odatse-XAFS: solver module for analyses of PTRF-XAFS spectrum data

Polarization-dependent Total Reflection Fluorescence X-ray Absorption Fine Structure (PTRF-XAFS) is a method to analyze material structures by the X-ray absorption spectra that reveal symmetries or electronic states of atoms. Especially, by using the total reflection, it is efficient for the analysis of surface structure.

Open Data Analysis Tool for Science and Engineering (ODAT-SE) provides a framework for applying a search algorithm to a direct problem solver to find the optimal solution. It has been developed by the name 2DMAT, and since version 3.0, it is organized as an open platform for data analysis by modularizing direct problem solvers and search algorithms.

For the analysis of X-ray spectra, a first-principle calculation software, FEFF, has been developed that provides theoretical prediction of X-ray spectroscopy from the information of atomic positions. odatse-XAFS is an adaptor library to use FEFF as a direct problem solver of ODAT-SE.

Prerequisites

• Required
  • python >= 3.9
  • numpy >= 1.14
  • pydantic >= 2.0
  • ODAT-SE >= 3.0
  • FEFF 8.5 light, or later

Install

• From PyPI (Recommended)
  • python3 -m pip install -U odatse-XAFS
    • If you install them locally, use --user option like python3 -m pip install -U --user
• From Source (For developers)
  1. update pip >= 19 by python3 -m pip install -U pip
  2. python3 -m pip install ODATSE_XAFS_ROOT_DIRECTORY to install odatse-XAFS package and odatse-XAFS command
  • ODATSE_XAFS_ROOT_DIRECTORY means the directory including this README.md file.

Simple Usage

• odatse-XAFS input.toml (use the installed script)
• python3 src/main.py input.toml (use the raw script)
• For details of the input file, see the document.

Files and directories of odatse-XAFS

• src/
  • source codes
• sample/
  • sample usages
• doc/
  • source files of documents (manuals)
• tests/
  • for automatic test
• LICENSE
  • license terms (GNU GPL v3)
• README.md
  • this file
• pyproject.toml
  • metadata for odatse-XAFS

License

This package is distributed under GNU General Public License version 3 (GPL v3) or later.

We hope that you cite the following references when you publish the results using 2DMAT / ODAT-SE: "Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures", Y. Motoyama, K. Yoshimi, I. Mochizuki, H. Iwamoto, H. Ichinose, and T. Hoshi, Computer Physics Communications 280, 108465 (2022).

Bibtex:

@article{MOTOYAMA2022108465,
  title = {Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures},
  journal = {Computer Physics Communications},
  volume = {280},
  pages = {108465},
  year = {2022},
  issn = {0010-4655},
  doi = {https://doi.org/10.1016/j.cpc.2022.108465},
  url = {https://www.sciencedirect.com/science/article/pii/S0010465522001849},
  author = {Yuichi Motoyama and Kazuyoshi Yoshimi and Izumi Mochizuki and Harumichi Iwamoto and Hayato Ichinose and Takeo Hoshi}
}

Copyright

© 2024- The University of Tokyo. All rights reserved. This software was developed with the support of "Project for advancement of software usability in materials science" of The Institute for Solid State Physics, The University of Tokyo.