pydefect

Pydefect is a robust, open-source Python library for point-defect calculations in non-metallic solids based on first-principle calculations with the VASP code.

Note: Units used in pydefect are eV for energy and angstrom for length following the vasp convention.

Installation instructions

Requirements

Python 3.7 or higher
vise
pymatgen
see requirements.txt for others

Latest stable version is released at PyPI repository, so one can download it using pip install pydefect.
After cloning the repository, it is possible to install pydefect using the python package manager pip. To do so, run this command in the directory containing setup.py:

pip install ./

Sometimes errors will be given if a specific version of a package is not installed. In this case try installing the exact versions that have been tested for use with pydefect with the following command:

pip install -r requirements.txt ./

This will install the package versions listed in the requirements.txt file. To prevent interference with other programmes, it is advised that a package management system like conda is used. This allows you to install dependencies in a particular environment so that they can be managed and recorded more easily. The commands above can then be executed in a conda environment (after installing pip in that environment).

For more information on how dependencies are managed in this branch see this blog post.

Executing this software

Detailed information is provided in the online manual at: https://kumagai-group.github.io/pydefect/

Files and directories included in pydefect distribution

  README                 : introduction
  LICENSE                : the MIT license 
  setup.py               : installation script
  requirements.txt       : list of required packages

  /pydefect/analyzer     : analysis tools for point-defect calculations
  /pydefect/chem_pot_diag: tools for calculating and drawing the chemical potential diagram
  /pydefect/cli          : command line interfaces
  /pydefect/corrections  : energy and eigenvalue correction related modules
  /pydefect/database     : database related to atoms and symmetries
  /pydefect/input_maker  : tools for generating VASP input files
  /pydefect/tests        : test files used mainly for unittests
  /pydefect/util         : useful tools

License

Python code is licensed under the MIT License.

Development notes

Bugs, requests and questions

Please use the Issue Tracker to report bugs, request features.

Code contributions

Although pydefect is free to use, we sincerely appreciate if you help us to improve this library. The simplest but most valuable contribution is to send the feature requests and bug reports.

Please report any bugs and issues at PyDefect's GitHub Issues page. Please use the "Fork and Pull" workflow to make contributions and stick as closely as possible to the following:

Code style follows PEP8 and Google's writing style.
Add unittests wherever possible including scripts for command line interfaces.

Tests

Run the tests using pytest pydefect. We also use integrated testing on GitHub via circleCI.

Citing pydefect

If pydefect has been used in your research, please cite the following paper.

"Insights into oxygen vacancies from high-throughput first-principles calculations"
Yu Kumagai, Naoki Tsunoda, Akira Takahashi, and Fumiyasu Oba
Phys. Rev. Materials 5, 123803 (2021)

Contact info

Yu Kumagai
yukumagai@tohoku.ac.jp

Tohoku University (Japan)

Shibu778/pydefect