DFT Tutorial

Beginner tutorial for Density Functional Theory (DFT) calculations using Quantum Espresso(QE) [1,2].

Required packages

• A working version of QE (>=6.4) needs to be installed/compiled and the executables needs to be located in the PATH environmental variable or specified manually in the variable BIN_DIR.
• A working version of gnuplot (>=5.0) (Some scripts will generate gnuplot files to plot the results. Other programs can also be used)
• A working version of XCrySDen (http://www.xcrysden.org/), a program that can visualize input and output files of QE.
• A working version of avogadro (https://avogadro.cc/), a program for creating and viewing molecular structures

Installing/Compiling QE

• QE can be installed from repository for Debian based linux distros (e.g.: Ubuntu) by running the command

  % sudo apt-get install quantum-espresso
  

  PS: The latest available version is shown at: https://packages.ubuntu.com/groovy/quantum-espresso (>6.5-1)

• QE can be compiled from source:

1. Download the desired release version from the GitHub page "https://github.com/QEF/q-e/releases".

2. Unzip/tar the downloaded package and go inside the folder.

3. From terminal run the commands

   % ./configure --prefix=path for installation
   % make all
   % make install
   

NOTE: options for the configuration / use of external libraries for optimized executables is beyond the purpose of this tutorial.

Downloading the exercises

To download the exercise repository, run

git clone https://github.com/cdhogan/DFT-basics.git DFT-basics
cd DFT-basics

The repository can be updated by running

git pull

Alternatively, you can download a static copy by browsing to https://github.com/cdhogan/DFT-basics , click the green Code button and Download zip (unzip to extract)

Overview of exercises

Bulk silicon (0_Si_bulk)

1. View an input file for a simple crystal and visualize it using xcrysden
2. Run a simple self-consistent calculation using pw.x
3. Determine the convergence with respect to the kinetic energy cutoff and k-point mesh
4. Determine the theoretical lattice parameter
5. Calculate a charge density and visualize it using XCrySDen
6. Generate a high-symmetry k-path using xcrysden and calculate a band structure using a non-self-consistent calculation

Two-dimensional boron nitride (1_BN)

1. How to use a supercell to simulate a material that is not periodic in all directions.
2. Compute the vacuum level and work function.

Graphene (2_Graphene)

1. Run calculation for a metallic/semimetallic system

Carbon monoxide molecule (3_CO)

1. Run a relax calculation and visualize the output using xcrysden
2. Run a calculation for a molecule (0D system)
3. Calculate the binding energy of a molecule
4. Visualize the HOMO and LUMO of a molecule (charge density for specific k-point and band)
5. Use a Lennard-Jones like potential to fit the data 'E_tot' vs 'bond length'

Optical properties and DOS (DOS_Opt)

1. Calculated the DOS and optical properties for systems of differing dimensionality

Computing arbitary materials (4_Create)

1. Set-up and calculate an arbitrary molecule
2. Make use of modern databases and tools to calculate an arbitrary crystal

Other folders

• Docs: Contain additional tutorials in pdf format
• Codes: Contain user-made code to analyze some of the data produced by QE
  1. broad.c (by Davide Grassano): Apply a gaussian broadening(to the y_n data) to a multicolumn file where the 1st column represents the x data and the 2nd,3rd,... columns represent the y_1, y_2, ... data.
  2. plot_pwbands.f90 (by C. Hogan): A code for generating plottable data from the pwscf output (obsolete)
• Pseudo: Contain the pseudopotential required to perform the exercises

Bibliography

1. P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, et al., Journal of physics: Condensed matter 21, 395502 (2009).
2. P. Giannozzi, O. Andreussi, T. Brumme, O. Bunau, M. B. Nardelli, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, M. Cococcioni, et al., Journal of Physics: Condensed Matter 29, 465901 (2017).