Using rigid bodies in diffpy.cmi

[Víctor Quezada]

Hello everyone,

I am reaching you out for advice on how to set up rigid bodies in diffpy.cmi, specifically, I need to build a hexaqua chromium (III) octahedra, fix the chromium position, restrain bond angles and distances and allow to rotate the octahedra through the equatorial and apical axis (first individually, then simultaneously). However, I have no idea on how to configure this in diffpy.cmi

I am aware that discrete structures can be defined by specifying atomic positions in xyz coordinates, but I don't know the language to apply the restrains and direct diffpy.cmi to iterate through the rotations of the chromium octahedra. Since this is a phosphonate-based MOF material, I would also like to explore the rotation of the phosphonate groups to explore other potential -PO(OH)2--(OH2)5Cr distances. This is a particular class of MOFs where the phosphonate groups are not coordinating to the Cr ions, but interacting through hydrogen bonding to the fully hydrated Cr octahedra. I am currently using a model obtained through Rietveld refinement, which describes most of the features but it fails to fit the two peaks around 2.5 A (see attached fit).

I have been educating myself in PDF and diffpy.cmi using the book "Atomic PDF analysis: A Primer" as I am not a PDF nor coding expert. I checked briefly  https://github.com/diffpy/cmi_exchange and couldn't find directions about this in the scripts description.

Any help, suggestions or directions for reading will be greatly appreciated.

I can provide more details if needed.

Best,

Victor Quezada Novoa, PhD.

Postdoctoral fellow

Shimizu research group

University of Calgary

[Tomasz Stawski]

Hi Victor,

I have implemented rigid bodies in this project:

https://github.com/BAMresearch/ZrV2O7-PDF-Refinement

Maybe have a look, and write if you have any questions.

Best regards,

Tomasz

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[Víctor Quezada]

Hello Tomasz,

Thank you very much for sharing this information, I will take a look and try my best to implement it in my system. For sure I will have some questions.

Best,

Victor 

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[Tomasz Stawski]

We are preparing a publication and I will be updating this repo next week. The code will stay the same but the documentation will be improved.

Best,

Tomasz

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[Simon Billinge]

wow, this is great, thanks Tomasz!

Back in the day Pavol Juhas and Dragica Prill did this using quaternions:

Dragica Prill, Pavol Juh´as, S. J. L. Billinge, and Martin U. Schmidt. “Towards solution and
refinement of organic crystal structures by fitting to the atomic pair distribution function”. In:
Acta Crystallogr. A 72.1 (2016), pp. 62–72. doi: 10.1107/S2053273315022457.

I am not sure if I can dig up the code or not, I will take a look.

S

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Simon Billinge

Professor of Materials Science

Director, CNSI (California NanoSystems Institute)

University of California, Santa Barbara

Tel: 805-893-8716 + Email: sbil...@ucsb.edu