doped: Python toolkit for robust and repeatable charged defect supercell calculations

doped: Python toolkit for robust and repeatable charged defect supercell calculations

15 April 2024 | Seán R. Kavanagh, Alexander G. Squires, Adair Nicolson, Irea Mosquera-Lois, Alex M. Ganose, Bonan Zhu, Katarina Brlec, Aron Walsh, and David O. Scanlon
doped is a Python package designed for the generation, pre- and post-processing, and analysis of defect supercell calculations. It aims to provide a robust, user-friendly, and efficient platform for conducting reproducible calculations of solid-state defect properties. The software is built to implement the defect simulation workflow in an efficient and flexible manner, combining reasonable defaults with full user control. doped includes functionalities for generating defect supercells, estimating charge states, selecting competing phases, and analyzing defect thermodynamics. It also provides automated symmetry and degeneracy handling, compatibility checking, and finite-size corrections. The package supports a wide range of DFT codes and is compatible with high-throughput architectures. doped has been used in several publications to manage defect simulation workflows. It includes features such as automated plotting, tabulation, and compatibility with other computational toolkits. The software is open-source and released under a Creative Commons Attribution 4.0 International License. The authors of the paper retain copyright but have released the work under the license. The software has been reviewed and published in the Journal of Open Source Software.doped is a Python package designed for the generation, pre- and post-processing, and analysis of defect supercell calculations. It aims to provide a robust, user-friendly, and efficient platform for conducting reproducible calculations of solid-state defect properties. The software is built to implement the defect simulation workflow in an efficient and flexible manner, combining reasonable defaults with full user control. doped includes functionalities for generating defect supercells, estimating charge states, selecting competing phases, and analyzing defect thermodynamics. It also provides automated symmetry and degeneracy handling, compatibility checking, and finite-size corrections. The package supports a wide range of DFT codes and is compatible with high-throughput architectures. doped has been used in several publications to manage defect simulation workflows. It includes features such as automated plotting, tabulation, and compatibility with other computational toolkits. The software is open-source and released under a Creative Commons Attribution 4.0 International License. The authors of the paper retain copyright but have released the work under the license. The software has been reviewed and published in the Journal of Open Source Software.
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