pymatgen-analysis-defects 2022.9.14

Pymatgen extension for defects analysis

📄 Full Documentation

This package is an extension to pymatgen for performing defect analysis. The package is designed to work with VASP inputs and output files and is meant to be used as a namespace package extension to the main pymatgen library. The new module has been redesigned to work closely with atomate2.

While the atomate2 automation framework is not required for this code to be useful, users are strongly encouraged to to adopt the atomate2 framework as it contains codified “best practices” for running defect calculations as well as orchestrating the running of calculations and storing the results.

Non-exhaustive list of features:

Reproducible definition of defects

Defects are defined based on the physical concept they represent, independent of the calculation details such as simulation cell size. As an example, a Vacancy defect is defined by the primitive cell of the pristine material plus a single site that represents the vacancy site in the unit cell.

Formation energy calculations

The formation energy diagram is a powerful tool for understanding the thermodynamics of defects. This package provides a simple interface for calculating the formation energy diagram from first-principles results.

The package handles the energy accounting of the chemical species for the chemical potential calcultions, which determines the y-offset of the formation energy.

Previous versions of the defects code

This package replaces the older pymatgen.analysis.defects modules. The previous module was used by pyCDT code which will continue to work with version 2022.7.8 of pymatgen.

Contributor

• Lead developer: Dr. Jimmy-Xuan Shen

• This code is a re-write of the defects analysis module of pymatgen from Dr. Danny Broberg and Dr. Shyam Dwaraknath.