[ase-users] BUG in bond lengths

[Michael Joseph Waters]

Hi Ron,

This is a good example of the bug. Can you file an issue for it?  https://gitlab.com/ase/ase/-/issues

When you do, if can provide a code example to demonstrate the bug it will greatly help the developers in fixing it.

Thanks,
-Mike
________________________________
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: Monday, September 9, 2024 11:59 AM
To: David Willock <WillockDJ at cardiff.ac.uk>
Cc: ase-users at listserv.fysik.dtu.dk <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] BUG in bond lengths

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<mailto:rcohen at carnegiescience.edu>



On Sat, Aug 31, 2024 at 7:04 AM David Willock <WillockDJ at cardiff.ac.uk<mailto: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<mailto:ase-users-bounces at listserv.fysik.dtu.dk>> on behalf of Ronald Cohen via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>
Sent: Friday, August 30, 2024 9:11:44 PM
To: ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk> <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>
Subject: [ase-users] BUG in bond lengths

External email to Cardiff University - Take care when replying/opening attachments or links.
Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.


I posted this before to https://matsci.org/<https://urldefense.com/v3/__https://matsci.org/__;!!Dq0X2DkFhyF93HkjWTBQKhk!X-qbNnn5BHDGUP-wH3Y3kPQlQlJOGBQqcuyIbvafUuyh6tesPx6jtmkwrDT6DwVBdLhmdIHJcSnQrVSd1RJWkDZWW8cQv7mJ2Rzb48YaKadL$> 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<https://urldefense.com/v3/__https://matsci.org/t/how-to-increase-bond-length-for-analysis-get-bonds/57295?u=ronald_cohen__;!!Dq0X2DkFhyF93HkjWTBQKhk!X-qbNnn5BHDGUP-wH3Y3kPQlQlJOGBQqcuyIbvafUuyh6tesPx6jtmkwrDT6DwVBdLhmdIHJcSnQrVSd1RJWkDZWW8cQv7mJ2Rzb40784u-i$>


---
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<mailto:rcohen at carnegiescience.edu>

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