First Principles Workshop

An introduction and hands-on tutorial with the

Quantum ESPRESSO

Quantum Espresso Hands-on

Tutorial

by N. T. Hung, A. R. T. Nugraha and R. Saito group

http://flex.phys.tohoku.ac.jp

1
 What we will do today
Hands-on #1: Total energy and relaxations for Silicon
Basic self consistent calculation (scf)
Convergence of total energy & plane waves cutoff (ecut)
Convergence of total energy & BZ sampling (k-point)
Lattice constant (vc-relax)
Files for practice
/silicon/ scf

ecut
Hands-on #1
k-point

vc-relax

rho Silicon
dos

bands

phonon
2
 Exercise #1
Do it by yourself: Graphene’s calculation!
Basic self consistent calculation (scf)
Convergence of total energy & plane waves cutoff (ecut)
Convergence of total energy & BZ sampling (k-point)
Lattice constant (vc-relax)
Files for exercise
/graphene/ scf

ecut
Hands-on #1
k-point

vc-relax

rho

dos

bands

phonon
3
 What we will do today
Hands-on #2: Charge density, Band structure, DOS, Phonon

Charge density (rho)

Density of states (dos)
Band structure (bands), Phonon dispersion (phonon)

Files for practice

/silicon/ scf

ecut

k-point

vc-relax

rho Silicon
dos
Hands-on #2
bands

phonon
4
 Exercise #2
Do it by yourself: Graphene’s calculation!

Charge density (rho) a 5

4
Density of states (dos) 3
2

Energy (eV)
Band structure (bands) 1
0
-1
Files for exercise -2
-3
/graphene/ scf -4
-5
Γ M K Γ DOS
ecut b 18
LO
15
TO

Frequency (100 cm-1 )

k-point 12
ZO
9
vc-relax
6 LA

rho 3 TA
ZA
0
Γ M K Γ DOS
dos
Hands-on #2
bands

phonon
5
 Structure of QE I/O file
Hands-on #1
Binary file
Text file Text file

input.in pw.x output.out

Notepad++, Notepad++,
Wordpad, vi, pw.x < input.in > output.out Wordpad, vi,
emacs, … (pw.exe for Windows users) emacs, …

Data file

tmp folder

6
 Structure of QE I/O file
Hands-on #1
Binary file
Text file Text file

input.in pw.x output.out

Notepad++, Notepad++,
Wordpad, vi, pw.x < input.in > output.out Wordpad, vi,
emacs, … (pw.exe for Windows users) emacs, …
Hands-on #2
Data file
Text & data file Binary file
tmp folder
band structure, pw.x,
phonon, ph.x, pp.x, Text file
charge density …
new input.in
gnuplot, xmgrace, pw.x < input.in > output.out
xcrysden, Vesta (pw.exe for Windows users)

7
 Structure of QE input file
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS
mixing_beta=0.7, Silicon
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

8
 Kohn-Sham equations
IN RUN OUT
Model: Physical quantities:
unit cell charge density
lattice vectors total energy
basis KS wavefunctions
KS energies
Physical approx:
xc-approximation
GGA, LDA, …

Numerical approx:
energy cut-off n-D 3D
k-points grid
SCF procedure

Solve Kohn-Sham equations


1 2
r + Vion (r) + VH [n(r)] + VXC [n(r)] i (r) = "i i (r)
2

External nuclear Hartree Exchange-correlation

potential potential potential
9
 Kohn-Sham equations

1 2
r + Vion (r) + VH [n(r)] + VXC [n(r)] i (r) = "i i (r)
2

H[n(r)]

Self-consistent field (SCF) method:

i (r) ! n(r) ! H[n(r)]

10
 Structure of QE input file
&CONTROL Construct Vion (r)
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/', Initial guess n(r)
outdir=‘../tmp/',
/
&SYSTEM
ibrav=2, Compute VH [n] + VXC [n]
celldm(1)=10.2625,
nat=2,
ntyp=1, Vef f = Vion + VH [n] + VXC [n]
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS ⇥ 1 2 ⇤
mixing_beta=0.7, Solve r + Vef f (r) i (r) = "i i (r)
conv_thr=1d-8,
2
/
ATOMIC_SPECIES X
Si 28.0855 Si.pbe-rrkj.UPF Compute n(r) = | i (r)|2
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic NO YES Energy
4 4 4 1 1 1 Self-consistent?
Forces

11
 Structure of QE input file
&CONTROL Construct Vion (r) ???
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/', Initial guess n(r)
outdir=‘../tmp/',
/
&SYSTEM
ibrav=2, Compute VH [n] + VXC [n]
celldm(1)=10.2625,
nat=2,
ntyp=1, Vef f = Vion + VH [n] + VXC [n]
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS ⇥ 1 2 ⇤
mixing_beta=0.7, Solve r + Vef f (r) i (r) = "i i (r)
conv_thr=1d-8,
2
/
ATOMIC_SPECIES X
Si 28.0855 Si.pbe-rrkj.UPF Compute n(r) = | i (r)|2
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic NO YES Energy
4 4 4 1 1 1 Self-consistent?
Forces

12
 Periodic boundary conditions
Crystal structure: Bravais lattice + Atomic basis

a1

a2

☞ Bravais lattice: (shape of unit cell & how it repeats). Specified by primitive
lattice vectors a1, a2, a3
R = n1a1 + n2a2 + n3a3, where n1, n2, n3 are integers.

☞ Atomic basis: how many atoms are in the unit cell, and how they are arranged.

13
 Periodic boundary conditions
4 Lattice types

7 Crystal classes

14
 Structure of QE input file
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir=‘../tmp/',
/
&SYSTEM ibrav = 1 (SC)
ibrav=2, ibrav = 2 (FCC)
celldm(1)=10.2625, ibrav = 4 (Hexagonal)
nat=2, …
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0, simple cubic:
/ v1 = a(1,0,0)
&ELECTRONS v2 = a(0,1,0)
mixing_beta=0.7, v3 = a(0,0,1)
conv_thr=1d-8,
/ face centered cubic:
ATOMIC_SPECIES v1 = (a/2)(-1,0,1)
Si 28.0855 Si.pbe-rrkj.UPF v2 = (a/2)(0,1,1)
ATOMIC_POSITIONS (alat) v3 = (a/2)(-1,1,0)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

15
 Structure of QE input file
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si', FCC structure
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1, v1 v2
ecutwfc=60.0,
ecutrho=720.0, v3
/
&ELECTRONS Silicon
mixing_beta=0.7,
conv_thr=1d-8,
/ face centered cubic:
ATOMIC_SPECIES v1 = (a/2)(-1,0,1)
Si 28.0855 Si.pbe-rrkj.UPF v2 = (a/2)(0,1,1)
ATOMIC_POSITIONS (alat) v3 = (a/2)(-1,1,0)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

16
 Structure of QE input file
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si', FCC structure
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2, unit bohr
celldm(1)=10.2625, a
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/ a a
&ELECTRONS
mixing_beta=0.7,
conv_thr=1d-8,
/ face centered cubic:
ATOMIC_SPECIES v1 = (a/2)(-1,0,1)
Si 28.0855 Si.pbe-rrkj.UPF v2 = (a/2)(0,1,1)
ATOMIC_POSITIONS (alat) v3 = (a/2)(-1,1,0)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic 1 bohr = 0.529177 Å
4 4 4 1 1 1

17
 Structure of QE input file
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si', FCC structure
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625, a
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/ a a
&ELECTRONS
mixing_beta=0.7,
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

18
 Structure of QE input file
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si', FCC structure
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625, a
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/ a a
&ELECTRONS
mixing_beta=0.7, Silicon
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

19
 Structure of QE input file
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si', FCC structure
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625, a
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/ a a
&ELECTRONS
mixing_beta=0.7, Silicon
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00 Mass of Si
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

20
 Structure of QE input file
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si', FCC structure
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2, PP file
celldm(1)=10.2625, a
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/ a a
&ELECTRONS
mixing_beta=0.7, Silicon
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

21
 Structure of QE input file
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si', FCC structure
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625, a
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/ a a
&ELECTRONS
mixing_beta=0.7,
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF atomic positions are in cartesian
ATOMIC_POSITIONS (alat) coordinates, in units of the lattice
Si 0.00 0.00 0.00 parameter.
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

22
How to check model structure

Xcrysden: http://www.xcrysden.org/ 23
How to check model structure

24
How to check model structure

Input file

25
How to check model structure

Silicon structure ✔ Input file

26
External nuclear potential
Construct Vion (r) ???

Initial guess n(r)

Compute VH [n] + VXC [n]

Vef f = Vion + VH [n] + VXC [n]

⇥ 1 2 ⇤
Solve r + Vef f (r) i (r) = "i i (r)
2

X
Compute n(r) = | i (r)|2

NO YES Energy
Self-consistent?
Forces

27
 External nuclear potential
Electrons experience a Coulomb valence valence
electrons
potential due to the nuclei with electrons
simple form:
core pseudo-
Z electrons potential
Vion =
r
But this leads to computational problems!

Pseudopotential (PP):
Replace the strong Coulomb
potential of the nucleus and
tightly bound core electrons by
an effective ionic potential
acting on the valence electrons. all-electron potential

28
 Pseudopotential
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS
mixing_beta=0.7,
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF Name of the pseudopotential file
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

29
 How to get pseudopotential
http://www.quantum-espresso.org/pseudopotentials/

Si.pbe-rrkj.UPF
type of exchange-
correlation functional
type of pseudopotential
30
 Pseudopotential
&CONTROL Si.pbe-rrkj.UPF
calculation='scf', <PP_INFO>
Generated using Andrea Dal Corso code (rrkj3)
restart_mode='from_scratch', Author: Andrea Dal Corso Generation date: unknown
Info: Si PBE 3s2 3p2 RRKJ3
prefix='si', 0 The Pseudo was generated with a Non-Relativistic Calculation
2.50000000000E+00 Local Potential cutoff radius
pseudo_dir='../pseudo/', nl pn l occ Rcut Rcut US E pseu
3S 1 0 2.00 2.50000000000 2.60000000000 0.00000000000
outdir='../tmp/', 3S 1 0 0.00 2.50000000000 2.60000000000 0.00000000000
3P 2 1 2.00 2.50000000000 2.70000000000 0.00000000000
/ 3D 3 2 0.00 2.50000000000 2.50000000000 0.00000000000
</PP_INFO>
&SYSTEM
ibrav=2, <PP_HEADER>
0 Version Number
celldm(1)=10.2625, Si Element
NC Norm - Conserving pseudopotential
nat=2, F Nonlinear Core Correction
SLA PW PBE PBE PBE Exchange-Correlation functional
ntyp=1, 4.00000000000 Z valence
-7.47480832270 Total energy
ecutwfc=60.0, 0.0000000 0.0000000 Suggested cutoff for wfc and rho
2 Max angular momentum component
ecutrho=720.0, 883 Number of points in mesh
2 3 Number of Wavefunctions, Number of Projectors
/ Wavefunctions nl l occ
3S 0 2.00
&ELECTRONS 3P 1 2.00
</PP_HEADER>
mixing_beta=0.7,
conv_thr=1d-8, <PP_MESH>
<PP_R>
/ 1.77053726905E-04 1.79729551320E-04 1.82445815642E-04 1.85203131043E-04
1.88002117930E-04 1.90843406086E-04 1.93727634813E-04 1.96655453076E-04
ATOMIC_SPECIES 1.99627519645E-04 2.02644503249E-04 2.05707082721E-04 2.08815947154E-04
2.11971796056E-04 2.15175339506E-04 2.18427298316E-04 2.21728404189E-04
Si 28.0855 Si.pbe-rrkj.UPF 2.25079399889E-04 2.28481039403E-04 2.31934088115E-04 2.35439322975E-04
2.38997532677E-04 2.42609517831E-04 2.46276091150E-04 2.49998077629E-04
ATOMIC_POSITIONS (alat) 2.53776314730E-04 2.57611652573E-04 2.61504954124E-04 2.65457095393E-04
2.69468965628E-04 2.73541467517E-04 2.77675517391E-04 2.81872045428E-04
Si 0.00 0.00 0.00 2.86131995864E-04 2.90456327206E-04 2.94846012447E-04 2.99302039285E-04
3.03825410344E-04 3.08417143402E-04 3.13078271619E-04 3.17809843768E-04
Si 0.25 0.25 0.25 3.22612924472E-04 3.27488594446E-04 3.32437950735E-04 3.37462106965E-04
3.42562193593E-04 3.47739358159E-04 3.52994765549E-04 3.58329598249E-04
K_POINTS automatic
4 4 4 1 1 1

31
 Plane wave expansion
In a periodic system we can write the KS states as a
superposition of plane waves:

1 X G i(k+G)·r
k,n (r) = ck,n e
⌦
G

G are vectors in reciprocal space.

The sum, in principle infinite, can be truncated:

~2 2
|k + G|  Ecut
2m

32
 Plane wave expansion
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1, ~2
ecutwfc=60.0, |k + G|2  Ecut
ecutrho=720.0, 2m
/
&ELECTRONS Units: Ry (1 Ry = 0.5 Ha = 13.6057 eV)
mixing_beta=0.7, For ultrasoft pseudopotentials we have also:
conv_thr=1d-8, ecutrho = usually 8-12 ⨉ ecutwfc
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

33
 Initial n(r)
Construct Vion (r) ✔

Initial guess n(r)

Compute VH [n] + VXC [n]

Vef f = Vion + VH [n] + VXC [n]

⇥ 1 2 ⇤
Solve r + Vef f (r) i (r) = "i i (r)
2

X
Compute n(r) = | i (r)|2

NO YES Energy
Self-consistent?
Forces

34
 Initial n(r)
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS startingwfc = ‘atomic’(DEFAULT)
mixing_beta=0.7, = ‘random’
conv_thr=1d-8, = ‘file’
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

35
 Sampling of the Brillouin zone
Many quantities we need to compute involve an integral over the BZ:
Z
1
Ā = A(k)d(k)
⌦BZ BZ

An example is the electronic density n(r):

1 XZ
2
n(r) = | i,k (r)| f (✏i,k ✏F )d(k)
⌦BZ i BZ

In practice the integral is discretized:

Z X
1
d(k) ! !k
⌦BZ BZ k

How do we choose the k points to include in the sum???

36
 Monkhorst and Pack (1976)

Example: square 2D lattice

4⨉4 k-points grid (16 points)

3 inequivalent point (IBZ)

4 ⇥ k1 ! !1 = 4/16 = 1/4
4 ⇥ k2 ! !2 = 4/16 = 1/4
8 ⇥ k3 ! !3 = 8/16 = 1/2
Z
1 1 1 1
A(k)d(k) ' A(k1 ) + A(k2 ) + A(k3 )
⌦BZ BZ 4 4 2

37
 Sampling of the Brillouin zone
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS
mixing_beta=0.7,
conv_thr=1d-8,
/
ATOMIC_SPECIES K_POINTS automatic
Si 28.0855 Si.pbe-rrkj.UPF nk1, nk2, nk3, k1, k2, k3
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00 nk1, nk2, nk3 as in Monkhorst-Pack
Si 0.25 0.25 0.25 grids k1, k2, k3 must be 0 ( no offset ) or
K_POINTS automatic 1 ( grid displaced by half a grid step in
4 4 4 1 1 1 the corresponding direction )

38
 QE run
Construct Vion (r) ✔

Initial guess n(r) ✔

Compute VH [n] + VXC [n]

Vef f = Vion + VH [n] + VXC [n]

⇥ 1 2 ⇤
Solve r + Vef f (r) i (r) = "i i (r)
2

X
Compute n(r) = | i (r)|2

NO YES Energy
Self-consistent?
Forces

39
 QE run
Construct Vion (r) ✔

Initial guess n(r) ✔

Compute VH [n] + VXC [n]

Si.pbe-rrkj.UPF

Vef f = Vion + VH [n] + VXC [n] GGA

⇥ 1 2 ⇤
Solve r + Vef f (r) i (r) = "i i (r)
2

X
Compute n(r) = | i (r)|2

NO YES Energy
Self-consistent?
Forces

40
 QE run
Construct Vion (r) ✔

Initial guess n(r) ✔

Compute VH [n] + VXC [n] ✔

Vef f = Vion + VH [n] + VXC [n] ✔
⇥ 1 2 ⇤
Solve r + Vef f (r) i (r) = "i i (r) Expensive
2

X
Compute n(r) = | i (r)|2

NO YES Energy
Self-consistent?
Forces

41
 Solve wave equation
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS diagonalization = ‘david’ (DEFAULT)
mixing_beta=0.7, = ‘cg’
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

42
 QE run
Construct Vion (r) ✔

Initial guess n(r) ✔

Compute VH [n] + VXC [n] ✔

Vef f = Vion + VH [n] + VXC [n] ✔
⇥ 1 2 ⇤
Solve
2
r + Vef f (r) i (r) = "i i (r) ✔
X
Compute n(r) = | i (r)|2

NO YES Energy
Self-consistent?
Forces

43
 QE run
Construct Vion (r) ✔

Initial guess n(r) ✔

Compute VH [n] + VXC [n] ✔

Vef f = Vion + VH [n] + VXC [n] ✔
⇥ 1 2 ⇤
Solve
2
r + Vef f (r) i (r) = "i i (r) ✔
X
Compute n(r) = | i (r)|2 ✔
NO YES Energy
Self-consistent?
Forces

44
 Self-consistency
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS
mixing_beta=0.7, Convergence threshold for self-consistency:
conv_thr=1d-8, estimated energy error > conv_thr (NO)
/
ATOMIC_SPECIES or energy error < conv_thr (YES)
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

45
 QE run
Construct Vion (r) ✔

Initial guess n(r) ✔

Compute VH [n] + VXC [n] ✔

Vef f = Vion + VH [n] + VXC [n] ✔
⇥ 1 2 ⇤
Solve
2
r + Vef f (r) i (r) = "i i (r) ✔
X
Compute n(r) = | i (r)|2 ✔
NO YES Energy
Self-consistent?
Forces

46
 new n(r)
&CONTROL
calculation='scf',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS Mix new and old density:
mixing_beta=0.7, 0.7 = 70% of the new density and
conv_thr=1d-8, 30% of old density at first step
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1

47
 QE run
Construct Vion (r) ✔

Initial guess n(r) ✔

Compute VH [n] + VXC [n] ✔

Vef f = Vion + VH [n] + VXC [n] ✔
⇥ 1 2 ⇤
Solve
2
r + Vef f (r) i (r) = "i i (r) ✔
X
Compute n(r) = | i (r)|2 ✔
NO ✔ YES Energy
Self-consistent?
Forces

48
 Total energy
$ pw.x <Si.scf.in> Si.scf.out &
$ vi Si.scf.out
or
$ grep ! Si.scf.out

49
 QE run
Construct Vion (r)
Fixed ions

Initial guess n(r)

Compute VH [n] + VXC [n]

Vef f = Vion + VH [n] + VXC [n] Move ions

⇥ 1 2 ⇤
Solve r + Vef f (r) i (r) = "i i (r)
2

X
Compute n(r) = | i (r)|2

NO YES Energy
Self-consistent?
Forces

50
 Structure optimization
&CONTROL
calculation=‘vc-relax',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir=‘../tmp/',
forc_conv_thr=1d-5,
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS
mixing_beta=0.7,
conv_thr=1d-8,
/
&IONS Broyden–Fletcher–Goldfarb–Shanno (BFGS)
ion_dynamics='bfgs',
/ algorithm is an iterative method for solving
&CELL unconstrained nonlinear optimization problems.
cell_dynamics='bfgs',
press=0.0,
press_conv_thr=0.5,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1
51
 Structure optimization
&CONTROL
calculation=‘vc-relax',
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir=‘../tmp/',
forc_conv_thr=1d-5,
/
&SYSTEM Cell lattice parameters and free (internal)
ibrav=2, coordinates of the atoms may be changed by
celldm(1)=10.2625,
nat=2, relaxation
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
/
&ELECTRONS
mixing_beta=0.7,
conv_thr=1d-8,
/
&IONS
ion_dynamics='bfgs',
/
&CELL
cell_dynamics='bfgs',
press=0.0,
press_conv_thr=0.5,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
4 4 4 1 1 1
52
 What we will do today
Hands-on #1: Total energy and relaxations for Silicon
Basic self consistent calculation (scf)
Convergence of total energy & plane waves cutoff (ecut)
Convergence of total energy & BZ sampling (k-point)
Lattice constant (vc-relax)
Files for practice
/silicon/ scf

ecut
Hands-on #1
k-point

vc-relax

rho Silicon
dos

bands

phonon
53
 Result
Hands-on #1

Basic self consistent calculation (scf)

/silicon/ scf

Command: $ pw.x <Si.scf.in> Si.scf.out

(pw.exe for Windows users)

54
 Result
Hands-on #1

Convergence of total energy & plane waves cutoff (ecut)

/silicon/ ecut

Command: $ pw.x <Si.ecut.#.in> Si.ecut.#.out

(pw.exe for Windows users)
Total energy (Ry)

Time (s)

Ecut (Ry) Ecut (Ry)

55
 Result
Hands-on #1

Convergence of total energy & BZ sampling (k-point)

/silicon/ k-point

Command: $ pw.x <Si.k-point.#.#.in> Si.k-point.#.#.out

(pw.exe for Windows users)

offset
Total energy (Ry)

no offset

Time (s)
no offset

offset

k points k points

56
 Result
Hands-on #1 a

Lattice constant (vc-relax) a

a
/silicon/ vc-relax Input:
Command: $ pw.x <Si.vc-relax.in> Si.vc-relax.out a = 10.2500 Bohr
(pw.exe for Windows users)
Output:
a = 10.3464 Bohr

57
 Exercise #1
Do it by yourself: Graphene’s calculation!
Basic self consistent calculation (scf)
Convergence of total energy & plane waves cutoff (ecut)
Convergence of total energy & BZ sampling (k-point)
Lattice constant (vc-relax)
Files for exercise
/graphene/ scf

ecut
Hands-on #1
k-point

vc-relax

rho

dos

bands

phonon
58
 Structure of QE I/O file
Hands-on #1
Binary file
Text file Text file

input.in pw.x output.out

Notepad++, Notepad++,
Wordpad, vi, pw.x < input.in > output.out Wordpad, vi,
emacs, … (pw.exe for Windows users) emacs, …
Hands-on #2
Data file
Text & data file Binary file
tmp folder
band structure, pw.x,
phonon, ph.x, pp.x, Text file
charge density …
new input.in
gnuplot, xmgrace, pw.x < input.in > output.out
xcrysden, Vesta (pw.exe for Windows users)

59
 Charge density
Command:
$ pw.x < Si.scf.in > Si.scf.out Step 1: SCF calculation (Hands-on #1)
$ pp.x < Si.pp.in > Si.pp.out Step 2: Visual charge density
(*.exe for Windows users)

Files for charge density

/silicon/ scf

ecut

k-point

vc-relax

rho

dos

bands

phonon
60
 Charge density
Command:
$ pw.x < Si.scf.in > Si.scf.out Step 1: SCF calculation (Hands-on #1)
$ pp.x < Si.pp.in > Si.pp.out Step 2: Visual charge density
(*.exe for Windows users)
Si.pp.in

&INPUTPP
outdir='../tmp/', Data of wavefunctions in step SCF
prefix='si',
plot_num=0,
/ VESTA: http://jp-minerals.org/vesta/en/
&PLOT
iflag=3,
output_format=6, Data of
fileout='si_rho.cube', charge
nx=64,ny=64,nz=64, density
/

61
Charge density

Charge density

Silicon atoms

62
 Density of states (DOS)
Command:
$ pw.x < Si.scf.in > Si.scf.out Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.nscf.in > Si.nscf.out Step 2: Non-SCF calculation
$ dos.x < Si.dos.in > Si.dos.out Step 3: Plot DOS
(*.exe for Windows users)

Files for density of states

/silicon/ scf

ecut

k-point

vc-relax

rho

dos

bands

phonon
63
 Density of states (DOS)
Command:
$ pw.x < Si.scf.in > Si.scf.out Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.nscf.in > Si.nscf.out Step 2: Non-SCF calculation
$ dos.x < Si.dos.in > Si.dos.out Step 3: Plot DOS
(*.exe for Windows users)
Si.nscf.in

&CONTROL
calculation='nscf', non-SCF calculation
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
nbnd=8,
occupations='tetrahedra', Linear tetrahedron method
/
&ELECTRONS
mixing_beta=0.7,
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
12 12 12 1 1 1 High density k-point 64
 Density of states (DOS)
Command:
$ pw.x < Si.scf.in > Si.scf.out Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.nscf.in > Si.nscf.out Step 2: Non-SCF calculation
$ dos.x < Si.dos.in > Si.dos.out Step 3: Plot DOS
(*.exe for Windows users)
Si.dos.in

&DOS
prefix='si',
outdir='../tmp/',
fildos='si.dos' Data file of DOS (state/eV)
emin=-9.0,
emax=16.0,
/ Command:
$ gnuplot < si_dos.gnu
2.5

2.0

1.5
DOS

1.0

0.5

0.0
-20 -15 -10 -5 0 5 10
ε (eV)
65
 Band structure
Command:
$ pw.x < Si.scf.in > Si.scf.out Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.nscf.in > Si.nscf.out Step 2: Non-SCF calculation
$ bands.x <Si.bands.in > Si.bands.out Step 3: Data of bands structure
$ plotband.x <Si.plotband Step 4: Plot band structure
(*.exe for Windows users)

Files for band structure

/silicon/ scf

ecut

k-point

vc-relax

rho

dos

bands

phonon
66
 Band structure
Command:
$ pw.x < Si.scf.in > Si.scf.out Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.nscf.in > Si.nscf.out Step 2: Non-SCF calculation
$ bands.x <Si.bands.in > Si.bands.out Step 3: Data of bands structure
$ plotband.x <Si.plotband Step 4: Plot band structure
(*.exe for Windows users)
Si.nscf.in
&CONTROL
calculation='bands', non-SCF calculation
restart_mode='from_scratch',
prefix='si',
pseudo_dir='../pseudo/',
outdir='../tmp/',
/
&SYSTEM
ibrav=2,
celldm(1)=10.2625,
nat=2,
ntyp=1,
ecutwfc=60.0,
ecutrho=720.0,
nbnd=8,
/
&ELECTRONS
mixing_beta=0.7,
conv_thr=1d-8,
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
K_POINTS {crystal_b} Selected special k-point coordinates
5
0.0000000000 0.0000000000 -0.5000000000 20 L
0.0000000000 0.0000000000 0.0000000000 30 Γ
-0.5000000000 0.0000000000 -0.5000000000 10 X
-0.3750000000 0.0000000000 -0.6250000000 30 U
0.0000000000 0.0000000000 0.0000000000 20 67
Γ
 XCrySDen k-Path

Xcrysden: http://www.xcrysden.org/ 68
XCrySDen k-Path

69
 Band structure
Command:
$ pw.x < Si.scf.in > Si.scf.out Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.nscf.in > Si.nscf.out Step 2: Non-SCF calculation
$ bands.x <Si.bands.in > Si.bands.out Step 3: Data of bands structure
$ plotband.x <Si.plotband Step 4: Plot band structure
(*.exe for Windows users)
Si.bands.in
&BANDS
outdir='../tmp/',
prefix='si',
filband='si.bands', Name of data file
/

70
 Band structure
Command:
$ pw.x < Si.scf.in > Si.scf.out Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.nscf.in > Si.nscf.out Step 2: Non-SCF calculation
$ bands.x <Si.bands.in > Si.bands.out Step 3: Data of bands structure
$ plotband.x <Si.plotband Step 4: Plot band structure
(*.exe for Windows users)
Si.plotband
si.bands Data file
-6.0 10
3.0
si.bands.xmgr 2.0
si.bands.ps 1.0
6.255 0.0
1.0 6.255 -1.0

Energy (eV)
-2.0
-3.0
-4.0
-5.0
-6.0
-7.0
-8.0
-9.0
-10.0
-11.0
-12.0

L Γ X U Γ

71
 Phonon
Command: Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.scf.in > Si.scf.out Step 2: Calculation of dynamical matrices on q-vectors
$ ph.x < Si.ph.in > Si.ph.out
$ q2r.x <Si.q2r.in > Si.q2r.out Step 3: Calculation of IFC's in real space
$ matdyn.x <Si.matdyn.in > Si.matdyn.out Step 4: A plot of the phonon DOS
(*.exe for Windows users)

Files for phonon

/silicon/ scf

ecut

k-point

vc-relax

rho

dos

bands

phonon
72
 Phonon
Command: Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.scf.in > Si.scf.out Step 2: Calculation of dynamical matrices on q-vectors
$ ph.x < Si.ph.in > Si.ph.out
$ q2r.x <Si.q2r.in > Si.q2r.out Step 3: Calculation of IFC's in real space
$ matdyn.x <Si.matdyn.in > Si.matdyn.out Step 4: A plot of the phonon DOS
(*.exe for Windows users)
Si.pp.in
phonon calc. Interatomic force constants (IFC’s) in real space
&inputph
outdir="../tmp/", q2r.x
prefix="si",
tr2_ph = 1d-14,
ldisp = .true.,
nq1=4, nq2=4, nq3=4, q-point
amass(1)=28.0855,
fildyn='si.dyn', ph.x
/

Si.q2r.in
&input
fildyn='si.dyn',
zasr='simple',
flfrc='si.fc',
/

Density functional
perturbation theory (DFPT):
direct calculation of second-
order derivatives of the energy

73
 Phonon
Command: Step 1: SCF calculation (Hands-on #1)
$ pw.x < Si.scf.in > Si.scf.out Step 2: Calculation of dynamical matrices on q-vectors
$ ph.x < Si.ph.in > Si.ph.out
$ q2r.x <Si.q2r.in > Si.q2r.out Step 3: Calculation of IFC's in real space
$ matdyn.x <Si.matdyn.in > Si.matdyn.out Step 4: A plot of the phonon DOS
(*.exe for Windows users)
Si.matdyn.in
&input
asr='simple',
dos=.true.,
amass(1)=28.0855,
flfrc='si.fc', Interatomic force constants (IFC’s) in real space
fldos='si.phdos',
nk1=50,nk2=50,nk3=50,
/ Data file of phonon DOS
Si (p=0, diamond phase)
0.10

0.09

Command: 0.08
$ gnuplot < si_phdos.gnu
0.07

0.06
φ-DOS

0.05

0.04

0.03

0.02

0.01

0.00
0 100 200 300 400 500 600
ω (cm-1)
74
 Exercise #2
Do it by yourself: Graphene’s calculation!

Charge density (rho) a 5

4
Density of states (dos) 3
2

Energy (eV)
Band structure (bands) 1
0
-1
Files for exercise -2
-3
/graphene/ scf -4
-5
Γ M K Γ DOS
ecut b 18
LO
15
TO

Frequency (100 cm-1 )

k-point 12
ZO
9
vc-relax
6 LA

rho 3 TA
ZA
0
Γ M K Γ DOS
dos
Hands-on #2
bands

phonon
75