Equilibrium defect concentrations and solute site preference in intermetallic compounds.

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

If not available already, use the following steps.

1. Install git if it's 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 ~~~~~~~~~~~ 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

1. Generate VASP input files for defect supercell calculations.
2. Parse the output files from VASP calculations.
3. 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.

1. Navigate to the 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. Alternatively you can try :

pip install . --user

1. 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

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.

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).

Version 2.0 ----------

Starting with version 1.9 (pre-release version of 2.0), the signature of the parser data is changing. So data files produced with PyDII codes with different versions may not work. Please report any bugs on the Issues tracker.

Optionally, instead of specifying mpid, users can use their own structures to run the PyDII calculations, as long as the structure is compatible with Pymatgen. Use the -h flag for more information.