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A Practical Introduction to Density Functional Theory

Rademaker, Louk

How to cite

RADEMAKER, Louk. A Practical Introduction to Density Functional Theory. 2020. doi:

10.48550/arXiv.2011.09888

This publication URL: https://archive-ouverte.unige.ch/unige:165812

Publication DOI: 10.48550/arXiv.2011.09888

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 SciPost Physics Lecture Notes Submission

A Practical Introduction to Density Functional Theory

L. Rademaker1*

1 Department of Theoretical Physics, University of Geneva, 1211 Geneva, Switzerland

* louk.rademaker@gmail.com
arXiv:2011.09888v1 [cond-mat.mtrl-sci] 19 Nov 2020

November 20, 2020

Abstract
These lecture notes contain a brief practical introduction to doing density func-
tional theory calculations for crystals using the open source Quantum Espresso
software. The level is aimed at graduate students who are studying condensed
matter or solid state physics, either theoretical or experimental.

Contents
1 Introduction: What is Density Functional Theory? 2
1.1 Born-Oppenheimer approximation 3
1.2 Hohenberg-Kohn theory 3
1.3 Approximating the functional 4
1.4 Kohn-Sham equation 5
1.5 Limitations 5

2 A Practical Guide 6
2.1 Wavefunction basis sets 7
2.2 Which functional? 7
2.3 Pseudopotentials 7
2.4 Quantum ESPRESSO 8
2.5 Materials Cloud 8

3 Example 1: Silicon 9
3.1 Self-consistent field 9
3.1.1 Writing the input file 9
3.1.2 Running the code 12
3.1.3 Reading the output 12
3.2 Homework: Find the lattice constant and bulk modulus of silicon 12
3.3 Bands 13
3.4 Try at home 15

4 Example 2: Graphene 15
4.1 Compute the band-structure 15

5 Example 3: WSe2 17

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5.1 Relax 18
5.2 Spin-orbit coupling 19

6 Further learning 20

References 21

Preface
These notes were developed for a short 4-hour course on density functional theory (DFT)
given in March 2020 at the University of Geneva. The lectures were the first instalment of
the ’ToolBoX’ series of lectures on different modern tools used in condensed matter physics.
We require basic knowledge of solid state physics and quantum mechanics - most importantly
band theory. Other than that, the idea is to be very practical. Making your hands dirty with
an actual calculation is, after all, the most reliable method of learning something.
Below, we will first give a speeding review of what DFT is in Sec. 1. How to prepare a DFT
calculation is discussed in Sec. 2. The remaining sections contain three hands-on examples of
real-world materials whose properties can teach us something about how to do DFT: silicon,
graphene and WSe2 . You are supposed to work out these examples yourself, but lazy students
can download the set of input files and pseudopotentials here: http://loukrademaker.nl/
dft_files/.This course is nowhere intended to make you a world-expert; rather, it gives you
a good head start and in Sec. 6 we mention some further places you can learn about DFT.

1 Introduction: What is Density Functional Theory?

Any material on earth, whether in crystals, amorphous solids, molecules or yourself, consists
of nothing else than a bunch of atoms, ions and electrons bound together by electric forces.
All these possible forms of matter can be explained by virtue of one simple equation: the
many-particle Schrödinger equation,
 
N 2 2 N 2Z Z
∂ X h̄ ∂ X e i j 
ih̄ Φ(r; t) = − + Φ(r; t). (1)
∂t 2mi ∂r2i |ri − rj |
i i<j

Here Φ(r; t) is the many-body wavefunction for N particles, where each particle has its own
mass mi , charge Zi and position ri . The only interaction is the Coulomb interaction e2 /r.
Despite its apparent simplicity, Eq. (1) is notoriously difficult to solve. This is where
density functional theory (DFT) comes in. Using a set of reasonable physical approximations
we can simplify the many-particle Schrödinger equation to something that we can actually
solve numerically.

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1.1 Born-Oppenheimer approximation

The first approximation arises from the physical problem we want to study: the ground state
of a collection of interacting ions and electrons. Because even the lightest ion is more than
a thousand times heavier than an electron, we will forget about the dynamics of the ions
all-together. This is known as the Born-Oppenheimer approximation. We then write the
time-independent Schrödinger equation for a collection of N electrons subject to the electric
potential created by the fixed ions,
 
N  2 2
 XN 2
X h̄ ∂ e
 − + V (ri ) +  Ψ(r) = E0 Ψ(r) (2)
2m ∂r2i |ri − rj |
i i<j

where ri are the positions of the electrons. The potential V (ri ) is created by the charged ions,
X e2 Zj
V (ri ) = − (3)
|ri − Rj |
j

where R is the (static) positions of the ions and Zj their charge. Note that the above
Hamiltonian – the left hand side of Eq. (2) – contains three terms: the kinetic energy (T ),
the potential energy (V ) and the interaction energy (U ).
The electronic density is obtained by integrating out all electron degrees of freedom except
one, Z
n(r) = d3 r2 · · · d3 rN |Ψ(r1 · · · rn )|2 . (4)

The total potential energy V is just given by the integral over the potential V (r) times the
density, Z
V = d3 rV (r)n(r). (5)

1.2 Hohenberg-Kohn theory

Assume we found a solution of Eq. (2), with ground state energy E0 and a certain electronic
density n(r). The strength of the Coulomb interaction and the mass of an electron are
constants of nature, so the only input that can possibly influence the electronic density n(r)
and the energy E0 of our ground state is our choice of potential V (r). In other words, the
ground state energy is a functional of the input potential,

E0 [V (r)] = FE [V (r)] (6)

A functional is nothing else than a function whose input is another function; in this case
the functional F takes as input the electric potential generated by the ions and outputs the
ground state energy based on Eq. (2).
At first this results seems counterintuitive. After all, the ground state energy clearly
contains the kinetic energy T , the interaction energy U and the potential energy. Only the
latter term explicitly depends on the potential. We can thus write the ground state energy in
terms of a separate functional for the kinetic and interaction energy, and the potential energy
Z
0
E[n(r)] = FE [V (r)] + d3 rV (r)n(r) (7)

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Hohenberg and Kohn [1] came to the elegant insight that the potential V (r) and electronic
density n(r) are conjugate variables. Other conjugate variables you may know are for example
pressure and volume in thermodynamics or momentum and position in classical physics. The
fact that the potential V (r) and the density n(r) are conjugate means you can equally well
describe any solution of Eq. (2) using the potential or the density.
Formally known as a Legendre transform (in the same way you go from the Hamiltonian
to the Lagrangian formulation of classical mechanics), we can change the functional of Eq. 7
to depend on the density n(r) rather than the potential V (r). This is the Hohenberg-Kohn
theorem: there exists a universal functional of electronic density, F[n(r)], such that for the
correct density n(r) it provides the ground state energy of Eq. (2),
Z
E[n(r)] = F[n(r)] + d3 rV (r)n(r). (8)

Knowing this functional, for any given potential V (r) we minimize the right hand side by
checking all possible electronic density distributions.
There are only two minor problems. We don’t know what this functional looks like. And
even if we did, we don’t know how to find the right electronic density.

1.3 Approximating the functional

The unknown functional F[n(r)] should describe the kinetic and interaction energy of a system
described by Eq. 2. Even though we cannot find its exact shape, we can look at its shape in
some limiting cases that we can solve.
We know that a free homogeneous electron gas with density n has a ground state energy
of
2/3
3h̄2 3π 2 5/3
E0 = n0 . (9)
10m
For a slowly varying electronic density, we can approximate the kinetic energy contribution
to the full functional F[n(r)] as the energy of Eq. (9) evaluated at each point separately,

2/3 Z
3h̄2 3π 2
T0 [n(r)] = d3 r(n(r))5/3 . (10)
10m
Furthermore, we know from perturbation theory that the lowest order energy contribution
from Coulomb interactions is given by the Hartree term,

e2 n(r)n(r0 )
Z
UH [n(r)] = d3 rd3 r0 . (11)
2 |r − r0 |

It is natural to write out the full functional as containing the homogeneous electron gas
term and the Hartree term. The remaining terms, though still unknown, should be small.
This unknown part is conventionally called the exchange-correlation potential Exc [n(r)]. The
full Hohenberg-Kohn functional, including the potential energy, is thus
Z
EHK [n(r)] = T0 [n(r)] + d3 rV (r)n(r) + UH [n(r)] + Exc [n(r)]. (12)

We will later discuss some general choices of exchange-correlation functionals in Sec. 2.2.

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1.4 Kohn-Sham equation

We replaced an intractable problem (solving Eq. (2)) with the task of minimizing an unknown
functional F[n(r)] over infinitely many possible electronic densities n(r). In the previous
section we already gave some first suggestions for the functional. But once we found it, how
to find the right electronic density n(r)?
Because the correct density minimizes the functional, we can find the functional by setting
it’s derivative to zero,
δF[n(r)]
= 0. (13)
δn(r)
Using the functional Eq. (12), we write out1

n(r0 ) 3 0 δExc [n(r)]

Z
δT [n(r)]
+ V (r) + d r + = 0. (14)
δn(r) |r − r0 | δn(r)

The idea of Kohn and Sham [2] was to treat this as if it is a single-particle problem. The first
term represents the kinetic energy, and the remaining terms form the Kohn-Sham potential

n(r0 ) 3 0 δExc [n(r)]

Z
VKS (r) = V (r) + d r + . (15)
|r − r0 | δn(r)

The Kohn-Sham equation is the single-particle Schrödinger equation with the potential given
by Eq. (15),
h̄2 ∂ 2
 
− + VKS (r) ψi (r) = i ψi (r). (16)
2m ∂r2
We solve these equations numerically, which is tractable because it’s just a linear differential
equation. The electronic density is obtained by occupying the N solutions ψi (r) with the
lowest energy,
XN
n(r) = |ψi (r)|2 . (17)
i=1

Now the electronic density obtained this way can be used to calculate a new Kohn-Sham
potential following Eq. (15). We continue this iterative procedure until we reach convergence.
A final comment is in order: in the above derivation we completely ignored the spin of
electrons. Of course, real electrons have spin so that you need that degree of freedom as well.
This does not change anything fundamental about how to use the Kohn-Sham equation.

1.5 Limitations
We have reached the end-goal: using the Born-Oppenheimer approximation, with an appro-
priate choice of functional, we use the Kohn-Sham equations to find the ground state energy
and electronic density of a system of interacting electrons and ions. This combination of
approximations and techniques is called density functional theory (DFT).
Despite is sometimes shaky assumptions, DFT turned out to be a resounding success. A
large majority of crystalline materials, many molecules and molecular structures have been
1
There is a small subtlety included in this equation: the kinetic component of the functional T [n(r)] should
not be the one obtained for the free homogeneous noninteracting electron gas of Eq. (10), but the one for a
noninteracting gas subject to the Kohn-Sham potential.

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explained using DFT. Walter Kohn – the man who was involved in both the Hohenberg-Kohn
theory and the Kohn-Sham equations – received the Nobel Prize for DFT in 1998. Mainly
because of this success, I assume, you want to learn DFT in this ToolBoX.
However, let me briefly shed some clouds over DFT’s success.

• A major limitation of DFT is that it is impossible to tell you the size of the errors that
exist due to the assumptions. If you get a self-consistent solution, that is nice, but only
a comparison with the experimental system will tell you whether it is a good solution.

• The electronic properties of many materials can be described using band theory, meaning
for every quasimomentum k we have a set of energies n (k). The solutions of the Kohn-
Sham equation Eq. (16) are commonly interpreted as these electronic bands. However,
it is important to bear in mind that in principle there is no connection to the actual
electronic energy levels in a material. It just turns out that, in many materials, the
Kohn-Sham energies happens to be a good approximation.

• As a corollary to the previous limitation: when using DFT for an insulator or semicon-
ductor, you can also compute the Kohn-Sham energy gap between the highest occupied
and lowest unoccupied state. This is not the actual gap of the semiconductor or insula-
tor. In practice, it turns out that DFT typically underestimates the real gap.

• Note that even if we had the exact functional, solving the corresponding Kohn-Sham
equations would not give you the exact solution for the ground state energy.

• Because the Kohn-Sham equations describe non-interacting electrons, many materials

with strong correlations cannot be described using DFT. In general, this is true for
materials with partially filled d or f -orbitals; or materials with localized electrons. In
particular, applying DFT to the class of high-temperature superconductors such as
cuprates, pnictides, and heavy fermions is relatively unsuccessful.

• Materials with ground state degeneracy – for example in the case of spontaneous sym-
metry breaking – are known to be difficult to compute using DFT.

• There is some subtlety involved in choosing the right functional. Commonly, functionals
become widely accepted because of a good overlap with experiments.

A good book to learn more about the theoretical side of DFT is Ref. [3].

2 A Practical Guide
DFT as introduced in the last section is a numerical technique – there are no analytical
expansions or solutions. And like many modern numerical techniques, it is better to use an
existing developed code than to write your own. There are numerous DFT software packages,
both open source and payed. In this section we will outline the most important choices we
need to make in order to start running some code.

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2.1 Wavefunction basis sets

The core of any code consists of computing the solutions to the Kohn-Sham equation. Because
this is a linear differential equation, we need to choose a basis over which we can expand the
Kohn-Sham equation. In this way, we transformed the continuum differential equation into a
matrix equation, for which there are many known techniques for diagonalizing it.
The two most popular choices of basis are plane waves (PW) and Gaussian type orbitals
(GTO). If you are interested in the structure of molecules, the most logical basis set is GTO
where you take a certain set of polynomials multiplied by a Gaussian envelope, to make sure
the electronic density remains close to the ions.
For crystals, on the other hand, the most logical basis set is plane waves ψ(k) = eik·r in
a box with periodic boundary conditions. Because this course is aimed at condensed matter
physicists, we will use a plane-wave code.
A full list of existing DFT codes, with their preferred basis set, is maintained on Wikipedia
[4].

2.2 Which functional?

In Sec. 1.3 we introduced some basic ideas regarding the precise shape of the functional.
We separated the kinetic energy of a noninteracting gas and the Hartree-Fock interaction
energy from the exchange-correlation functional. Here we will discuss in more detail some
possible exchange-correlation functionals that have been proposed, without any attempt at
being encyclopedic.
It is known – see for example the textbook [5], chapter 5 – that the energy of the homo-
geneous electron gas can be expanded in powers of the Fermi momentum kF ∼ n1/3 . Kohn
and Sham [2] suggested to use these analytical results for the exchange-correlation functional,
which is now known as the local density approximation (LDA).
A natural next step is to have a functional that not only depends on the density n(r)
but also on its derivative ∇n(r). Such functionals are known as generalized gradient approx-
imations (GGA). [6] A popular version of a GGA functional is the Perdew–Burke-Ernzerhof
functional (PBE) [7] - its publication is cited more than 100000 times! In this work we will
use the PBE functional, since it reproduces experimental band-structures relatively accurate.

2.3 Pseudopotentials
Are we ready to start computing? Well, not yet. If we are interested in doing DFT for a
crystal, we would give our code the size of the unit cell, the type of atoms and their positions.
For example, silicon has an fcc crystal structure with two atoms per unit cell. Silicon itself is
element number 14, which means there are 28 electrons per unit cell. However, both physically
and numerically it is nonsensical to include all 28 electrons in our calculation.
Physically speaking, the electronic configuration of silicon is Ne 3s2 3p2. The core elec-
trons, given by the electronic configuration of neon, are completely irrelevant in the physics
of binding a silicon crystal. Numerically, the fact that a bare atomic core has a diverging
potential 1/r creates a lot problems. Both these problems can be solved by putting a pseu-
dopotential at the position of the silicon atoms. A pseudopotential is a smeared-out potential
that includes the charge of the physically irrelevant core electrons, that is therefore more
numerically stable than the diverging 1/r potential of a bare atomic core. Using a pseu-

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dopotential for silicon, for example, means you now do DFT with only the four outermost
electrons, known as the valence electrons.
Like with the choice of functional, there are many different ways to compute a pseudopo-
tential. In fact, most pseudopotentials are tailored to work with certain functionals, so in
these notes we will use pseudopotentials that work well with the PBE functional.

2.4 Quantum ESPRESSO

Now we are ready to select a DFT implementation. In these notes we will use the open-source
plane-wave DFT code Quantum ESPRESSO (http://www.quantum-espresso.org/). Its
development was started in Trieste, Italy, but has by now many contributors from all around
the world. If you ever use Quantum ESPRESSO scientifically, make sure you explicitly
acknowledge the code and cite their original journal publications [8, 9].
Our first task is to install Quantum ESPRESSO on your own computer. The simulations
we will do in these lecture notes are light enough that they can be done on a standard laptop.
The full source package of Quantum ESPRESSO can be downloaded from

https://www.quantum-espresso.org/download

If you are comfortable doing so, you can install Quantum ESPRESSO using the source
package. Otherwise, on the above webpage you will also find links for stable binaries for
typical platforms such as Windows. For Mac OS X I recommend using MacPorts (https:
//www.macports.org/), which has a port called quantum-espresso. It automatically takes
care of dependencies, such as OpenMPI and Fortran libraries.

2.5 Materials Cloud

We will use the pseudopotential libraries collected by Materials Cloud, [10, 11] an online tool
and repository for doing DFT calculations developed by the EPFL and the ETH. On their
website, they have collected various pseudopotentials, benchmarked them, and selected for
each element the best choice of pseudopotential.
We will download their collection of pseudopotentials, which are all computed for the PBE
functional.

1. Go to the website https://www.materialscloud.org/, and navigate to the Discover

page using the top menu.

2. Click on Standard solid-state pseudopotentials (SSSP).

3. You will see a periodic table (see Fig. 1). By clicking on the button that reads Pseudo,
you will download a tar.gz file containing all the pseudopotentials.

4. Once you downloaded the library, look into the folder. You will see files with names like
Si.pbe-n-rrkjus_psl.1.0.0.UPF and C.pbe-n-kjpaw_psl.1.0.0.UPF. These are the
pseudopotentials for silicon and carbon, respectively. Directly after that, you can see
that these pseudopotentials are computed for the PBE functional.

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Figure 1: The Standard solid-state pseudopotentials library from Materials Cloud [10, 11]
contains for all elements a choice of pseudopotential, which can be downloaded on https:
//www.materialscloud.org/.

3 Example 1: Silicon
Silicon is one of the most abundant materials on earth, and one of the most used in modern
technology. It is therefore logical that we start with silicon as the first material we are going
to study.
To start off, create a folder where we will do all of our calculations, with three subfolders:
silicon, out and pseudo. Then move the pseudopotential file for silicon that we downloaded
from Materials Cloud into the pseudo directory.

3.1 Self-consistent field

3.1.1 Writing the input file
Quantum ESPRESSO works with input files. These are text-only files that contain all the
parameters that you want to give to your code. We will now build together an input file
for computing the ground state of a silicon crystal. Note that all possible parameters are
summarized in the file INPUT_PW.txt or INPUT_PW.html that came with the source package.
So let’s get coding! Open your favorite plain text editor, and create a new file called
silicon.scf.in. The input file we will create is structured with cards, of the form &NAME ... /.
The first card named CONTROL describes calculation parameters.
& CONTROL
calculation = ’ scf ’
prefix = ’ silicon ’
outdir = ’ ../ out / ’

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pseudo_dir = ’ ../ pseudo / ’

tprnfor = . true .
verbosity = ’ high ’
/

• calculation decides what calculation we will do. Choose ’scf’, which is short for
self-consistent field calculation. It is the default option of Quantum ESPRESSO. In
the scf-mode, the self-consistent loop described in Sec. 1 is done to find the ground state
energy and the electronic density.

• prefix is the name of your set of calculations. This allows you to later use the output
of this calculation in further calculations, for example to obtain the band structure.

• outdir is the directory where all the detailed output files will be put, in files of the form
prefix.xml and prefix.save, with the exception of the command line output.

• pseudo_dir is the directory where you put the pseudopotentials.

• The last two flags are optional. We set tprnfor true, which means the code will calculate
and output the forces acting on the ions. This is a useful way to check that your proposed
crystal structure is stable. We also set verbosity to high, which means the output file
will contain a lot of extra information, such as the calculated symmetry representations
of the crystal. I can really advise to run both with high and low verbosity and to
compare the output files.

The next card describes the system we are studying. What kind of lattice, how many
atoms, and what are the cut-offs for our plane wave basis.
& SYSTEM
ibrav = 2
celldm ( 1 ) = 10 . 2
nat = 2
ntyp = 1
occupations = ’ fixed ’
ecutwfc = 30
ecutrho = 120
/
& ELECTRONS
/

• ibrav selects the type of Bravais unit cell. In the case of silicon, we choose 2, which
is the number for face-centered cubic (fcc). In this crystal structure, the lattice vectors
are
a1 = a/2(−1, 0, 1); a2 = a/2(0, 1, 1); a3 = a/2(−1, 1, 0), (18)
where a is the lattice constant given in celldm(1), see also Fig. 2, left side. The
parameter celldm(1) is given in atomic units, meaning Bohr radii. A full list of possible
Bravais lattices can be found in the file INPUT_PW.txt.

• nat is the total number of atoms per unit cell, ntyp is the total number of different
atoms per unit cell. In fcc silicon, there is only one type (silicon) but two atoms per
unit cell.

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• occupations tells the code how to occupy the computed Kohn-Sham states. fixed
means we just occupy all the states below the Fermi level and empty all the states
above. Choose this option for insulators; however, for metals (such as graphene in the
next section) we need a different option.

• Recall that Quantum ESPRESSO uses a plane-wave basis to describe the wavefunc-
tions. We should tell the system how many plane waves should be included in the
calculation. This is characterized by a kinetic energy cut-off ecutwfc, which implies
2
|k|2
that we take all the plane waves with momenta such that h̄ 2m ≤ ecutwfc. The pa-
rameter is given in Rydberg units (1 Ry = 13.606 eV). On the Materials Cloud website,
see Fig. 1, there is a suggested minimum wavefunction cut-off for every pseudopotential,
which for silicon is 30 Ry. Making it larger makes the code slower, but should give a
more accurate result.

• The code not only stores the plane waves of the electronic states, but also directly the
density distribution. Therefore a second cut-off is necessary, ecutrho. Because density
scales as the square of wavefunctions, and the kinetic energy scales as the square of the
momentum, we need to include a density cut-off at least four times ecutwfc. For our
case, exactly four times suffices.

• The card &ELECTRONS allows us to tell the system how to solve the Kohn-Sham equation.
In our case, we just use the default values. However, we need to include the card!

The third part of the input contains explicit information about the atoms: their pseu-
dopotentials and positions.
ATOMIC_SPECIES
Si 28 . 086 Si . pbe - n - rrkjus_psl . 1 . 0 . 0 . UPF
ATOMIC_POSITIONS alat
Si 0 . 00 0 . 00 0 . 00
Si 0 . 25 0 . 25 0 . 25

• Below the line ATOMIC_SPECIES you list all the types of atoms that exist in your unit
cell. In our case, it is just silicon. For each type of atom, you give its name (Si), its
atomic mass in units of u (28.086), and the relevant pseudopotential file name.

• After ATOMIC_POSITIONS you list the positions of all the atoms. The flag alat means
the positions are given in cartesian coordinates in units of the lattice parameter a
(celldm(1)). Alternatively, one can use angstrom (cartesian coordinates in Angstrom)
or crystal (multiples of the primitive lattice vectors). Here we have a silicon atom at
the origin, and a second silicon atom at a( 14 , 14 , 14 ).

In the final part of the input we tell the code at which momentum points we will do the
calculation.
K_POINTS automatic
6 6 6 1 1 1

The simplest option is to choose the flag automatic, which generates a Monkhorst-Pack
grid [12]. The first three numbers indicate the number of k-points in each of the three
directions ( 6 6 6). The last three provide a possible offset in each direction: 0 means no

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offset and thus the inclusion of high-symmetry points like Γ; 1 means that you place the
momentum points exactly in between the points generated by 0. A finer momentum mesh is
generated if you choose 1, so that is what we will choose typically.

3.1.2 Running the code

Congratulations, you have now written your first DFT input file! To run it, simply use the
following command on the command line:

pw.x -in silicon.scf.in > silicon.scf.out

The program pw.x is the main component of Quantum ESPRESSO. It takes the input
file silicon.scf.in and does the self-consistent calculation of the ground state energy and
density. On most modern computers, it should not take longer than a few seconds for a system
as simple as silicon.

3.1.3 Reading the output

The heavy part of the output is sent to the output directory ../out/. The human-readable
part is saved in the file silicon.scf.out. Let’s read through it together.
The beginning of the output file lists the properties of this calculation, many of them were
given by your input file. Some of them were implicit, yet properly picked up. For example,
on line 45 you can see that the program will use the PBE exchange-correlation functional.
On line 39 we read that we are going to use 4 Kohn-Sham states, with spin degeneracy this
corresponds to 8 electrons per unit cell. After that follows properties of the crystal structure,
including its symmetries, and the list of momentum points in our grid.
Just before the actual calculation starts, the program estimates the amount of memory
needed for this calculation, in the line Estimated max dynamical RAM per process. This
might be useful to know for more complicated crystal structures, but for silicon this poses no
problems.
Between the lines Self-consistent Calculation and End of self-consistent calculation the
self-consistent DFT loop is iterated until we have reached convergence. After this, the file
contains for each momentum point the resulting energies of the Kohn-Sham states. This is
directly followed by:
highest occupied level ( ev ) : 6 . 2506

! total energy = - 22 . 83862400 Ry

This is the main output of a DFT calculation: the ground state energy. For clarity, the code
also includes the energy of the highest occupied level. This is not exactly the same as the
Fermi level, because there might be occupied states with a higher energy at momentum points
that were not included in your momentum grid.

3.2 Homework: Find the lattice constant and bulk modulus of silicon
a. The ground state energy by itself is not a measurable quantity. However, one of the ideas
of DFT is that we can find the lattice constant of a crystal by calculating the ground state
energy as a function of the input lattice constant, E0 (a). The predicted actual lattice constant

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Silicon (FCC) band structure

10

Dispersion [eV]
0

-5

L Γ X W Γ

Figure 2: Left: Crystal structure of face-centered cubic silicon. Right: Band structure of
silicon as computed using the steps of Sec. 3.3.

is where this function is minimal. So can you predict with your DFT code the lattice constant
of silicon?
Hint: Write a code that automatically generates input files with different values of the
lattice constant a. Then extract the total energy for every value of a.
b. In the previous exercise you calculated the function E0 (a). The change of energy
under uniform compression is characterized by the bulk modulus. What is the value of the
bulk modulus you calculated?

3.3 Bands
Strictly speaking, the Kohn-Sham energies do not correspond to anything physical. However,
it turns out that they are a pretty good approximation to the electron band energies of weakly
interacting materials. Therefore it is instructive to calculate the Kohn-Sham energies for many
points in the Brillouin zone, to get a sense of silicons band structure.
A calculation of the bands can only be done after you finished a self-consistent field calcu-
lation with the same parameters . This is because the bands calculation takes the electronic
density (and thus the Kohn-Sham potential) obtained in an scf calculation, and recomputes
the Kohn-Sham energies for a new set of chosen momentum points. A good starting point
for the bands calculation input file is therefore to copy the scf input file to a new file called
silicon.bands.in. If you want to write your own bands file from scratch, make sure it has
the same prefix as the previous self-consistent field calculation.
At three points, we will change this new input file. First, we need to tell the code that we
want to calculate the band structure, so replace the calculation line with this:
calculation = ’ bands ’

For an insulator or semiconductor like silicon, the default setting is that only occupied bands
will be computed. If we are interested in the band gap, we also need to calculate the unoccu-
pied bands. To achieve this, add to the &SYSTEM card a line that says we want to calculate 8
bands:
nbnd = 8

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The final change we need is to the momentum point grid. A customary way to visualize a
bandstructure is to choose a path in the Brillouin zone and compute the bands along this path.
This can be done by the command tpiba_b, which means that the K_POINTS are in units of
2π/a. The subscript _b indicates that we can define a path for a bandstructure calculated.
For a path L – Γ – X – W – Γ, we replace the old K_POINTS card by
K_POINTS tpiba_b
# tpiba_b = k - points in units of 2pi /a , in format for band calculation
# number of k - points ( use high - symmetry points only )
5
# kx , ky , kz , n . of points between this and next one
0 . 5 0 . 5 0 . 5 20
0 . 0 0 . 0 0 . 0 30
0 . 0 0 . 0 1 . 0 30
0 . 0 1 . 0 1 . 0 30
0.0 0.0 0.0 0

Notice that here we added some comment lines (the one starting with #). These will be
ignored by the code, and can be useful for our own understanding of the input files. Here,
the comments explain us that we have a path with 5 momentum points, and that we have 20
momentum points in between L and Γ, and so forth.
We can run the bands calculation with this command,
pw.x -in silicon.bands.in > silicon.bands.out
It might take a few seconds longer than the scf calculation, because we have more momentum
points.
The output file silicon.bands.out starts out with listing the parameters of the calcula-
tion. After the line Band Structure Calculation it will calculate the Kohn-Sham energies
of each desired momentum point. At the end of the calculation, you will find lines looking
like this:
End of band structure calculation

k = 0 . 5000 0 . 5000 0 . 5000 ( 754 PWs ) bands ( ev ) :

- 3 . 3153 - 0 . 6624 5 . 1803 5 . 1803 7 . 9984 9 . 7300 9 . 7300 14 . 1551

k = 0 . 4750 0 . 4750 0 . 4750 ( 748 PWs ) bands ( ev ) :

- 3 . 3519 - 0 . 6101 5 . 1849 5 . 1849 8 . 0036 9 . 7355 9 . 7355 14 . 1635

It signals the end of the calculation, and then it will list for each momentum point all the
Kohn-Sham energies in eV. The momentum points themselves are given in units of 2π a where
a is the lattice constant (celldm(1)).
The Quantum ESPRESSO code itself comes with a set of post-processing tools, one of
them allows you to plot the band-structure thus calculated. You can also import the output
file into your favorite tool (Python, Mathematica, Matlab, GNUplot) and plot it there. The
resulting band-structure is shown in Fig. 2, right. Notice it is very similar to the actual
band-structure!
The band gap calculated using this code is about 0.8 eV, significantly smaller than the
actual band gap in silicon of about 1.1 eV. This is common among DFT calculations of
semiconductors. On the other hand, many qualitative features – including the fact that
silicon has an indirect band gap – are reproduced with our simple calculation!

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3.4 Try at home

Congratulations, you have successfully predicted the properties of a material, purely from
first principles! To get comfortable with this technique, try some other three-dimensional
semiconductors, and calculate their lattice constant and band-structure.

1. First try other zincblende structures like C-diamond, β-SiC, and GaAs.

2. Next, calculate a different crystal structure: rock-salt NaCl. Can you find in PW_input.txt
how to program its simple cubic structure?

3. Finally, study hexagonal α-SiC. Which one has a lower ground state energy, α- or β-SiC?

4 Example 2: Graphene
The study of silicon in the previous section allows you to calculate crystal and electronic band
structures of any three-dimensional semiconductor. In the remainder of these notes, we will
switch gears and introduce a few new concepts: we discuss how to deal with metals, with
two-dimensional materials, and how we can optimize the structure within a unit cell, and how
to have more complicated unit cells.
Graphene is a perfect material to do this. It is, as you know, a two-dimensional semi-metal
with a hexagonal unit cell.

4.1 Compute the band-structure

As with the silicon, we need to write input files for a self-consistent calculation first. Make
a new folder graphene and start an input file named graphene.scf.in. The first card,
&CONTROL, is the same as in the silicon case but with only the prefix changed to graphene.
The &SYSTEM card will have some significant changes. Let’s write it out in its full totality,
& SYSTEM
assume_isolated = ’ 2D ’
ibrav = 4
celldm ( 1 ) = 4 . 65
celldm ( 3 ) = 6
nat = 2
ntyp = 1
occupations = ’ smearing ’
smearing = ’ mv ’
degauss = 1 . 5000000000d - 02
ecutwfc = 45
ecutrho = 180
/
& ELECTRONS
/

• In the standard DFT implementation, we have periodic boundary conditions in all three
direction. The command assume_isolated = ’2D’ ensures that there is no periodicity
(neither in the charge density nor in the Coulomb interactions) in the z-direction.

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• Graphene has an hexagonal lattice, which has ibrav = 4. The lattice vectors are given
by √
a1 = a(1, 0, 0); a2 = a(− 12 , 23 , 0); a3 = a(0, 0, c/a), (19)
where as before a =celldm(1) in Bohr, and c/a =celldm(3) is the ratio between the
horizontal and vertical lattice size. The value for celldm(3) should be such that, for
our 2d set-up in graphene, the vertical unit cell size should be large than the cut-off of
the pseudopotentials – in this case at least 20 Bohr.

• In the case of a metal or semimetal, just computing the occupied Kohn-Sham energies
is very numerically unstable. Tiny changes can lead to different shapes of the Fermi
surface. It is therefore necessary to smear the occupations of the Kohn-Sham states,
which is ensured by setting occupations = ’smearing’. We then also need to set which
type of smearing we will use; here we opted for Marzari-Vanderbilt (mv) smearing [13],
with a width set by degauss in Ry units.

• Notice we changed the wavefunction and density cut-offs.

The last part of the input file tells us where the carbon atoms are going to be, and our
choice of momentum points. The only subtleties are in the placement of the carbon atoms,
see Fig. 3, left, and in the choice of K_POINTS: because we have a two-dimensional system we
only need one momentum point in the z-direction.
ATOMIC_SPECIES
C 12 . 0107 C . pbe - n - kjpaw_psl . 1 . 0 . 0 . UPF
ATOMIC_POSITIONS alat
C 0 . 000000 0 . 000000 0 . 000000
C 0 . 000000 0 . 5773503 0 . 000000
K_POINTS automatic
9 9 1 1 1 1

Run the self-consistent field calculation by

pw.x -in graphene.scf.in > graphene.scf.out

The next step is to make our bands calculation input file. Like before, we can just copy the scf
input file to a new file graphene.bands.in. Make sure you change the type of calculation,
and the list of K_POINTS. For the latter, I suggest a path Γ – M – K – Γ. Because K and M are
particularly easily expressed in terms of the reciprocal lattice vectors, we write the K_POINTS
in units crystal_b:
K_POINTS crystal_b
4
0 . 000000 0 . 000000 0 . 000000 40
0 . 500000 0 . 000000 0 . 000000 20
0 . 333333 0 . 333333 0 . 000000 40
0 . 000000 0 . 000000 0 . 000000 0

In the silicon case we explicitly asked the code to compute more than just the occupied
bands, using nbnd. Because we are computing a (semi)metal, using the smearing flag, the
code automatically calculates some unoccupied bands as well. We do not need to specify the
number of bands nbnd.
As before, the bands calculation can now be run by the command

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Graphene band structure

Dispersion [eV]
-5

- 10

- 15
Γ M K Γ

Figure 3: Left: The honeycomb crystal structure of graphene. Right: Band structure of
graphene with the Dirac cone clearly visible.

WSe2 band structure

-3
Dispersion [eV]

-4

-5

-6

-7
Γ M K Γ

Figure 4: Left: Crystal structure of WSe2 . Right: Final band-structure with spin-orbit
coupling, with a sizeable spin-orbit splitting at K of ∆vSOC = 0.4 eV.

pw.x -in graphene.bands.in > graphene.bands.out

The resulting band-structure, with the characteristic Dirac cone at the Fermi level, can be
seen in Fig. 3.

5 Example 3: WSe2
The third and final material that allows us to learn some new features of DFT is monolayer
WSe2 . In-plane it has a honeycomb lattice structure, with on one sublattice the W atoms,
and on the other sublattice two Se atoms, displaced in the positive/negative z-direction, as
shown in Fig. 4, left. Using lattice relaxation calculations, we will be able to find the exact
displacement of the Se atoms. Furthermore, WSe2 is a semiconductor with sizeable spin-orbit
coupling, and we will show how to include that.

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5.1 Relax
In a relaxation calculation, the DFT code not only computes the ground state energy but also
the derivative of the energy with respect to atomic displacements. This corresponds to the
forces acting on each atom. If your initial guess of atomic positions is not stable, there will
be nonzero forces. The code will suggest a new set of atomic positions based on the direction
of those forces. By repeating this until you have no more forces acting on the atoms, you
have relaxed the structure and minimized the ground state energy. We will use this feature
to calculate the position of the Se atoms in monolayer WSe2 .
As before, we start by making a new folder wse2 with in there an input file, which we will
call wse2.relax.in. We will calculate the position of the Se atoms, using a relax calculation.
The first card of the input file therefore contains the lines
calculation = ’ relax ’
prefix = ’ wse2 ’

In the &CONTROL card we can also include a force convergence threshold forc_conv_thr, which
determines how close to zero we want the final forces to be. In our simple calculation we only
need to use the default value, so we do not need include it in our input file.
The remainder of the input file looks like this:
& SYSTEM
assume_isolated = ’ 2D ’
ibrav = 0
nat = 3
ntyp = 2
occupations = ’ fixed ’
ecutwfc = 30
ecutrho = 120
/
& ELECTRONS
/
& IONS
/
ATOMIC_SPECIES
W 183 . 840 W_pbe_v1 . 2 . uspp . F . UPF
Se 78 . 960 Se_pbe_v1 . uspp . F . UPF
ATOMIC_POSITIONS angstrom
W 0 . 000000 0 . 000000 0 . 000000 0 0 0
Se 0 . 000000 1 . 919689645 1 . 500000 0 0 1
Se 0 . 000000 1 . 919689645 - 1 . 500000 0 0 1
K_POINTS automatic
8 8 1 1 1 1
CELL_PARAMETERS angstrom
3 . 32500000 0 . 0000000000 0 . 0000000000
- 1 . 66250000 2 . 8795344676 0 . 0000000000
0 . 00000000 0 . 0000000000 32 . 0000000000

• In the &SYSTEM card, we reverted back to fixed occupations since WSe2 is a semicon-
ductor. Notice how we changed the cut-offs and the number of atoms and types of
atoms.

• Because we are interested in the atomic positions, it is worthwhile to write out the
lattice vectors and the initial atomic positions explicitly in units of Angstrom. We can

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do so by selecting ibrav = 0, meaning we have a free form of the unit cell. We should
then explicitly write out the three unit vectors in a new card called CELL_PARAMETERS.

• We are interested in finding the z-position of the Se atoms. We know already that their
in-plane coordinates are given by the honeycomb lattice, which are given as the second
and third column of the lines after ATOMIC_POSITIONS angstrom. In the third column
we put the z-position. We set W at z = 0, and we guess an initial distance of the Se atoms
at z = ±1.5 A. The last three numbers indicate which atomic position coordinates we will relax .
For the Se atoms, 0 0 1 means we keep the x, y coordinates fixed, and will minimize
the ground state energy with respect to the z-coordinate.

• We do need to include a new card &IONS, where we can specify the properties of the
atomic displacements the code will do. Having this card empty just means we choose
the default values, but for a relax calculation it has to be there!

Run the pw.x code as usual. In the output file wse2.relax.out you can see the two
self-consistent loops. Given a set of atomic positions, the ground state energy and forces
are calculated. If the forces are larger than the threshold, a new set of atomic positions is
proposed after the line saying ATOMIC_POSITIONS. After a few iterations, we have reached
convergence and we find the following lines containing the final coordinates:
Begin final coordinates

ATOMIC_POSITIONS ( angstrom )
W 0 . 000000000 0 . 000000000 0 . 000000000 0 0 0
Se 0 . 000000000 1 . 919689645 1 . 678711660 0 0 1
Se 0 . 000000000 1 . 919689645 - 1 . 678711660 0 0 1
End final coordinates

We predict the distance between the two Se atoms to be 3.36 Å.

5.2 Spin-orbit coupling

In the above lattice relaxation calculation we did not take into account spin-orbit coupling. In
general, spin-orbit coupling becomes more important the heavier the element is, which in our
case applies to the tungsten (W). Because spin-orbit will likely not influence the position of
the Se atoms, we take the atomic positions from the previous calculations and do the standard
scf followed by bands to calculate the bandstructure of WSe2 . Only this time, we will have
spin-orbit coupling.
Make the wse2.scf.in and wse2.bands.in input files. You can combine the elements
from the wse2.relax.in and graphene.bands.in. Make sure you copy the atomic positions
from the previous relax output file into our new input files. To turn on spin-orbit coupling,
we need to add the following two lines to the &SYSTEM card:
lspinorb = . true .
noncolin = . true .

The first term turns on spin-orbit coupling, and the second allows for noncollinear spins (so not
only up and down but also superpositions). Additionally, we need to have a fully relativistic pseudopotential to s
In the W pseudopotential we have used so far, you can find the following line:
The Pseudo was generated with a Scalar - Relativistic Calculation

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Because Scalar-Relativistic implies no spin-orbit coupling, we need to find a new pseu-

dopotential that is fully relativistic! Many different types of pseudopotentials can be down-
loaded from the Quantum ESPRESSO website. Go to https://www.quantum-espresso.
org/pseudopotentials/ps-library/, and download a full relativistic ultra-soft pseudopo-
tential (USPP) for tungsten (W) that works with the PBE functional. After that, update the
line in the input files where you give the pseudopotential:
ATOMIC_SPECIES
W 183 . 840 W . rel - pbe - spn - rrkjus_psl . 1 . 0 . 0 . UPF

Finally, the amount of valence electron per W is 14 and per Se is 6, meaning the code computes
26 electrons. If you want also to see the conduction bands, I suggest putting nbnd = 32 or
higher.
As before, run the scf first, followed by a bands calculation. You can check in the output
files that the number of Kohn-Sham energies is now equal to the number of electrons. Before
we included spin-orbit coupling, the spin degeneracy meant we just needed half the amount
of Kohn-Sham energies.
The final band structure is shown in Fig. 4, right. As before, the band gap (here about
1.3 eV) is smaller than experimentally detected (1.7 eV in monolayers). Notably, the valence
band at the K point is split due to the spin-orbit coupling, with a splitting of ∆vSOC = 0.4 eV,
comparable to what is measured in experiments. [14]

6 Further learning
You now have learned the basics of how to compute crystal structures and electronic bands
using density functional theory, implemented in the plane-wave tool Quantum ESPRESSO.
But there is much more to DFT than just this. There are some additional tools that we
haven’t discussed, such as the possibility to compute phonon dispersions, Raman or optical
spectra, and wannierization. We also haven’t looked into modern developments of functionals,
such as the inclusion of Van der Waals interactions, hybrid functionals or strong correlations
(LDA+U, GW or DFT+DMFT).
Luckily, there are many online courses available that are more in-depth than this short
ToolBox.

• The Materials Cloud webpage also contains a set of lectures, including notes, exercises
and videos, on how to do DFT with Quantum ESPRESSO. You can find them here:
https://www.materialscloud.org/learn/.

• Many universities have their classes on density functional theory online, for example MIT
has https://ocw.mit.edu/courses/materials-science-and-engineering/3-320-atomistic-comput
labs/sections

• The source manual of Quantum ESPRESSO named pw_user_guide.pdf, which comes

with downloading the source package, contains a lot of information on what you can do
with the code. The source package also contains examples on how to use the code, see
the folder PW/examples for input files and ideas for pw.x. You can also look at examples
of other parts of the code, such as PHonon/examples, that show you how to compute
phonon dispersions.

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Acknowledgements
These notes would not exist without the enthusiasm of the ToolBoX organizers João Ferreira
and Michael Sonner. I would also like to thank Marco Gibertini for discussions.

Funding information L.R. acknowledges funding from the SNSF in the form of an Am-
bizione grant.

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