VASP: Molecular Dynamics in the NVT Ensemble

本教程算力资源采用「单卡 RTX4090」。

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

When performing molecular dynamics simulation in VASP, there is no need to provide force field parameters, only the initial structure of the atoms. VASP will solve the forces on the atoms by orthogonalizing the electron wave function, and then solve Newton's equations of motion to simulate the motion trajectory of the atoms.

1. Tutorial Content

This tutorial will demonstrate molecular dynamics in the NVT ensemble. Through this tutorial, you will learn about VASP molecular dynamics.Core command tag：Take NVT as an example.

MDALGO = 2
SMASS = -1

Users can modify tags as needed to achieve molecular dynamics simulations of other different ensembles.

Effect examples

2. Input file description

This tutorial will use INCAR, POSCAR, KPOINTS, and POTCAR as input files.

1. INCAR

SYSTEM = Si
ISYM   = 0        ! 无对称性

! ab initio
PREC   = Normal   ! 普通精度
IVDW   = 10       ! 考虑 vdw 修正

ISMEAR = 0      ! 高斯占据
SIGMA  = 0.02   ! 高斯展宽 0.02eV

ENCUT  = 300    ! 波函数截断能量 300eV
EDIFF  = 1e-5   ! 电子步精度 1e-5eV

LWAVE  = F      ! 不保存波函数
LCHARG = F      ! 不保存电荷
LREAL  = F      ! 不投影到实空间计算

! 分子动力学
IBRION = 0        ! 原子坐标更新模式为分子动力学
NSW    = 500    ! 步数为 500
POTIM  = 5      ! 时间间隔为 5fs

! NVT 系综
MDALGO = 2        ! NVT 系综设置       
SMASS =-1          ! NVT 系综设置
TEBEG = 500       ! 开始和结束的温度
TEEND = 500       ! 保持一致为 500K
ISIF   = 2        ! 保持原胞体积不变

2. POSCAR

In order to simplify the calculation, only a small supercell of 8 atoms is used this time.

Si
   1.00000000000000
     5.4654798508000004    0.0000000000000000    0.0000000000000000
     0.0000000000000000    5.4654798508000004    0.0000000000000000
     0.0000000000000000    0.0000000000000000    5.4654798508000004
   Si
     8
Direct
  0.0000000000000000  0.0000000000000000  0.0000000000000000
  0.5000000000000000  0.5000000000000000  0.0000000000000000
  0.5000000000000000  0.0000000000000000  0.5000000000000000
  0.0000000000000000  0.5000000000000000  0.5000000000000000
  0.2500000000000000  0.2500000000000000  0.2500000000000000
  0.7500000000000000  0.7500000000000000  0.2500000000000000
  0.7500000000000000  0.2500000000000000  0.7500000000000000
  0.2500000000000000  0.7500000000000000  0.7500000000000000

3. KPOINTS

In order to reduce computational resources, only 2x2x2 k grid points are selected.

Not only Gamma point
 0
Gamma
 2 2 2
 0 0 0

4. POTCAR

The system corresponds to the pseudopotential combination of elements, here it is the pseudopotential of Si.

Procedure

1. Clone and start the container

After waiting for the loading to complete, click Open Workspace

2. Upload files

2.1 Open Terminal

2.2 Enter the following command to enter the directory

cd md

2.3 Upload the prepared silicon pseudopotential. This tutorial has already prepared other files.

Here you can useOfficial website examplePseudopotential POTCAR file in

Place the file in the directory

3. Enter the following command to run vasp

mpirun -n 1 vasp_std

4. View atomic trajectories

After vasp is finished running, you can download the atomic trajectory file.

Use ovito to open and export the animated image.