How to calculate the Phonon and Thermal properties using the Phonopy code (Supercell method)

 Phonopy code is developped to calculate the phonon and thermal properties plus some other functionalities.

To install the code click on the following link:

How to install Phonopy Code to calculate Phonon and Thermal properties

 

There are 2 ways to do phonon calculations which are:

1- Supercell method based upon finite differences technique

2- DFPT method based upon Density Functional Perturbative Theory

For more information check the following links:

https://www.vasp.at/wiki/index.php/Phonons:_Theory#Finite_differences

https://www.vasp.at/wiki/index.php/Phonons_from_finite_differences 

http://cmt.dur.ac.uk/sjc/thesis_prt/node39.html 

 

We will use the supercell method and calculate the DOS and Band structure of NiS2. 

 
We need some input files and some scripts.

 POSCAR

Si O
   1.00000000000000
     4.2266540199664249    0.0000000000000000    0.0000000000000000
     0.0000000000000000    4.2266540199664249    0.0000000000000000
     0.0000000000000000    0.0000000000000000    2.6888359272289208
 2   4
Direct
  0.0000000000000000  0.0000000000000000  0.0000000000000000
  0.5000000000000000  0.5000000000000000  0.5000000000000000
  0.3067891334429594  0.3067891334429594  0.0000000000000000
  0.6932108665570406  0.6932108665570406  0.0000000000000000
  0.1932108665570406  0.8067891334429594  0.5000000000000000
  0.8067891334429594  0.1932108665570406  0.5000000000000000

 

INCAR

  PREC = Accurate
IBRION = -1
 ENCUT = 500
 EDIFF = 1.0e-08
ISMEAR = 0; SIGMA = 0.01
 IALGO = 38
 LREAL = .FALSE.
 LWAVE = .FALSE.
LCHARG = .FALSE.

 

KPOINT

KPOINTS  
0
Gamma
18 18 6
0 0 0

 

Creation of POTCAR of SiO2 using POTCAR-Si and POTCAR-O

cat POTCAR-Si POTCAR-O > POTCAR

 

POTCAR-Si

POTCAR-O

 

Script phon.sh for phonon calculations

#!/bin/bash

# Command to run vasp in current directory
RUN_VASP="vasp_std"

N=$(ls POSCAR-* | wc -l)
echo $N

for s in $(eval echo "{001..$N}")

do
    d=${s%%.POSCAR}
    
    mkdir disp-$d

(
     cd disp-$d
     cp  ../INCAR INCAR
     cp  ../POTCAR POTCAR
     cp  ../KPOINT KPOINT
     cp ../POSCAR-$d POSCAR
     
     
$RUN_VASP

      cd ..
)

done

 

Calculation

1- Creation of displacement POSCARs

% conda activate phonopy 

(phonopy) % phonopy -d --dim="2 2 3"

 

You should find the files, SPOSCAR, phonopy_disp.yaml, and POSCAR-{number} as follows:

% ls
INCAR KPOINT phonopy_disp.yaml  POSCAR  POSCAR-001  POSCAR-002  POSCAR-003  SPOSCAR

SPOSCAR is the perfect supercell structure, phonopy_disp.yaml contains the information on displacements, and POSCAR-{number} are the supercells with atomic displacements. POSCAR-{number} corresponds to the different atomic displacements written in phonopy_disp.yaml.

 

2- Phonon calculations

chmod +x phon.sh

./phon.sh 

 

3- Calculation of sets of forces

% phonopy -f disp-001/vasprun.xml disp-002/vasprun.xml disp-003/vasprun.xml

or

% phonopy -f disp-{001..003}/vasprun.xml

 

Post-process

In the post-process,

1. Force constants are calculated from the sets of forces

2. A part of dynamical matrix is built from the force constants

3. Phonon frequencies and eigenvectors are calculated from the dynamical matrices with the specified q-points.

For mesh sampling calculation, prepare the following setting file named, e.g., mesh.conf:

ATOM_NAME = Si O
DIM = 2 2 3
MP = 8 8 8

The density of states (DOS) is plotted by:

% phonopy -p mesh.conf

 

 Thermal properties are calculated with the sampling mesh by:

% phonopy -t mesh.conf

You should check the convergence with respect to the mesh numbers. Thermal properties can be plotted by:

% phonopy -t -p mesh.conf  

Projected DOS is calculated by the following setting file named, e.g., pdos.conf:

ATOM_NAME = Si O
DIM = 2 2 3
MP = 8 8 8
PDOS = 1 2, 3 4 5 6

and plotted by:

% phonopy -p pdos.conf 

 

Band structure is calculated with the following setting file named, e.g., band.conf by:

ATOM_NAME = Si O
DIM =  2 2 3
BAND = 0.5 0.5 0.5  0.0 0.0 0.0  0.5 0.5 0.0  0.0 0.5 0.0

The band structure is plotted by:

% phonopy -p band.conf 

 

In either case, by setting the -s option, the plot is going to be saved in the PDF format. If you don’t need to plot DOS, the (partial) DOS is just calculated using the --dos option.