Installation of ODAT-SE

Prerequisites

  • Python3 (>=3.9)

    • The following Python packages are required:

      • tomli >= 1.2 : For reading configuration files in TOML format

      • numpy >= 1.14 : For numerical calculations

    • Optional packages (required for specific optimization methods):

      • mpi4py : For parallelization and speedup when using grid search

      • scipy : For optimization using the Nelder-Mead method

      • physbo (>=2.0) : For Bayesian 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:

  • Total Reflection High-energy Positron Diffraction (TRHEPD) – odatse-STR package A high-precision method for surface structure analysis.

  • Surface X-ray Diffraction (SXRD) – odatse-SXRD package An X-ray diffraction method for investigating atomic arrangements at surfaces and interfaces.

  • Low-energy Electron Diffraction (LEED) – odatse-LEED package An electron diffraction method for studying crystal structures of solid surfaces.

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.toml

Verifying the installation

To verify that the installation was completed successfully, run the following commands:

$ odatse --version
$ odatse --help

How to uninstall

To uninstall the ODAT-SE module, please run the following command:

$ python3 -m pip uninstall ODAT-SE

If you need to uninstall related optional packages individually, you can run similar commands for each package.