分子动力学入门

课上：八个水分子为例的分子动力学。

分子动力学

步骤

建模

在 MS 中建立模型，上传，vaspkit-106。

结构优化

INCAR 为：

详情

[zjb@op geo2]$ cat INCAR 
Global Parameters
 ISTART =  0            (Read existing wavefunction; if there)
# ISPIN =  2           (Spin polarised DFT)
 ICHARG =  2         (Non-self-consistent: GGA/LDA band structures)
 LREAL  = .FALSE.          (Projection operators: automatic)
 ENCUT  =  400        (Cut-off energy for plane wave basis set, in eV)
 PREC   =  Normal       (Precision level)
 LWAVE  = .FALSE.        (Write WAVECAR or not)
 LCHARG = .FALSE.        (Write CHGCAR or not)
 NPAR   = 4           (Max is no. nodes; don't set for hybrids)
 ALGO   = Fast

Electronic Relaxation
ISMEAR =  0            (Gaussian smearing; metals:1)
SIGMA  =  0.05         (Smearing value in eV; metals:0.2)
EDIFF  =  1E-04        (SCF energy convergence; in eV)

Ionic Relaxation
NSW    =  100          (Max electronic SCF steps)
IBRION =  2            (Algorithm: 0-MD; 1-Quasi-New; 2-CG)
POTIM  =  0.3
#ISIF   =  2            (Stress/relaxation: 2-Ions, 3-Shape/Ions/V, 4-Shape/Ions)
EDIFFG = -1E-02        (Ionic convergence; eV/AA)
# ISM =  2            (Symmetry: 0=none; 2=GGA; 3=hybrids)

需要把 walltime 加长，课上演示失败的原因就是到了 walltime。我加到了 01:30:00。

疑惑：怎样迅速达到收敛？这个硬生生跑完了 100 步...

分子动力学

在结构优化基础上，对 INCAR 做如下修改

Ionic Relaxation
 NSW    =  100          (Max electronic SCF steps)
 IBRION =  0            (Algorithm: 0-MD; 1-Quasi-New; 2-CG)
 POTIM  =  1
 SMASS  =  0
 TEBEG  =  350
 TEEND  =  350
# ISIF   =  2            (Stress/relaxation: 2-Ions, 3-Shape/Ions/V, 4-Shape/Ions)
# EDIFFG = -1E-02        (Ionic convergence; eV/AA)
# ISM =  2            (Symmetry: 0=none; 2=GGA; 3=hybrids)

结果分析

使用 grep T= stdout 查看数据。使用 grep T= stdout > md-data.txt 将数据保存到 md-data.txt 文件，下载，导入 Origin。