Harvard SEAS AP275 Computational Design of Materials Spring 2018

Problem Set 2: First-Principles Energy Methods

Problem 1 (10 points): Convergence of absolute energies with respect to cutoff energies.

A Using the Quantum ESPRESSO PWscf package, calculate the energy of Ge in the
diamond structure as a function of plane-wave cutoff energy. A good range to try is 5-
80 Ry, doing calculations at increments of 5 Ry. When changing the cutoff, make sure
to keep the other variables (lattice constant, k-points, etc) fixed and to record them.
Record and plot your final results. Specify when you reach the level of convergence of
around 5 meV/atom (convert this to Ry/atom). Note that the code calculates energy
per primitive cell.

B Do you see a trend in your calculated energies and calculation time with respect to the
cutoff? Is this what you expect and why?

C In Problem Set 1, we used a cubic unit cell. Here, we use the primitive cell. What are
the advantages and disadvantages of both methods?

Problem 2 (10 points): Convergence of absolute energies with respect to k-points.

A Using PWscf, calculate the energy as a function of the size of the k-point grid used
to integrate the Brillouin zone. For each grid, record the number of unique k-points.
Record the computational time. When changing the size of the k-point grid, make sure
to keep your other variables fixed (lattice constant, plane-wave cutoff, etc). One may
choose a lower cutoff than the “converged” cutoff in the last problem. There are some
“cross effects” in doing so, however we assume these are small.

B Do you see a trend in your calculated energies and computation times with respect to
the k-point grid size? If you see a trend, is this what you expect and why?

Problem 3 (10 points): Convergence of forces with respect to plane-wave cutoff energies.

Oftentimes we are interested in quantities other than energies. In this problem, we will
be calculating forces on atoms. Displace a Ge atom +0.05 in the z direction (fractional
coordinates). Keeping other parameters fixed, calculate the forces on a Ge atom as a function
of the kinetic energy cutoff. A good force value would be converged to within around 10
meV/Angstrom (convert this to Ry/bohr, since PWscf gives forces in Ry/bohr). Record
relevant parameters (lattice parameter, k-points, unique k-points, etc). A good k-point grid
to use is 4 × 4 × 4. Plot and record your results.

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Problem 4 (10 points): Convergence of forces with respect to k-points.

Using PWscf, calculate the force on a Ge atom displaced +0.05 in the z direction (in frac-
tional coordinates) as a function of k-point grid size. Keep all other parameters fixed. Record
your relevant conditions (lattice parameter, cutoffs, etc).

Problem 5 (5 points): Convergence of energy differences with respect to energy cutoffs.

In practice only energy differences have physical meaning, as opposed to absolute energy
scales, which can be arbitrarily shifted. Therefore, it is important to understand the conver-
gence properties. Using PWscf, calculate the energy difference between two Ge cyrstals at
different lattice parameters, as a function of cutoff. For example, you could calculate the en-
ergy of Ge at the experimental lattice parameter (10.70 bohr), and then calculate the energy
using another value close to it (10.75 bohr, for example), take the difference between the two
energies, and repeat for many energy cutoffs. Make sure to keep your other variables (lattice
constant, k-points, etc) fixed while changing the cutoff. Record all relevant parameters such
as the lattice constant, k-points, and so on. A good energy difference is converged to around
5 meV/atom (convert this to Ry/atom).

Problem 6 (10 points): Comparing Problems 1, 2, 3, 4, and 5.

How do the cutoff requirements change when looking at absolute energies, looking at forces,
and looking at energy differences? How do the k-point grid requirements change? Can you
explain the differences in the requirements and the rates of convergence?

Problem 7 (45 points): Equilibrium lattice constant and bulk modulus.

In this problem you will calculate the equilibrium lattice constant and bulk modulus of Ge.
Usually, we are interested in quantities such as forces or energy differences, not absolute
energies. Therefore, for this problem use the cutoff and k-point criteria that you determined
for the force and energy difference calculation. (In general, to be absolutely safe you should
test convergence specifically for the quantity you are interested in. So, ideally, we would test
convergence of lattice constant as a function of energy cutoff and k-point grid size, but we
are not going to do this.)
A Calculate the equilibrium lattice constant of Ge in the diamond structure from first
principles using PWscf. The experimental value is 10.7 bohr. How does the experi-
mental value compare with the calculated value? Is this expected? Make sure to record
all the relevant parameters (k-points, cutoffs, etc).
B Calculate the bulk modulus of Ge in the diamond structure. Here you will need to
derive some (simple) equations and then apply them to compute a material’s property,
a very typical scenario in computational science.

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The bulk modulus is a measure of the stiffness of a material. It is defined as

∂P
B = −V0 ,
∂V
where P is the pressure on the material, V is its volume, and V0 is its equilibrium
volume. Derive an expression for the bulk modulus that you can use it. Use finite
difference approximation for derivatives. How does your value compare with the ex-
perimental value of ≈76 GPa?

C Solve problem 7A by directly minimizing the energy using structure optimization ca-
pability of Quantum Espresso. Think about what type of calculation the code should
do, find the required parameters in the online documentation and modify the Python
workflow accordingly. Compare with the results of problem 7A where you directly
scanned over lattice parameter values.

Hints: Remember that P = −∂E/∂V . Remember that PWscf calculates energies per prim-
itive unit cell. Be careful about unit conversions.

OPTIONAL Extra Credit Question 1 (20 points):

Calculate the elastic constants C11 , C12 , and C44 for Ge using first-principles energy methods.
You will need to perform proper deformations of the unit cell and to lower the symmetry. You
will have 8 atoms in the unit cell for diamond structure. Use the same (reduced) symmetry
for the original (not deformed) unit cell in order to make correct energy comparisons. You
may want to look up convenient expressions relating the elastic constants specifically in cubic
crystals.

OPTIONAL Extra Credit Question 2 (20 points):

Compute and plot the band structure of Ge. You will need to change the original calculation
mode to

calculation = ’bands’

and provide the list of k points along high some symmetry directions (in section K P OIN T S)
for which you want to compute the Kohn-Sham eigenvalues. The proper format of the
input file is very important. The details can be found in the PWscf manual. Look up the
relevant high symmetry directions and special k-points for the diamond crystal, which is
the same space group as Si and Ge. Include the valence bands and the 4 lowest conduction
bands. (change parameter nbnd) Compare your result with the band structure found in the
literature.

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Lab 2 Handout:
Quantum Espresso DFT Code

1 The First-Principles Code: Quantum Espresso

We will be using the PWscf code included in the Quantum-Espresso package as our first-
principles code. Quantum-Espresso is a full ab initio package implementing electronic struc-
ture and energy calculations, linear response methods (to calculate phonon dispersion curves,
dielectric constants, and Born effective charges) and third-order anharmonic perturbation
theory. Inside this package, PWscf is the code we will use to perform total energy calcula-
tions. PWscf uses both norm-conserving pseudopotentials (PP) and ultrasoft pseudopoten-
tials (US-PP), within density functional theory (DFT). In addition to basic self-consistent
plane-wave calculations (PWscf module) Quantum-Espresso has capabilities for ab-initio
molecular dynamics, vibrational and optical spectroscopy, dielectric and magnetic response,
and tools for ionic and electronic transport. Quantum-Espresso is free under the condi-
tions of the GNU GPL. Further information (including online manual) can be found at the
Quantum-Espresso website (http://www.quantum-espresso.org/. There are many other
first-principles codes that one can use, for a full up-to-date listing see

https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software

The rest of this handout will show how to get energies and forces using the PWscf code in
Quantum-Espresso. Some helpful unit conversions are the following:

1 bohr = 1 a.u. (atomic unit) = 0.529177249 Å (Angstrom)

1 Ry (Rydberg) = 13.6056981 eV
1 eV = 1.60217733 × 10−19 J

2 How to run PWscf

2.1 Environment setup
For the computations related to Lab 2 you will be using the same VirtualBox VM envi-
ronment. Please refer to the document on the class website for the initial setup of the
VM, in case you need to repeat the first steps. The Quantum Espresso code is located
in /home/bond/Software/qe-6.0, and the compiled binary executable is already linked to
/home/bond/bin/pw.x. The code includes an extensive set of examples demonstrating its
different capabilities in /home/bond/Software/qe-6.0/Examples/PW.

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• First we will need to setup the environment for this lab.

Edit your /.profile file to specify a new environment variable that tells the scripts
the location of pseudopotentials for the DFT calculations:
export ESPRESSO_PSEUDO=$HOME’/Software/qe-6.0/pseudo’
and check that you have the variable pointing to the Quantum Espresso PWscf binary:
export PWSCF_COMMAND=$HOME’/bin/pw.x’
For these changes to take effect, you will need to close and restart the terminal shell
windows. Alternatively, you can run the following command to update your environ-
ment: $ source ~/.profile

• Each atom in a DFT calculation is typically modeled with a pseudopotential, that

smoothly approximates the chemically irrelevant core electrons without affecting the
valence electrons. The pseudopotential library for Quantum Espresso is here:
http://www.quantum-espresso.org/pseudopotentials/
We will need an LDA pseudopotential for Germanium for this lab, so let’s download it
$ cd /home/bond/Software/qe-6.0/pseudo
$ wget http://www.quantum-espresso.org/wp-content/uploads/upf_files/Ge.pz-bhs.UPF

• Now download the workflow automation tools and Python plugins for Quantum Espresso
that you will be adapting to solve exercises in this lab.
bond@vmint ~ $ cd ~/Software/labutil/
bond@vmint ~/Software/labutil $ git pull
If you changed the plugins and samples in this directory while working on the previous
assignment, the git command will notice this and will prompt you to ’merge’ your
changes. Do not do this. Instead, backup any of your changes by renaming this folder
to something else, for instance:
bond@vmint ~/Software/labutil $ cd ..
bond@vmint ~/Software $ mv labutil/ my_labutil
Then repeat the initial procedure steps to set up a fresh repository (see previous lab):
bond@vmint ~/Software $ git clone https://github.com/bkoz37/labutil.git
If, however, git does not detect any changes when you do git pull, it will simply
download and update the files.
Copy the sample files to your working directory.
bond@vmint ~/Software/labutil/lab2_samples $ cp * ~/WORK/Lab2/

• You are now ready to run DFT calculations.

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2.2 Running a PWscf example

Once you are in your working directory for this lab, take a look at the sample file pwscf.in. It
contains the input information needed to do run to compute the energy of a germanium(Ge)
unit cell using PWscf. If you edit the file with your favourite editor (vi, emacs, nano etc ).
It will look like this

&control
calculation = ’scf’
tstress = .true.
tprnfor = .true.
pseudo_dir = ’/home/bond/Software/qe-6.0/pseudo’
outdir=’/home/bond/WORK/Lab2/Problem1/test’
/
&system
ibrav = 0
nat = 2
ntyp = 1
ecutwfc = 30
/
&electrons
diagonalization = ’david’
mixing_beta = 0.5
conv_thr = 1e-07
/
K_POINTS automatic
4 4 4 0 0 0
ATOMIC_SPECIES
Ge 72.61 Ge.pz-bhs.UPF
CELL_PARAMETERS {angstrom}
0.0 2.5 2.5
2.5 0.0 2.5
2.5 2.5 0.0
ATOMIC_POSITIONS {angstrom}
Ge 0.00000 0.00000 0.00000
Ge 1.25000 1.25000 1.25000

The most relevant lines for the calculations related to this lab are the following:

• The line

calculation = ’scf’

indicates the task to be performed. That this is a ’self-consistent field’ calculation

(scf) to find the energy of the system using the iterative Kohn-Sham procedure. You

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can change this line to do non-self-consistent calculations, if for example we wanted to

compute the band structure of a material. In that case you would specify calculation
= ’bands’ to run the pw.x in the same folder as the results of the scf run. It will
perform a non-self-consistent calculation to get the eigenvalues at specified k-points
(see below) based on the charge density that is already present in the folder.

• The line

tprnfor = .true.

indicates that forces will be printed out. A similar line appears for the stress.

• The line

pseudo dir = ’/home/bond/Software/qe-6.0/pseudo’

indicates the location of the pseudopotential file that describes the behaviour of inner
electrons for each Ge atom . The code will look for the pseudopotential file in that
directory.

• The line

outdir dir = ’/home/bond/WORK/Lab2/Problem1/test’

indicates the directory where temporary files (wavefunction, charge density) will be
written. We will be running each calculation and writing the output file to the same
folder, for convenience.

• The lines

ibrav = 0
nat = 2
ntyp = 1

indicate that our unit cell will be completely specified by its cell vectors using the
CELL PARAMETERS block, as described below. We also tell the code that we have two
atoms (nat = 2) of the same (ntyp = 1) species in it. These parameters will be
automatically filled in by our Python plugin, based on the information it finds in the
structure object.

• The line

ecutwfc = 30.0

indicates that a plane-wave kinetic energy cutoff of 30 Ry will be used. Plane-waves

with higher energies will not be included into the basis to describe our wavefunctions.
This number will need to be changed until you are sure that the calculations are well
converged with respect to the size of the basis (see next section).

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• Ge 72.61 Ge.pz-bhs.UPF indicates the atom label (Ge), atomic mass unit number for
Ge and the name (choice) of pseudopotential to be used.

• The lines

ATOMIC_POSITIONS {angstrom}
Ge 0.00000 0.00000 0.00000
Ge 1.25000 1.25000 1.25000

indicate where the two atoms in the unit cell are located.

• The lines

K POINTS automatic
4 4 4 0 0 0

indicate that the Morkhost-Pack grid of k-points to be used contains 4 × 4 × 4 points,

and it is not displaced from the origin. This number will need to be changed until you
are sure that the calculations are well converged with respect to the size of the k-points
grid (see next section).

• The full listing and description of all input file keywords is located here:
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html

We are ready now to run our first PWscf calculation. Just type

bond@vmint ~/WORK/Lab2 $ pw.x < pwscf.in > pwscf.out

After a few seconds if everything goes well you should have in your directory a file called
pwscf.out. All relevant information is there. To look at the total energy of the system type
in command line

grep total pwscf.out

At the end you will find lines containing something like

! total energy = -15.99179135 ryd

total stress (a.u.) (kbar) P= -20.27

so here you can see the total value of the energy for the cell (your number might be slightly
different) and the total stress. Note that the final occurrence of total energy will have an
exclamation point by it. This something that you can use to hunt for it manually, for example
by typing

grep ’^!’ *.out

which will search all files terminated by .out in the current directory, looking for lines that
start with an exclamation point.
At the end of the file, it is written how long your program took to run. For example:

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PWSCF : 0.34s CPU 0.36s WALL

Your numbers may be different from these.
There will also be lines which say:
number of k points= 8
cart. coord. in units 2pi/alat
k(1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0312500
k(2) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.2500000
k(3) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.1250000
k(4) = ( 0.0000000 0.5000000 0.0000000), wk = 0.1875000
k(5) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.7500000
k(6) = ( 0.5000000 0.0000000 0.5000000), wk = 0.3750000
k(7) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0937500
k(8) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.1875000
This records the number of unique k-points that were calculated. Some points from original
4 × 4 × 4 = 64 mesh are symmetry related(identical) and have the same energy so the code
doesn’t compute them more than once. They are then weighted differently. The weights
add up to 2, an idiosyncrasy of this program. Your numbers will be different if you use a
different k-point mesh.

2.3 Using functional workflows to run PWscf multiple times

In order to check the numerical convergence of your calculations with respect to energy cutoff
and number of k-points, you will have to run PWscf multiple times with different values for
those parameters. Instead of creating many different input files by hand and using them one
by one to run PWscf, we will do this more efficiently by using automated Python plugins
that will create input files for you, run the binary code, and parse out the necessary results
from the output file. This way all your work is contained within Python functions connected
together into a reusable workflow. An example that you can start from and modify for this
lab is now in your folder ~/WORK/Lab2/, where it is safe to be modified. (Note: do not
modify files in your labutil folder, it is only used to download lab samples.)
By modifying the Python workflow, you can loop over plane-wave cutoffs, k-point grids,
and lattice constants. You can create your own naming scheme for labeling directories
containing each calculation. Use the runpath variable in the script and set it dynamically
as you like.

3 Numerical convergence issues

3.1 Plane waves
Remember that we are dealing with infinite systems using periodic boundary conditions.
This means that we can use the Bloch theorem to help us solve the Schrdinger equation.
The Bloch theorem states that
ψnk = eikr unk (r),

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with X
unk (r) = cG eiGr .
G

In these equations, ψnk (r) is the wavefunction, unk (r) is a function that is periodic in the
same way as the lattice, the sum goes over all (at least in principle) reciprocal lattice vectors
G, and the cG are coefficients in the basis expansion. In this case, our basis functions
(i.e., what we expand in) are plane waves. They are called plane waves because surfaces of
constant phase are parallel planes perpendicular to the direction of propagation. Remember
that limiting the plane-wave expansion to the infinite, but numerable and discrete set of G
vectors that are integer multiples of the three primitive lattice vectors, we are selecting plane
waves that have a periodicity compatible with the periodic boundary conditions of our direct
lattice.
In actual calculations, we have to limit the plane wave expansion at some point (i.e.,
stop taking more values of G). This is called the planewave cutoff. Cutoffs are always given
in energy units (such as Rydberg or eV) corresponding to the kinetic energy of the highest
G. Note: The units of reciprocal lattice are the inverse of the direct lattice, or 1/length.
However, we can convert 1/length to energy units (remember that λν = c and that E = hν,
where λ is a wavelength, ν is a frequency, and E is an energy).
Problem 1 is designed to test cutoff convergence issues. You can always take a higher
cutoff than you need, but the calculations will take longer.

3.2 K-points
Because of the Bloch theorem, we need to solve a Schrödinger-like Kohn-Sham equation (i.e.
iterate selfconsistently the diagonalization of a M × M matrix, where M is the number of
basis functions) everywhere in the first Brillouin zone (if you dont know what a Brillouin
zone is, its time to go over the concepts of direct and reciprocal lattice). In practice, we
do this for a finite number of k values (e.g., the coarse grained k-point ”Monkhorst-Pack”
mesh), and get a value for E at each k. To obtain a value for E, the energy of the crystal,
we need to integrate over the first Brillouin zone, where the bands are occupied (and divide
by the volume). Thus, summing over a finite number of k points is an approximation to
performing an integral. You will need to make sure you have enough k-points to have a
converged value for the energy.

3.3 Summary about numerical convergence

For all first-principles calculations, you must pay attention to two numerical convergence
issues. The first is the energy cutoff, which is the cutoff for the wavefunction expansion. The
second is number of k-points, which measures how well your discrete grid has approximated
the continuous integral.

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4 Hints for Solving the Problems

In order to solve the problems in Problem Set 2, you will have to run several PWscf calcula-
tions. You can organize your runs any way you like. One way is to make directories for each
calculation that you do, and name your folders accordingly. Or you can modify the plugins
to do it differently. Good organization may save you headache in the long run (but is totally
up to you).

4.1 Problems 1 and 2

In problem 1 we check the convergence of the total energy with respect to the plane-wave
cutoff. All the variables except the plane-wave cutoff should keep the same value in all the
runs. Check the total energies to decide when the calculations are converged.
Problem 2 will test the convergence of the energy with increasing the density of the k-
point grid. We will be testing k-point grid convergence and cutoff convergence separately.
So, set your cutoff to something lower, such as 30 Ry (or some other cutoff that you have used
already in Problem 1). There are some cross effects in testing cutoff and k-point separately,
however we assume these are small. You may also want to test denser grids. You will also
want to record the number of unique k-points (that is, unique by symmetry). This is near
the beginning of the output file, and looks something like this:

number of k points= 8

Your calculation will scale roughly as the number of unique k-points. You can verify this
with the timing information.

4.2 Problems 3 and 4

In problems 1 and 2, the forces on Ge are zero in the x, y, and z directions. This is because of
symmetry, which cancels out forces. In problems 3 and 4, we will create forces by displacing
a Ge atom +0.05 (fractional coordinates) in the z direction. To do this, remember how to
move at atom using ASE (see IPython notebook). The forces will appear in the output file
after the total energies. It will look something like this:

Forces acting on atoms (Ry/au):

atom 1 type 1 force = 0.00000000 0.00000000 0.11794007

atom 2 type 1 force = 0.00000000 0.00000000 -0.11794007

Total force = 0.235880 Total SCF correction = 0.000005

The numerical value for your forces may be slightly different from the above example. Forces
are given in units of Ry/bohr, but the Python plugin converts them to eV/atom. Record
this number, and retest the convergence issues with respect to cutoffs and k-points.

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5 FAQ
• I get a message: Note: The following floating-point exceptions are sig-
nalling: IEEE DENORMAL
This just a low-level warning from the GNU compiler not being happy with a floating
point numeric convention in the PWscf code. Ignore it.

• How precisely do I need to get the lattice parameter?

Lattice parameters are typically listed to within 0.01 Å. There are applications when
higher precision is required; this is not one of them.

• The energies when you move an atom (the force calculations) are higher
than when you don’t?
This is correct. Remember equilibrium has the lowest energy. Equilibrium for this
structure has Ge atoms at (0, 0, 0) and at (0.25, 0.25, 0.25). As a side note the forces
will give you an idea of how far you are from equilibrium (they tell you which direction
the atoms “want” to move). The stresses tell you which direction the cell parameters
“want” to change to reach equilibrium.

• My energy versus lattice constant plot is jagged.

There are a number of solutions to this; the easiest is to raise the energy cutoff.

• The weights of the k-points add up to 2, not 1.

Yes. This is a feature of the code. Dont worry about it.

• How is “convergence of energy” defined?

You say that your energy is converged to X Rydbergs when Etrue − En = X (En is
the current energy). How do you know Etrue ? In practice you might take your energy
at the highest cutoff (or k-grid, or whatever) that you calculated — if that seems
converged, you might call that Etrue . The most important thing is that you do not
define convergence as En+1 − En , where n is a step in energy cutoff (or k-grid, or
whatever).
You do need to be careful though. It is possible to get false or accidental convergence
as well. That is, your energy at a 2 × 2 × 2 k-grid may be the same as the energy at
a 8 × 8 × 8 k-grid, but the energy at a 4 × 4 × 4 might be very different from both of
these. In this case, you aren’t really converged at a 2 × 2 × 2 k-grid.

• I don’t understand convergence of energy and forces. It seems that, as a

percentage of the absolute value, energies converge much faster.
Sometimes you are interested in an absolute value, rather than a percentage value. For
instance, let’s say you can measure the length to within 1 mm. If you measure the
length of an ant, in terms of percentage error, you may be off by 50% or more. If you
measure the length of an elephant, in terms of absolute error, you may be off by 0.01%.
But usually you don’t care as long as you are to within 1 mm. Errors on forces are the

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same. Don’t worry about the percentage errors so much. You could always arbitrarily
decrease the percentage errors on the forces by taking a bigger displacement. From
experience, we know that a good error on energy differences is around 5 meV/atom.
From experience, we also know that a good error on forces is 10 meV/Å. These are
just values that we know, because we have done many first-principles calculations in
the past. This is what you should look for.

• Does PWscf use LDA or GGA? DFT or Hartree Fock?

PWscf uses DFT. It has both LDA and GGA implemented, but in this lab we only
use LDA.

• My energies are really different from Lab 1. What is the “correct” scale I
should be looking for?
Remember that absolute energies do not usually mean very much. We are mostly
interested in energy differences. Also, the reference energies are different. In lab 1, the
reference energy (when atoms are infinitely far apart) is 0. In lab 2, this is not the
case. The absolute energies can shift a lot, depending on which reference energies you
take.

• Why do I take k-point grids with the same number of points per direction?
Can I take other k-point grids?
For this material, we take the same number of k-points per direction because the three
lattice directions are equivalent. This is not always true. The “best” k-point meshes
are those that sample k-space evenly in all directions. Thus, for a tetragonal cell (with
a = b, c = 2a, and all angles 90 degrees) we might take a 8 × 8 × 4 mesh. Think about
why this is so. (Note that if a lattice vector is longer in real space, it is shorter in
k-space).

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