Installation

pip install doped  # install doped and dependencies

Alternatively if desired, doped can also be installed from conda with:

conda install -c conda-forge doped

Setup POTCARs and Materials Project API

To generate VASP POTCAR input files, and auto-determine INCAR settings such as NELECT for charged defects, your POTCAR directory needs to be setup to work with pymatgen (via the ~/.pmgrc.yaml file).

Instructions:

1. Set the VASP pseudopotential directory and your Materials Project API key in $HOME/.pmgrc.yaml (pymatgen config file) as follows:

PMG_VASP_PSP_DIR: <Path to VASP pseudopotential top directory>
PMG_MAPI_KEY: <Your MP API key obtained from https://legacy.materialsproject.org/open>

Within your VASP pseudopotential top directory, you should have a folder named POT_GGA_PAW_PBE/potpaw_PBE.54/POT_GGA_PAW_PBE_54 which contains POTCAR.X(.gz) files, generated using pmg config.

2. If you have not previously setup your POTCAR directory in this way with pymatgen, then follow these steps:

   mkdir temp_potcars  # make a top folder to store the unzipped POTCARs
   mkdir temp_potcars/POT_PAW_GGA_PBE  # make a subfolder to store the unzipped POTCARs
   mv potpaw_PBE.54.tar.gz temp_potcars/POT_PAW_GGA_PBE  # copy in your zipped VASP POTCAR source
   cd temp_potcars/POT_PAW_GGA_PBE
   tar -xzf potpaw_PBE.54.tar.gz  # unzip your VASP POTCAR source
   cd ../..  # return to the top folder
   pmg config -p temp_potcars psp_resources  # configure the psp_resources pymatgen POTCAR directory
   pmg config --add PMG_VASP_PSP_DIR "${PWD}/psp_resources"  # add the POTCAR directory to pymatgen's config file ($HOME/.pmgrc.yaml)
   rm -r temp_potcars  # remove the temporary POTCAR directory
   

3. If this has been successful, you should be able to run the shell commands:

   pmg potcar -s Na_pv
   grep PBE POTCAR
   

   Which should then show PAW_PBE Na_pv {date} as the output (you can ignore any pymatgen warnings about recognising the POTCAR type).

4. If this does not work, you may need to add this to the .pmgrc.yaml file:

   PMG_DEFAULT_FUNCTIONAL: PBE  # whatever functional label your POTCARs have
   

   Note the Materials Project API key is required for determining the necessary competing phases to calculate in order to determine the chemical potential limits (required for defect formation energies). This should correspond to the legacy MP API, with your unique key available at: https://legacy.materialsproject.org/open.

Developer Installation

If you want to use the example files from the tutorials or run the package tests, you will need to clone the doped GitHub repository:

1. Download the doped source code using the command:

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

1. Navigate to root directory:

cd doped

1. Install the code, using the command:

pip install -e .

Requirements

doped requires pymatgen>=2022.10.22 and its dependencies.