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VASP Combined With Phonopy to Calculate the Specific Heat Capacity of Silicon

Run this Tutorial Online

VASP stands for Vienna Ab initio Simulation Package (The VASP Manual – VASP Wiki) is a computer program for atomic-scale material modeling from first principles, such as electronic structure calculations and quantum mechanical molecular dynamics.

PhonopyWelcome to phonopy — Phonopy v.2.37.1) is a Python toolkit for computing phonon band structures, thermal properties, group velocities, and other phonon-related quantities at the harmonic and quasi-harmonic levels.

Under the simple harmonic approximation, the specific heat capacity shared by phonons isSpecific derivationYou can check it out on Phonopy’s official website.

Tutorial Content

This tutorial will use an automated script to demonstrate the calculation process using Phonopy. Through this tutorial, you will learn the basic process of specific heat capacity calculation:

  1. Prepare perturbation difference supercell structure
  2. Calculate the total energy of all structures
  3. Calculate the force constant matrix
  4. Calculation of the specific heat capacity of silicon from the force constant matrix

Input File

The input file contains

├── POSCAR-unitcell
├── clean.sh
├── run.sh
└── run_vasp.sh
├── pt
│   ├── INCAR
│   ├── KPOINTS
│   └── POTCAR

POSCAR-unitcell

Si #硅结构
   5.38930000000000
     0.0000000000000000    0.5071343999939496    0.5071343999939496
     0.5071343999939496    0.0000000000000000    0.5071343999939496
     0.5071343999939496    0.5071343999939496    0.0000000000000000
   2
Direct
  0.8750000000000000  0.8750000000000000  0.8750000000000000
  0.1250000000000000  0.1250000000000000  0.1250000000000000

clean.sh

#!/bin/bash
rm -r *.yaml thermal_properties.pdf
 band.yaml FORCE_SETS vasp poscar *out SPOSCAR 
# 删除不必要文件

run.sh

#!/bin/bash
rm -r vasp poscar

#准备微扰差分超胞结构
##########################
phonopy -d --dim 2 2 2 --pa auto -c POSCAR-unitcell
mkdir poscar
mv POSCAR-unitcell pp
mv POSCAR-* poscar/
##########################


#计算所有结构的总能
##########################
mkdir vasp
cd vasp
Pnum=$(ls -l ../poscar/  -IR | grep "^-" | wc | awk -F ' ' '{print $1}')
cp ../run_vasp.sh .

t_head="for i in {1.."
t_tail="}"
sed -i "3c ${t_head}${Pnum}${t_tail}"  run_vasp.sh #生成 vasp 计算脚本

./run_vasp.sh
##########################

cd ../


mv pp POSCAR-unitcell

#计算力常数矩阵
##########################
phonopy -f vasp/*/vasprun.xml > pfcout
##########################

#根据力常数矩阵计算比热容
##########################
phonopy-load --mesh 31 31 31 -t -p -s
##########################

run_vasp.sh

#!/bin/bash
#计算 vasp 流程自动脚本
for i in {1..8}
do
rm -r $i
mkdir $i
cd $i
ii=$(printf "%03d" $i)
cp ../../poscar/POSCAR-${ii} POSCAR
cp ../../pt/* .
mpirun -n 1 vasp_std
cd ../

done

Files in folder pt

INCAR standard static calculation

ISTART =  1            (若有波函数、读取波函数)
ISPIN  =  1            (非极化计算)

Static Calculation
ISMEAR =  0            (高斯占据)
SIGMA  =  0.05         (高斯展宽)
NELM   =  60           (最大电子步)
EDIFF  =  1E-08        (SCF 收敛精度)

KPOINTS

K-Spacing Value to Generate K-Mesh: 0.040
0
Gamma
   4   4   4
0.0  0.0  0.0

POTCAR

The pseudopotential combination of the corresponding elements in the system, here is the pseudopotential of Si

Getting Started

1. Clone the container

Find the tutorial working directory and clone the container

2. Set up the container

Select 4090 — Pay as you go — vasp 6.3.0-cuda11.8 — Workspace

2

After loading, open the workspace

3

Open Terminal

4

Unzip the package

unzip Cv_dft.zip

Enter the directory

cd Cv_dft

Upload the prepared silicon pseudopotential

Here you can useOfficial website examplePut the pseudopotential POTCAR in the directory

5

3. Install the phonopy environment

Enter the following command to install the phonopy environment

conda install -c conda-forge phonopy

Then enter y and press Enter to agree to the installation

6

4. Run the script

Run the script by typing:

chmod 777 *.sh

./run.sh

5. View the “Specific Heat v Temperature” graph

The final calculated result will be output in pdf

7

View the file thermal_properties.pdf

8

We can see in the terminal that the specific heat capacity ends up being 48.8006881 J/K/mol.

Here we need to convert the units to the common units J/K/kg. There are 2 atoms in the unit cell, and the molar mass of the unit cell is 0.056kg/mol. Let's do a simple conversion:

48.8006881/0.056 J/K/kg = 871.4408589285714 J/K/kg

It can be seen that the final results are consistent with the paper "Study on thermal properties of silicon single crystals based on lattice dynamics (I) - Lattice dynamics and specific heat" is consistent with the result of 888.03 J/K/kg.