zhubonan / doped

Collection of Python modules & functions to perform and process solid-state defect calculations

Defect Oriented Python Environment Distribution (doped)

This is a (mid-development) Python package for managing solid-state defect calculations, geared toward VASP. Much of it is a modified version of the excellent PyCDT.
See this link for the original PyCDT paper.

Defect formation energy plots are templated from AIDE and follow the aesthetics philosopy of sumo, both developed by the dynamic duo Adam Jackson and Alex Ganose.

Example Jupyter notebooks (the .ipynb files) are provided in examples to show the code functionality and usage.

Requirements

doped requires pymatgen<2022.8.23 and its dependencies.

Installation

• Because of breaking changes made to the pymatgen defects code in version 2022.8.23, doped requires pymatgen<2022.8.23, which is installed automatically when installing doped. However, as discussed briefly below and in the example notebooks, the ShakeNBreak approach is highly recommended when calculating defects in solids, and this package has been updated to be compatible with the latest version of pymatgen. As such, it is recommended to install doped in a virtual python environment as follows:

conda create -n doped  # create conda environment named doped
conda activate doped  # activate doped conda environment
pip install doped  # install doped package and dependencies

And then use this environment whenever using doped. Instead of conda you can also use venv to setup virtual environments, see here for more.

If you want to use the example files, you should clone the repository and install with pip install -e . from the doped directory.

2. (If not set) Set the VASP pseudopotential directory in $HOME/.pmgrc.yaml as follows::

  PMG_VASP_PSP_DIR: <Path to VASP pseudopotential top directory>

Within your VASP pseudopotential top directory, you should have a folder named POT_GGA_PAW_PBE which contains the POTCAR.X(.gz) files (in this case for PBE POTCARs).

(Necessary to generate POTCAR files, auto-determine INCAR settings such as NELECT for charged defects...) See here if you have issues with this.

3. (Optional) Set the Materials Project API key in $HOME/.pmgrc.yaml as follows::

  MAPI_KEY: <Your mapi key obtained from www.materialsproject.org>

(For pulling structures and comparing properties with the Materials Project database).

ShakeNBreak

As shown in the example notebook, it is highly recommended to use the ShakeNBreak approach when calculating point defects in solids, to ensure you have identified the groundstate structures of your defects. As detailed in the theory paper, skipping this step can result in drastically incorrect formation energies, transition levels, carrier capture (basically any property associated with defects). This approach is followed in the doped example notebook, with a more in-depth explanation and tutorial given on the ShakeNBreak website.

Summary GIF:

SnB CLI Usage:

Developer Installation

1. Download the doped source code using the command:

  git clone https://github.com/SMTG-UCL/doped

2. Navigate to root directory:

  cd doped

3. Install the code, using the command:

  pip install -e .

Acknowledgments

doped has benefitted from feedback from many users, in particular members of the Walsh and Scanlon research groups who have used / are using it in their work. Direct contributors are listed in the Contributors sidebar above; including Seán Kavanagh, Katarina Brlec, Adair Nicolson and Sabrine Hachmioune. Code to efficiently identify defect species from input supercell structures was contributed by Dr Alex Ganose.