[ase-users] problem removing rotation and translation in NEB calculations

[Peterson, Andrew]

I've encountered the same thing (but with NWChem). There is no problem in
how the algorithm runs, it's just that the final energy loses its
information on energy and forces, which makes our standard tools for
looking at NEB results break.

The problem is: at each step along the NEB calculation, the
`minimize_rotation_and_translation` function is called on each image except
the 0th (initial state). That is, image 1's rotations and translations are
minimized with respect to image 0, then image 2 with respect to image 1,
etc., until the final image's rotations and translations are minimized with
respect to its previous image. From ASE's perspective, that final image's
atomic positions have changed, which automatically deletes the energy and
force information. (Even though we "know" that the energy should stay the
same and the forces should stay the same, within some
rotation/translation.) By default ASE's NEB algorithm never re-calculates
the final image, so in the resulting trajectory that final image never has
saved energy/force results (except possibly at step 0).

It's not obvious to me what the solution is. We certainly don't want to
re-calculate that final image at every NEB step just to be able to make
plots. Artificially adding back the energy and forces to that image also
seems problematic. Perhaps we could make the plotting tools more tolerant
to missing images?

On Tue, Aug 20, 2019 at 3:45 PM Charles-Alexandre Mattelaer via ase-users <
ase-users at listserv.fysik.dtu.dk> wrote:

> Dear ASE community
>
> I've stumbled upon a peculiar behaviour of the NEB module when removing
> rotation and translation. When enabling the removal, I don't get an energy
> for the final image which results in no plots (when e.g. subtracting this
> energy from the rest to obtain relative energies) and also errors when
> trying to apply the NEB analysis.
>
> I've added example input that generate said problem (trajectory files
> seemed to big, even when extracting the last NEB path). No problem
> analyzing the trajectory where rotation and translation was allowed. I do
> believe that this problem occurs with other (external?) calculators as
> well. (Haven't tried it for this particular case.)
>
> It seems that rotation and translation becomes a problem during this
> calculation ( i see drifting of the molecule which leads to convergence
> issues) so it would be handy if I could properly enable this option.
>
> Any help would be appreciated!
>
> Kind regards
>
> Charles-Alexandre Mattelaer
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-- 
Andrew Peterson
Associate Professor
Brown University School of Engineering
Barus & Holley 247
184 Hope Street
Providence, RI 02912
(401) 863-2153
http://brown.edu/go/catalyst
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