Modelling Materials with Density Functional Theory

Introduction

This is the lab material for the Imperial College London, Department of Materials course "MSE404: Modelling Materials with Density Functional Theory".

This course is intended to introduce students to the modelling of materials with density-functional theory (DFT). In the labs we will use the free, open-source DFT code Quantum Espresso, but while the format of the input files may change in other DFT codes, the general principles will be the same. The labs will also briefly introduce student to the use of the Linux OS and how it enables the effective use of computational resources, as well as showing students some simple scripting, analysis, and visualization tools.

Structure of the Labs

The labs are organised as follows:

• Lab 1: Getting started in Linux
• Lab 2: Quantum Espresso Input and Output
• Lab 3: Converging your Calculations
• Lab 4: The Electronic Band Structure and Density of States
• Lab 5: Forces, Stresses and Structures
• Lab 6: Vibrational Frequencies and Normal Modes
• Lab 7: Finite Temperature Properties
• Lab 8: Spin Polarization and Magnetic Systems
• Lab 9: Optical Properties and Time-Dependent Density Functional Theory

Additional Material:

• Calculating Useful Properties from Total Energies
• Examining the Charge Density and Wavefunction
• The Hydrogen Atom and Electron Spin
• The Tetrahedron Method for Densities of States
• Optical Properties and Time-Dependent Density Functional Theory

Extras:

• Setting up a virtual machine
• More Useful Linux Commands
• Plotting with Gnuplot
• Bash and Shell Scripting
• Running in Parallel

How to Use this Material

The latest version of the course is available online at https://imperialcollegelondon.github.io/MSE404-MM/. The text source files named readme.md in the various directories use markdown. You can download the whole repository and view them in a terminal, or read them at the Github site https://imperialcollegelondon.github.io/MSE404-MM/.

Each lab is designed to be self-contained. The webpage will show the general direction and explain the concepts, while the input files and scripts are stored in directories located along side the readme.md file, labeled by their apparences in the text.

There will be code blocks like the one below in the text

echo "Hello World"

which are meant to be run in the terminal. And you can click the icon on the right to copy the code to your clipboard.

There will also be inline annotations () like the one below:

program hello
    print *, "Hello World" !(1)
end program hello

1. Print the string "Hello World" to the terminal.

You can click on the annotation to see the explanation.

There will also be admonitions like the one below:

Coder's Tip [important]

Don'f forget to add comments to your code to explain what you are doing!

Coder's Tip [side-note]

Don't forget to sleep and eat! (well, this is important too!)

where important/optional information is given. Also, the Tasks will also be marked as admonitions like the one below:

Taks 1 - Read me

Read this readme.md file.

Admin resources

• Contributing
• Server config

Acknowledgements

• Original materials provided by Éamonn Murray (https://gitlab.com/eamonnmurray/MaterialsModelling)
• Contributors: Simão João, Christopher Cheung, Jordan Edwards, Chengcheng Xiao, Indrajit Maity, Valerio Vitale, Laura Ratcliff and Johannes Lischner.
• Webpage refreshed by Chengcheng Xiao, 2024.