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Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package

The design of X-ray optics based on diffraction from crystals depends on the accurate calculation of the structure factors of their Bragg reflections over a wide range of temperatures. In general, the temperature dependence of the lattice parameters, the atomic positions and the atomic thermal vibra...

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Autores principales: Sutter, John P., Pittard, James, Filik, Jacob, Baron, Alfred Q. R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9348876/
https://www.ncbi.nlm.nih.gov/pubmed/35974725
http://dx.doi.org/10.1107/S1600576722005945
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author Sutter, John P.
Pittard, James
Filik, Jacob
Baron, Alfred Q. R.
author_facet Sutter, John P.
Pittard, James
Filik, Jacob
Baron, Alfred Q. R.
author_sort Sutter, John P.
collection PubMed
description The design of X-ray optics based on diffraction from crystals depends on the accurate calculation of the structure factors of their Bragg reflections over a wide range of temperatures. In general, the temperature dependence of the lattice parameters, the atomic positions and the atomic thermal vibrations is both anisotropic and nonlinear. Implemented here is a software package for precise and flexible calculation of structure factors for dynamical diffraction. α-Quartz is used as an example because it presents the challenges mentioned above and because it is being considered for use in high-resolution X-ray spectroscopy. The package is designed to be extended easily to other crystals by adding new material files, which are kept separate from the package’s stable core. Python 3 was chosen as the language to allow the easy integration of this code into existing packages. The importance of a correct anisotropic treatment of the atomic thermal vibrations is demonstrated by comparison with an isotropic Debye model. Discrepancies between the two models can be as much as 5% for strong reflections and considerably larger (even to the level of 100%) for weak reflections. A script for finding Bragg reflections that backscatter X-rays of a given energy within a given temperature range is demonstrated. The package and example scripts are available on request. Also discussed, in detail, are the various conventions related to the proper description of chiral quartz.
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spelling pubmed-93488762022-08-15 Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package Sutter, John P. Pittard, James Filik, Jacob Baron, Alfred Q. R. J Appl Crystallogr Research Papers The design of X-ray optics based on diffraction from crystals depends on the accurate calculation of the structure factors of their Bragg reflections over a wide range of temperatures. In general, the temperature dependence of the lattice parameters, the atomic positions and the atomic thermal vibrations is both anisotropic and nonlinear. Implemented here is a software package for precise and flexible calculation of structure factors for dynamical diffraction. α-Quartz is used as an example because it presents the challenges mentioned above and because it is being considered for use in high-resolution X-ray spectroscopy. The package is designed to be extended easily to other crystals by adding new material files, which are kept separate from the package’s stable core. Python 3 was chosen as the language to allow the easy integration of this code into existing packages. The importance of a correct anisotropic treatment of the atomic thermal vibrations is demonstrated by comparison with an isotropic Debye model. Discrepancies between the two models can be as much as 5% for strong reflections and considerably larger (even to the level of 100%) for weak reflections. A script for finding Bragg reflections that backscatter X-rays of a given energy within a given temperature range is demonstrated. The package and example scripts are available on request. Also discussed, in detail, are the various conventions related to the proper description of chiral quartz. International Union of Crystallography 2022-07-28 /pmc/articles/PMC9348876/ /pubmed/35974725 http://dx.doi.org/10.1107/S1600576722005945 Text en © John P. Sutter et al. 2022 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Research Papers
Sutter, John P.
Pittard, James
Filik, Jacob
Baron, Alfred Q. R.
Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package
title Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package
title_full Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package
title_fullStr Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package
title_full_unstemmed Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package
title_short Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package
title_sort calculating temperature-dependent x-ray structure factors of α-quartz with an extensible python 3 package
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9348876/
https://www.ncbi.nlm.nih.gov/pubmed/35974725
http://dx.doi.org/10.1107/S1600576722005945
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