PyDII

Equilibrium defect concentrations and solute site preference in intermetallic compounds.

Requirements

PyDII requires Python 3.4+, Pymatgen, SymPy, and Monty packages and optionally VASP for full functionality.

Source Code

Obtaining

If not available already, use the following steps.

Install git if it's not already packaged with your system.
Download the PyDII source code using the command:
```
git clone https://github.com/pydii/pydii.git
```

Code Description

The PyDII source code is in the folder ROOT_FOLDR/pydii. The ROOT_FOLDR is also named pydii. The root folder contains additional files for setup and one examples folder that can be used to test the code.

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

Generate VASP input files for defect supercell calculations.
Parse the output files from VASP calculations.
Generate defect concentration, defect formation energy, and chemical potential data.

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

Installation

Navigate to the PyDII root directory
```
cd pydii
```
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. Alternatively you can try

pip install . --user
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, which you can add to your .bashrc file
```
export PATH=$PATH:PYDII_ROOTDIR
export PYTHONPATH=$PYTHONPATH:PYDII_ROOTDIR
```

Materials Project API key

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

Examples

From the PyDII root directory, go to the 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: Ding, H. et al, Computer Physics Communications, 193, (2015).

mbkumar / pydii-1