Introduction

What is ODAT-SE ?

ODAT-SE is a framework for applying a search algorithm to a direct problem solver to find the optimal solution. As the standard direct problem solver, the experimental data analysis software for two-dimensional material structure analysis is prepared. The direct problem solver gives the deviation between the experimental data and the calculated data obtained under the given parameters such as atomic positions as a loss function used in the inverse problem. The optimal parameters are estimated by minimizing the loss function using a search algorithm. For further use, the original direct problem solver or the search algorithm can be defined by users. In the current version, for solving a direct problem, ODAT-SE offers the wrapper of the solver for the total-reflection high-energy positron diffraction (TRHEPD), the surface X-ray diffraction (SXRD), and the low-energy electron diffraction (LEED). As algorithms, it offers the Nelder-Mead method, the grid search method, the Bayesian optimization method, the replica exchange Monte Carlo method, and the population annealing Monte Carlo method.

What is odatse-SXRD ?

sxrdcalc [1] has been developed as a software package for the analyses of the surface X-ray diffraction data, which calculates the X-ray diffraction intensity from surface, the Patterson map of experimental data, and the fitting of model structure to the experimental data by Levenberg-Marquadt method or simulated annealing method. odatse-SXRD is an adaptor library to use sxrdcalc as a direct problem solver of ODAT-SE. It was originally developed as a component of 2DMAT v2.x, and has been restructured as a separate module to be used with ODAT-SE and sxrdcalc.

[1] W. Voegli, et. al., Applied Surface Science 252, 5259 (2006).

License

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

Copyright (c) <2020-> 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. We hope that you cite the following reference when you publish the results using 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}
}

Version Information

odatse-SXRD

  • v1.0.0: 2024-11-25

ODAT-SE

  • v3.0.0: 2024-11-25

2DMAT

  • v2.1.0: 2022-04-08

  • v2.0.0: 2022-01-17

  • v1.0.1: 2021-04-15

  • v1.0.0: 2021-03-12

  • v0.1.0: 2021-02-08

Main developers

ODAT-SE, odatse-SXRD, 2DMAT has been developed by following members.

  • ODAT-SE v3.0.0 -, odatse-SXRD v1.0.0 -

      1. Motoyama (The Institute for Solid State Physics, The University of Tokyo)

      1. Yoshimi (The Institute for Solid State Physics, The University of Tokyo)

      1. Aoyama (The Institute for Solid State Physics, The University of Tokyo)

      1. Hoshi (National Institute for Fusion Science)

  • 2DMAT v2.0.0 -

      1. Motoyama (The Institute for Solid State Physics, The University of Tokyo)

      1. Yoshimi (The Institute for Solid State Physics, The University of Tokyo)

      1. Iwamoto (Department of Applied Mathematics and Physics, Tottori University)

      1. Hoshi (Department of Applied Mathematics and Physics, Tottori University)

  • 2DMAT v0.1.0 - v1.0.1

      1. Motoyama (The Institute for Solid State Physics, The University of Tokyo)

      1. Yoshimi (The Institute for Solid State Physics, The University of Tokyo)

      1. Hoshi (Department of Applied Mathematics and Physics, Tottori University)