Framework for first-principles calculations of charged dopants and defects in 2D materials

qdef2d [tentative name, work-in-progress] is a python package that aims to help automate and accelerate the setting up and post-processing of charged defect calculations in 2D materials. This will enable the rapid and robust evaluation of defect structures, formation energies, and electronic properties for different types of defects in a wide range of 2D materials to create a new database of defects in 2D and layered bulk materials. The modules and scripts are currently set up to work with VASP input/output files and the University of Florida's high performance computing cluster, HiPerGator.

Requirements:

• python3 environment with the following packages installed: numpy, pymatgen, pandas (+ openpyxl), matplotlib
• download the sxdefectalign2d script which we will be using to apply the Freysoldt-Neugebauer 2D charge correction scheme.

qdef2d package:

qdef2d
|-- io
|   |-- vasp
|   |   |-- incar.py
|   |   |-- kpoints.py
|   |   |-- submit.py
|   |   |-- parse_energies.py
|   |-- database
|       |-- database_entry.py
|-- defects
|   |-- core.py
|   |-- gen_defect_supercell.py
|   |-- setup_defect_calcs.py
|   |-- calc_Eform_uncorr.py
|   |-- calc_Eform_corr.py
|   |-- corrections
|       |-- SPHInX_input_file.py
|       |-- alignment_correction_2d.py
|       |-- apply_corrections_2d.py
|       |-- parse_corrections.py
|-- logging.py
|-- osutils.py
|-- slabutils.py

• incar.py, kpoints.py, submit.py: functions for generating VASP input files, job submission script
• parse_energies.py: function/script to parse total energies from VASP OUTCARs and save into a pandas dataframe.
• database_entry.py: functionalities related to creating, manipulating, and reading simple database entries [should be replaced with interface to actual mongodb database, e.g. on MaterialsWeb]
• core.py: defines Defect object, includes functionalities for creating different types of defects
• gen_defect_supercell.py, setup_defect_calcs.py: functions/scripts to generate defect supercell, VASP input files for defect supercell calculations
• calc_Eform_uncorr.py, calc_Eform_corr.py: functions/scripts to evaluate the un-corrected and corrected defect formation energies and save into a pandas dataframe.
• SPHInX_input_file.py, alignment_correction_2d.py, apply_corrections_2d.py, parse_corrections.py: functions/scripts to generate the input file for the charge correction, apply the charge correction, and parse the results into a pandas dataframe.
• logging.py, osutils.py, slabutils.py: additional utility functions

Additional documentation can be found in the source codes, accessed via the help() function, or with the --h flag from the command line.

Jupyter tutorials:

These jupyter notebooks demonstrate how to make use of the modules and scripts in qdef2d to set up, execute, and analyze the results of DFT calculations to obtain various properties of 2D materials. They are meant to be executed on HiPerGator, where pre-calculated examples can also be found.

• tutorial_2D_pristine.ipynb: general tutorial about how to calculate some basic properties (lattice constant, band structure, dielectric tensor) of pristine 2D materials.
• tutorial_2D_defects.ipynb: tutorial about how to correctly evaluate the formation energies of charged defects in 2D materials.

Authors:

Anne Marie Z. Tan

How to cite:

BibTex entry for this Github repository::

   @misc{charged-defects-framework,
     title        = {Framework for first-principles calculations of charged dopants and defects in 2D materials},
     author       = {A. M. Z Tan},
     year         = 2019,
     publisher    = {GitHub},
     journal      = {GitHub repository},
     howpublished = {\url{https://github.com/aztan2/charged-defects-framework}},
     url          = {https://github.com/aztan2/charged-defects-framework},
     doi          = {}
   }