New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
The recommended way of marking substitutional disorder #251
Comments
p103 and 104 of IT Vol G 1st Edition state that occupational disorder can either be described as above, or else a dummy atom type can be created and the |
Thank you for the useful reference! Slight deviation regarding the terminology. It seems that what I called substitutional disorder (based on [1]) is referred to as compositional disorder in IT Vol. G 1st Edition so I will be using this term from now on. Also, occupational disorder seems to be a synonym of positional disorder at least from the way these terms are used in p105 and p212 (definition of Regardless, now it is completely clear that there are two formalised ways of describing compositional disorder (same site approach and dummy site approach). However, one question still remains -- can the [1] https://ocw.mit.edu/courses/chemistry/5-067-crystal-structure-refinement-fall-2009/lecture-notes/MIT5_067F09_lec4.pdf |
Interesting. I think that the authors of the Volume and definitions had in mind groups of bonded atoms when defining the |
The core DMG have no objections to compositional disorder being described using |
Relevant core DMG discussion can be found at https://www.iucr.org/__data/iucr/lists/coredmg/msg00414.html. |
The definitions were updated and a few example CIF files were added by merging PR #343. I will leave to @jamesrhester to close this issue in case he still wants to keep it open as a reminder to also update the text in Volume G. Also, I will reiterate my question from the last comment of PR #343. I noticed that the disorder example that was provided in the DDL1 version of the dictionary as part of the ATOM_SITE category description (see https://github.com/COMCIFS/DDL1-legacy-dictionaries/blob/28e20dc928790dceb889716d2bed435fc10c4c79/dictionaries/cif_core.dic#L850) is no longer available in the DDLm dictionary. Maybe this example should be restored or a similar one reintroduced? |
Yes, the missing example should be returned, it is very helpful. |
One popular way of expressing substitutional disorder in CIF files relies on grouping atoms with partial occupancies based on their identical coordinates. For example, the following fragment:
Indicates that one site is simultaneously occupied by Sr/La, another by O1/F1 and the third one by O2/F2. This type of markup conveys the general idea, however, it feels somewhat imprecise due to the potential rounding errors that one has to take into account while comparing the coordinates, etc. Also I was not able to find official documentation that describes this approach (I would be happy to get a reference, though).
Alternative approach uses the
_atom_site.disorder_group
and_atom_site.disorder_assembly
data items from theCIF_CORE
dictionary to group the disordered atoms in a more formal machine-readable way. However, it not clear if this approach is legit, since the definitions of both of these items explicitly use the term "positional disorder" and do not mention "substitutional disorder" at all. Previous example, rewritten using the_atom_site.disorder_*
items:Are there any COMCIFS recommendations on marking substitutional disorder? Can the
_atom_site.disorder_*
data items be used for this purpose?The text was updated successfully, but these errors were encountered: