Installation of ODAT-SE

Prerequisites

  • Python3 (>=3.9)

    • The following Python packages are required.

      • tomli >= 1.2

      • numpy >= 1.14

    • Optional packages

      • mpi4py (required for grid search)

      • scipy (required for Nelder-Mead method)

      • physbo (>=2.0, required for Baysian optimization)

How to download and install

You can install the ODAT-SE python package and the odatse command following the instructions shown below.

  • Installation using PyPI (recommended)

    • python3 -m pip install ODAT-SE

      • --user option to install locally ($HOME/.local)

      • If you use ODAT-SE[all], optional packages will be installed at the same time.

  • Installation from source code

    1. git clone https://github.com/issp-center-dev/ODAT-SE

    2. python3 -m pip install ./ODAT-SE

      • The pip version must be 19 or higher (can be updated with python3 -m pip install -U pip).

  • Download the sample files

    • Sample files are included in the source code.

    • git clone https://github.com/issp-center-dev/ODAT-SE

How to run

In ODAT-SE, the analysis is carried out by using a predefined optimization algorithm Algorithm and a direct problem solver Solver.

$ odatse input.toml

See Search algorithms for the predefined Algorithm and Direct Problem Solver for the Solver.

The direct problem solvers for analyses of experimental data of two-dimensional material structure are provided as separate modules. To perform these analyses, you need to install the modules and the required software packages. At present, the following modules are provided:

  • odatse-STR module for Total Refrection High-energy Positron Diffraction (TRHEPD)

  • odatse-SXRD module for Surface X-ray Diffraction (SXRD)

  • odatse-LEED module for Low-energy Electron Diffraction (LEED)

If you want to prepare the Algorithm or Solver by yourself, use the ODAT-SE package. See (For developers) User-defined algorithms and solvers for details.

The program can be executed without installing odatse command; instead, run src/odatse_main.py script directly as follows. It would be convenient when you are rewriting programs.

$ python3 src/odatse_main.py input

How to uninstall

Please type the following command:

$ python3 -m pip uninstall ODAT-SE