[Cod-bugs] overlap problem for 563 crystals

[Saulius Gražulis]

Dear Bob,

thank you for your report.

On 2023-04-07 05:38, bob wrote:
> I am writing to bring to your attention an issue with the COD ID (see 
> codID-563). There seems to be an atomic overlap problem with 563 
> structures, specifically with the COD-1510278 as can be seen in the 
> attached image.
> Could you kindly investigate this issue and let me know if it can be 
> rectified? I would greatly appreciate your assistance in this matter.

The issue that you are reporting is not a bug but an intended 
description of the structures, at least in the COD 1510278. In this 
entry, the two atoms, Au and Pt, are on exactly the same site (xyz = 0.0 
0.0 0.0), and have occupancies 0.5, meaning that this is 50:50 ratio 
Pt:Au alloy; each site in such crystal is either Au or Pt with 50% 
probability (thus the entry reports a /substitutional alloy /[1]/)/. 
Whether this is indeed a correct alloy structure needs to be consulted 
in the original paper 
(https://doi.org/10.1524/zpch.1985.144.144.223/html), but from the data 
perspective the description is correct.

Other entries in the COD might have different reasons for the atoms to 
be too close – substitutional disorder, incorrectly marked positional 
disorder, incorrectly solved or recorded structures, etc. When we find 
incorrect descriptions, we do correct them manually, but this is a very 
time-consuming work, so we cannot promise to fix all issues quickly, and 
we have to triage them by importance.

Thus, it is ultimately your responsibility as a COD user to interpret 
COD structures as was intended by the authors (as in the case of COD 
1510278), and to filter our those structures that are not suitable for 
your investigation for one reason or another.

Sincerely yours,
Saulius

Refs.:

[1] Wikipedia. Alloy; sect. "Mechanisms" (2023). URL: 
https://en.wikipedia.org/wiki/Alloy [accessed 2023-04-07T09:44+03:00]

-- 
Dr. Saulius Gražulis
Vilnius University, Life Science Center, Institute of Biotechnology
Saulėtekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)
phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366

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