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VASP+DFPT+Phonopy 计算声子过程

發布時間：2024/1/3 综合教程 24 生活家

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以Ammonia為例,基本翻譯自http://atztogo.github.io/phonopy/vasp.html#how-to-run。

1. 結構優化. 輸入文件如下：

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

--------------------------------------------------------------------------------

由于聲子對結構優化比較敏感，這兒的 PREC=accurate.

2. 構建優化過的單胞

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. 構建超胞（但是不需要計算）,并且重命名SPOSCAR為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計算.

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.

注意的參數是IBRION=8 和 NSW=1.

5. 計算Force Constant

1 phonopy --fc vasprun.xml

6. 計算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

總結

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