Equilibrium defect concentrations and solute site preference in intermetallic compounds

pydii requires pymatgen, sympy and monty packages and optionally VASP for full functionality.

If not available already, use the following steps.

1. Install git, if not already packaged with your system.

2. Download the pydii source code using the command:

   git clone https://github.com/pydii/pydii.git

Code Description ~~~~~~~~~~~ PyDII source code is in the folder ROOT_FOLDR/pydii. The ROOT_FOLDR is also named pydii. The root folder additional files for setup and one Examples folder that can be used to test run the code.

Within the pydii folder, the essential functionality is implemented in dilute_solution_model.py. Scripts to generate input files for VASP calculations, parsing vasp runs, and generate defect concentrations are in the scripts subfolder. The scripts

1. generate VASP input files for defect supercell calculations,
2. parse the output files from VASP calculations, and
3. generate defect concentration, defect formation energy and chemical potential data.

To test the programs fully, VASP is required. If VASP installation is not found, POTCAR file is not generated in step 1 and step 2 can not be performed. In case, the user uses alternative density functional packages for first principles calculations, the input to step 3 should be preparared in the json format given in examples/NiAl_mp-1487/mp-1487_raw_defect_energy.json. Contact the authors for any addition details.

1. Navigate to pydii root directory :

   cd pydii

2. Install the code, using the command :

   python setup.py install

   The command tries to obtain the required packages and their dependencies and install them automatically. Access to root may be needed if virtualenv is not used.

3. The package can be installed at non-standard locations using the command :

   python setup.py install --prefix PYDII_ROOTDIR

   where PYDII_ROOTDIR is your choice of directory. In UNIX/Linux environments, add PYDII_ROOTDIR to PATH and PYTHONPATH variables by the following commands :

   export PATH=$PATH:PYDII_ROOTDIR
   export PYTHONPATH=$PYTHONPATH:PYDII_ROOTDIR    

PyDII makes use of Materials Project (MP) database to get the crystal structure of the intermetallic. To access the MP database, MP API key is required. Please refer to https://materialsproject.org/open to obtain MP API key).

From the pydii, go to examples folder by typing:

cd examples

The examples folder contains two subfolders for Al3V and NiAl intermetallic systems. For a description of the compounds and how to generate the defect concentration profiles, refer to the manuscript.