VASP+DFPT+Phonopy 计算声子过程
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VASP+DFPT+Phonopy 计算声子过程
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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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