Metadata-Version: 2.3
Name: odatse-XAFS
Version: 1.0.0
Summary: PTRF-XAFS solver module for ODAT-SE: data-analysis software of quantum beam diffraction experiments for 2D material structure
License: GPL-3.0-or-later
Author: 2DMAT developers
Author-email: 2dmat-dev@issp.u-tokyo.ac.jp
Requires-Python: >=3.9
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Dist: ODAT-SE (>=3,<4)
Requires-Dist: numpy (>=1.14,<2.0)
Requires-Dist: pydantic (>=2,<3)
Project-URL: Repository, https://github.com/2DMAT/odatse-XAFS
Description-Content-Type: text/markdown

# 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)](https://github.com/issp-center-dev/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](https://feff.phys.washington.edu/), 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.

[source/master]: https://github.com/2DMAT/odatse-XAFS/
[source/develop]: https://github.com/2DMAT/odatse-XAFS/tree/develop
[ci/master/badge]: https://github.com/2DMAT/odatse-XAFS/workflows/Test/badge.svg?branch=master
[ci/master/uri]: https://github.com/2DMAT/odatse-XAFS/actions?query=branch%3Amaster
[doc/en/badge]: https://img.shields.io/badge/doc-English-blue.svg
[doc/ja/badge]: https://img.shields.io/badge/doc-Japanese-blue.svg
[doc/master/en/uri]: https://2DMAT.github.io/odatse-XAFS/manual/master/en/index.html
[doc/master/ja/uri]: https://2DMAT.github.io/odatse-XAFS/manual/master/ja/index.html
[doc/develop/en/uri]: https://2DMAT.github.io/odatse-XAFS/manual/develop/en/index.html
[doc/develop/ja/uri]: https://2DMAT.github.io/odatse-XAFS/manual/develop/ja/index.html

