odatse-STR: solver module for analyses of TRHEPD data

Open Data Analysis Tool for Science and Engineering (ODAT-SE) is 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.

sim-trhepd-rheed has been developed as a simulator software package for the total-reflection high-energy positron diffraction (TRHEPD) and the reflection high energy electron diffraction (RHEED). It takes atom positions as input and calculates the Rocking Curve of the diffraction intensity. The program is written in Fortran and runs on ordinary Linux environment. odatse-STR is an adaptor library to use sim-trhepd-rheed as a direct problem solver of ODAT-SE.

Prerequisites

• Required
  • python >= 3.9
  • numpy >= 1.14
  • pydantic >= 2.0
  • ODAT-SE >= 4.0
  • sim-trhepd-rheed >= 1.0.2

Supported versions of ODAT-SE

odatse-STR is maintained in two release lines, one for each major version of ODAT-SE. Choose the odatse-STR version that matches your ODAT-SE installation.

• odatse-STR 1.1.x requires ODAT-SE 4.0 or later and does not work with ODAT-SE 3.x. It follows the solver API of ODAT-SE 4: user programs that create the Solver object themselves must call odatse.mpi.setup() first (programs using odatse.initialize() or the odatse-STR command are not affected), and the solver-level MPI parallelization of ODAT-SE 4 (--nsolve greater than 1) is not supported because sim-trhepd-rheed runs serially.
• odatse-STR 1.0.x works with ODAT-SE 3.x (3.1 or later is recommended). Bug fixes are backported to this line, but new features are not.
• The main branch holds the latest line. To obtain the 1.0.x line for ODAT-SE 3, check out the release-1.0 branch or a v1.0.* tag, for example git clone -b release-1.0 https://github.com/2DMAT/odatse-STR.git, or download the corresponding archive from the Releases page.

Install

• From Source
  1. update pip >= 19 by python3 -m pip install -U pip
  2. python3 -m pip install ODATSE_STR_ROOT_DIRECTORY to install odatse-STR package and odatse-STR command
  • ODATSE_STR_ROOT_DIRECTORY points to the directory including this README.md file.
  • If you install them locally, use --user option like python3 -m pip install -U --user

Simple Usage

• odatse-STR 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-STR

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

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

© 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.