Author: John Kitchin

Introduction to this book

This book serves two purposes: 1) to provide worked examples of using DFT to model materials properties, and 2) to provide references to more advanced treatments of these topics in the literature. It is not a definitive reference on density functional theory. Along the way to learning how to perform the calculations, you will learn how to analyze the data, make plots, and how to interpret the results. This book is very much “recipe” oriented, with the intention of giving you enough information and knowledge to start your research. In that sense, many of the computations are not publication quality with respect to convergence of calculation parameters.

You will read a lot of python code in this book. I believe that computational work should always be scripted. Scripting provides a written record of everything you have done, making it more probable you (or others) could reproduce your results or report the method of its execution exactly at a later time.

This book makes heavy use of many computational tools including:

• Python

  • Module index

• Atomic Simulation Environment (ase)

• numpy

• scipy

• matplotlib

• emacs

  • org-mode This book is written in org-mode, and is best read in emacs in org-mode. This format provides clickable links, easy navigation, syntax highlighting, as well as the ability to interact with the tables and code. The book is also available in PDF.

• git This book is available at jkitchin/dft-book

• vasp This is the Python module used extensively here. It is available at jkitchin/vasp

The DFT code used primarily in this book is VASP.

• VASP wiki

• VASP Manual

Similar code would be used for other calculators, e.g. GPAW, Jacapo, etc… you would just have to import the python modules for those codes, and replace the code that defines the calculator.

Review all the hyperlinks in this chapter.

Acknowledgments

I would like to thank Zhongnan Xu for sending me some examples on magnetism. Alan McGaughey and Lars Grabow for sending me some NEB examples. Matt Curnan for examples of phonons.

Many thanks to students in my class who have pointed out typos, places of confusion, etc… These include Bruno Calfa, Matt Curnan, Charlie Janini, Feng Cao, Gamze Gumuslu, Nicholas Chisholm, Prateek Mehta, Qiyang Duan, Shubhaditya Majumdar, Steven Illes, Wee-Liat Ong, Ye Wang, Yichun Sun, Yubing Lu, and Zhongnan Xu.