[ase-users] BUG in bond lengths

[Ronald Cohen]

I can't believe I am still writing on this, but I didn't realize how bad it
was. The bond lengths are just completely wrong. For example for tetragonal
P4mm perovskite:

This is from get_bonds and get_values:

There are 6 Ti-O bonds.
1.807929755388571 1.807929755388571 1.7549750000519997
1.807929755388571 1.807929755388571 1.7549750000519997
The average Ti-O bond length is 1.7902781702763804. Min is 1.7549750000519997.




And these are the correct values:

Ti-O neighbors= [0 6 2 2 2]
[1.875109   1.80792976 1.80792976 1.80792976 1.80792976 1.754975
 1.80792976 1.80792976 1.80792976 1.80792976 1.875109   1.754975  ]
Average: 1.810300503592381 Min: 1.754975000052

Bonds misses the 1.875109 bond.

Ron

---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen at carnegiescience.edu



On Sat, Aug 31, 2024 at 7:04 AM David Willock <WillockDJ at cardiff.ac.uk>
wrote:

> It looks like both lists contain the same values but the first is notably
> longer than the second. Are you able to check with a P1 version of the
> structure so there is no symmetry to take account of in the cif file, and
> check that minimum image convention is applied in both cases?
>
> Best wishes
> David
>
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> ------------------------------
> *From:* ase-users <ase-users-bounces at listserv.fysik.dtu.dk> on behalf of
> Ronald Cohen via ase-users <ase-users at listserv.fysik.dtu.dk>
> *Sent:* Friday, August 30, 2024 9:11:44 PM
> *To:* ase-users at listserv.fysik.dtu.dk <ase-users at listserv.fysik.dtu.dk>
> *Subject:* [ase-users] BUG in bond lengths
>
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> ateb/agor atodiadau neu ddolenni.
>
> I posted this before to https://matsci.org/ but now I am convinced it is
> a bug. I am trying to find a set of atomic distances that are not normal
> near neighbor bonds--they are second neighbors, in different distorted
> perovvkites.
>
> It seems the bond lengths from ase are incorrect! Attached is a simple
> code that computes the atomic distances two ways, and there are two
> different answers. get_values seems to just be incorrect. Using
> ase.neighborlist.neighbor_list is close but still slightly off. I include a
> pdf of the code output, the code, the input, and also the output from
> Mercury from CCDC. Link to discussion on matsci:
> https://matsci.org/t/how-to-increase-bond-length-for-analysis-get-bonds/57295?u=ronald_cohen
>
>
> ---
> Ronald Cohen
> Extreme Materials Initiative
> Earth and Planets Laboratory
> Carnegie Institution for Science
> 5241 Broad Branch Rd., N.W.
> Washington, D.C. 20015
> rcohen at carnegiescience.edu
>
>
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