geng,
>
> Am Do., 16. Jan. 2020 um 19:20 Uhr schrieb GENG SUN via ase-users
> <ase-users at listserv.fysik.dtu.dk>:
> >
> > Hello ASE users,
> >
> > I found that when I switch on remove_rotation_and_translation=True in
> NEB module of ASE, the trajectory generated by the optimizers (BFGS for
> example) will not contain any energies and forces calculated. This will
> cause some difficulties to monitor the process of NEB calculations.
> >
> > Is there a simple way to fix that?
>
> The rotation and translation invalidates the previously calculated
> energies for all images.
>
> The energies won't be plotted unless *all* images have energies.  The
> energies are calculated for intermediate images during NEB, but not
> initial and final images, since those don't move.
>
> Therefore: Most likely you just need to recalculate them manually for
> initial and final image and they should all show up.
>
> Best regards
> Ask
>
> >
> > Thank you very much in advance.
> >
> > Best,
> >
> > Geng
> > _______________________________________________
> > ase-users mailing list
> > ase-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
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