zoukankan      html  css  js  c++  java
  • VASP+DFPT+Phonopy 计算声子过程

    以Ammonia为例,基本翻译自http://atztogo.github.io/phonopy/vasp.html#how-to-run。

    1. 结构优化. 输入文件如下:

    INCAR
    !System settings
       SYSTEM = Ammonia
       PREC   =  accurate    low, normal, accurate
       ISTART =      0     job   : 0-new  1-cont  2-samecut
       ICHARG =      2     charge: 0-INIWAV 1-CHGCAR 2-atom 10-nonself
       ISPIN  =      1     spin polarized? 1:no 2:yes
       INIWAV =      1     0-jellium 1-rand
    
    !Electronic Relaxation
       ENCUT  =   200.0 eV
       NELM   =   1000     max e SC
       NELMIN =      2     min e SC
       NELMDL =     -5     non-SC +:every -:first
       EDIFF  = 1.0E-6     stopping-criterion for ELM
       LREAL  =   Auto     real-space projection
       ALGO   =   fast     normal:38(D) fast:38-48(RMM) all:58 damped:53
    
       !IMIX = 4
       !AMIX = 0.1
       !BMIX = 0.0001
       !WC = 1000
       !INIMIX = 1
       !MIXPRE = 1
       !MAXMIX = -45
    
    !Ionic relaxation
       EDIFFG = -0.0005    stopping-criterion for IOM +:energy -:force
       NSW    =     500    number of steps for IOM
       !NBLOCK =      1     inner block ionic cfg-XDATCAR, scale T
       !KBLOCK =   1000     outer block PCF-PCDAT,DOS-DOSCAR
       IBRION =      2     ionic relax: 0-MD 1-static 2-CG 3-dampedMD
       ISIF   =      2
       POTIM  =   1.0     time-step for ionic-motion
       !TEBEG  =  600.0
       !TEEND  =  600.0     temperature during run
       SMASS  =     -1     -3:micro -2:const -1:scaled >=0:Nose mass
    
    !DOS related values:
       !EMIN   =  10.00
       !EMAX   = -10.00     energy-range for DOS
       !NEDOS = 300
       ISMEAR =      0     1,2:metal -5,0:sem/ins
       SIGMA  =   0.05     broadening in eV
       !RWIGS  = -1.0 -1.0 -1.0
       !NBANDS = 10       actual number of bands in calculation
    
    !Write flags
       !NWRITE =      2     long runs use 0 or 1
       LWAVE  = .FALSE.     write WAVECAR
       LCHARG = .FALSE.     write CHGCAR
       LVTOT  = .FALSE.    write LOCPOT, local potential
       LELF   = .FALSE.    write electronic localiz. function (ELF)
       !LORBIT = 11
       !LAECHG = .TRUE.
       !LADDGRID = .TRUE.
    
    !Parallel flags
       NPAR   =      8     # of nodes
       LPLANE =  .FALSE.
       LSCALU = .FALSE.
       LSCALAPACK = .FALSE.
    
    
    
    POSCAR
    Ammonia_rlx
    1.0
        5.1305  0.0  0.0
        0.0 5.1305 0.0
        0.0 0.0 5.1305
        N H
    4 12
    Cart
           1.0789441   1.0789441   1.0789441
           1.4863058   4.0515558   3.6441941
           3.6441941   1.4863058   4.0515558
           4.0515558   3.6441941   1.4863058
           1.9095721   1.3477823   0.5710246
           1.9942253   3.2209279   3.9130323
           3.1362746   0.6556779   3.7827176
           4.5594753   4.4748221   1.2174676
           1.3477823   0.5710246   1.9095721
           1.2174676   4.5594753   4.4748221
           3.2209279   3.9130323   1.9942253
           0.5710246   1.9095721   1.3477823
           0.6556779   3.7827176   3.1362746
           4.4748221   1.2174676   4.5594753
           3.9130323   1.9942253   3.2209279
           3.7827176   3.1362746   0.6556779
    
    KPOINTS
    Automatic mesh
    0
    MP
     5  5  5
     0  0  0
    
    --------------------------------------------------------------------------------

    由于声子对结构优化比较敏感,这儿的 PREC=accurate.

    2. 构建优化过的单胞

    1 cp CONTCAR POSCAR
    Ammonia_rlx                             
       1.00000000000000     
         5.1304999999999996    0.0000000000000000    0.0000000000000000
         0.0000000000000000    5.1304999999999996    0.0000000000000000
         0.0000000000000000    0.0000000000000000    5.1304999999999996
       N    H 
         4    12
    Direct
      0.2173355638189437  0.2173355638189437  0.2173355638189437
      0.2826644166897822  0.7826644166897819  0.7173355638189437
      0.7173355638189437  0.2826644166897822  0.7826644166897819
      0.7826644166897819  0.7173355638189437  0.2826644166897822
      0.3844041525928144  0.2739307062557181  0.1256929444364981
      0.3743070360722207  0.6155958474071853  0.7739307062557181
      0.6256929444364983  0.1155958474071856  0.7260692742530075
      0.8743070360722203  0.8844041525928147  0.2260692742530077
      0.2739307062557181  0.1256929444364981  0.3844041525928144
      0.2260692742530077  0.8743070360722203  0.8844041525928147
      0.6155958474071853  0.7739307062557181  0.3743070360722207
      0.1256929444364981  0.3844041525928144  0.2739307062557181
      0.1155958474071856  0.7260692742530075  0.6256929444364983
      0.8844041525928147  0.2260692742530077  0.8743070360722203
      0.7739307062557181  0.3743070360722207  0.6155958474071853
      0.7260692742530075  0.6256929444364983  0.1155958474071856
     
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00
      0.00000000E+00  0.00000000E+00  0.00000000E+00

    3. 构建超胞(但是不需要计算),并且重命名SPOSCAR为POSCAR

    1 python /home/zjyx/softwares/phonopy-1.10.10/bin/phonopy --vasp -c POSCAR-unitcell -d --dim="4 4 4"

    4. 用VASP做DFPT计算.

    INCAR文件:

    !System settings
       SYSTEM = Ammonia
       PREC   =  normal    low, normal, accurate
       ISTART =      0     job   : 0-new  1-cont  2-samecut
       ICHARG =      2     charge: 0-INIWAV 1-CHGCAR 2-atom 10-nonself
       ISPIN  =      1     spin polarized? 1:no 2:yes
       INIWAV =      1     0-jellium 1-rand
    
    !Electronic Relaxation
       ENCUT  =   200.0 eV
       NELM   =   1000     max e SC
       NELMIN =      2     min e SC
       NELMDL =     -5     non-SC +:every -:first
       EDIFF  = 1.0E-6     stopping-criterion for ELM
       LREAL  =   Auto     real-space projection
       ALGO   =   fast     normal:38(D) fast:38-48(RMM) all:58 damped:53
    
       !IMIX = 4
       !AMIX = 0.1
       !BMIX = 0.0001
       !WC = 1000
       !INIMIX = 1
       !MIXPRE = 1
       !MAXMIX = -45
    
    !Ionic relaxation
       EDIFFG = -0.0005    stopping-criterion for IOM +:energy -:force
       NSW    =       1    number of steps for IOM
       !NBLOCK =      1     inner block ionic cfg-XDATCAR, scale T
       !KBLOCK =   1000     outer block PCF-PCDAT,DOS-DOSCAR
       IBRION =      8     ionic relax: 0-MD 1-static 2-CG 3-dampedMD
       ISIF   =      2
       POTIM  =   1.0     time-step for ionic-motion
       !TEBEG  =  600.0
       !TEEND  =  600.0     temperature during run
       SMASS  =     -1     -3:micro -2:const -1:scaled >=0:Nose mass
    
    !DOS related values:
       !EMIN   =  10.00
       !EMAX   = -10.00     energy-range for DOS
       !NEDOS = 300
       ISMEAR =      0     1,2:metal -5,0:sem/ins
       SIGMA  =   0.05     broadening in eV
       !RWIGS  = -1.0 -1.0 -1.0
       !NBANDS = 10       actual number of bands in calculation
    
    !Write flags
       !NWRITE =      2     long runs use 0 or 1
       LWAVE  = .FALSE.     write WAVECAR
       LCHARG = .FALSE.     write CHGCAR
       LVTOT  = .FALSE.    write LOCPOT, local potential
       LELF   = .FALSE.    write electronic localiz. function (ELF)
       !LORBIT = 11
       !LAECHG = .TRUE.
       !LADDGRID = .TRUE.
    
    !Parallel flags
       !NPAR   =      8     # of nodes
       LPLANE =  .FALSE.
       LSCALU = .FALSE.
       LSCALAPACK = .FALSE.

    注意的参数是IBRION=8 和 NSW=1.

    5. 计算Force Constant

    1 phonopy --fc vasprun.xml

    6. 计算Band structure

    1 phonopy --dim="4 4 4" -c POSCAR-unitcell band.conf -p -s

    其中band.conf 文件如下:

    DIM = 4 4 4
    PRIMITIVE_AXIS = 1.0 0.0 0.0  0.0 1.0 0.0  0.0 0.0 1.0
    BAND = 0.0 0.0 0.0  0.0 0.5 0.0  0.5 0.5 0.0  0.5 0.5 0.5
    BAND_LABELS = Gamma X M R
    FORCE_CONSTANTS = READ
  • 相关阅读:
    win2008R2超过激活期,但是一个小时之后就会自动强制关机的问题
    SQL数据库中出现大量用户登录错误怎么解决
    VMware上安装centos 6.3 不能联网问题
    最简单的正则表达式
    双向认证SSL原理
    【虚拟机】在VMware中安装Server2008之后配置网络连接的几种方式
    win7 windows server 2008R2下 https SSL证书安装的搭配(搭配https ssl本地测试环境)
    使用word优雅的添加代码并上传到博客园(附:批量取消图片超链接方法)
    IIS服务器多域证书使用443端口解决方案
    服务器证书安装配置指南(IIS7)
  • 原文地址:https://www.cnblogs.com/zjyx/p/6592579.html
Copyright © 2011-2022 走看看