VASP+FDM+Phonopy 计算声子过程
2024-05-13 12:00:10
以Ammonia为例，基本翻译自：https://atztogo.github.io/phonopy/procedure.html#tutorial.
1. 结构优化. 输入文件如下：
INCAR !System settingsSYSTEM = AmmoniaPREC = accurate low, normal, accurateISTART = 0 job : 0-new 1-cont 2-samecutICHARG = 2 charge: 0-INIWAV 1-CHGCAR 2-atom 10-nonselfISPIN = 1 spin polarized? 1:no 2:yesINIWAV = 1 0-jellium 1-rand!Electronic RelaxationENCUT = 200.0 eVNELM = 1000 max e SCNELMIN = 2 min e SCNELMDL = -5 non-SC +:every -:firstEDIFF = 1.0E-6 stopping-criterion for ELMLREAL = Auto real-space projectionALGO = 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 relaxationEDIFFG = -0.0005 stopping-criterion for IOM +:energy -:forceNSW = 500 number of steps for IOM!NBLOCK = 1 inner block ionic cfg-XDATCAR, scale T!KBLOCK = 1000 outer block PCF-PCDAT,DOS-DOSCARIBRION = 2 ionic relax: 0-MD 1-static 2-CG 3-dampedMDISIF = 2POTIM = 1.0 time-step for ionic-motion!TEBEG = 600.0!TEEND = 600.0 temperature during runSMASS = -1 -3:micro -2:const -1:scaled >=0:Nose mass!DOS related values:!EMIN = 10.00!EMAX = -10.00 energy-range for DOS!NEDOS = 300ISMEAR = 0 1,2:metal -5,0:sem/insSIGMA = 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 1LWAVE = .FALSE. write WAVECARLCHARG = .FALSE. write CHGCARLVTOT = .FALSE. write LOCPOT, local potentialLELF = .FALSE. write electronic localiz. function (ELF)!LORBIT = 11!LAECHG = .TRUE.!LADDGRID = .TRUE.!Parallel flagsNPAR = 8 # of nodesLPLANE = .FALSE.LSCALU = .FALSE.LSCALAPACK = .FALSE.POSCAR Ammonia_rlx 1.05.1305 0.0 0.00.0 5.1305 0.00.0 0.0 5.1305N H 4 12 Cart1.0789441 1.0789441 1.07894411.4863058 4.0515558 3.64419413.6441941 1.4863058 4.05155584.0515558 3.6441941 1.48630581.9095721 1.3477823 0.57102461.9942253 3.2209279 3.91303233.1362746 0.6556779 3.78271764.5594753 4.4748221 1.21746761.3477823 0.5710246 1.90957211.2174676 4.5594753 4.47482213.2209279 3.9130323 1.99422530.5710246 1.9095721 1.34778230.6556779 3.7827176 3.13627464.4748221 1.2174676 4.55947533.9130323 1.9942253 3.22092793.7827176 3.1362746 0.6556779KPOINTS Automatic mesh 0 MP5 5 50 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 0.00000000000000000.0000000000000000 5.1304999999999996 0.00000000000000000.0000000000000000 0.0000000000000000 5.1304999999999996N H 4 12 Direct0.2173355638189437 0.2173355638189437 0.21733556381894370.2826644166897822 0.7826644166897819 0.71733556381894370.7173355638189437 0.2826644166897822 0.78266441668978190.7826644166897819 0.7173355638189437 0.28266441668978220.3844041525928144 0.2739307062557181 0.12569294443649810.3743070360722207 0.6155958474071853 0.77393070625571810.6256929444364983 0.1155958474071856 0.72606927425300750.8743070360722203 0.8844041525928147 0.22606927425300770.2739307062557181 0.1256929444364981 0.38440415259281440.2260692742530077 0.8743070360722203 0.88440415259281470.6155958474071853 0.7739307062557181 0.37430703607222070.1256929444364981 0.3844041525928144 0.27393070625571810.1155958474071856 0.7260692742530075 0.62569294443649830.8844041525928147 0.2260692742530077 0.87430703607222030.7739307062557181 0.3743070360722207 0.61559584740718530.7260692742530075 0.6256929444364983 0.11559584740718560.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+000.00000000E+00 0.00000000E+00 0.00000000E+00
3. 构建超胞
1 python /home/zjyx/softwares/phonopy-1.10.10/bin/phonopy --vasp -c POSCAR-unitcell -d --dim="4 4 4"
在这一步后，将会产生若干个POSCAR-??? 文件，可以用以下script将其移动到对应的文件夹内以方便后续计算。同时，也需在当前文件夹内准备好待用的其他输入文件。需要改的参数有INCAR里的IBRION， NSW和KPOINTS里的mesh points.
script:
1 #! /usr/bin/env python
2
3 '''
4 mv all POSCAR-??? files to a new created disps directories, and
5 copy other inputs files to the all subdirectries
6 '''
7
8 import os
9 import sys
10 from shutil import copy, move
11
12 other_inp = ['INCAR', 'KPOINTS', 'POTCAR']
13
14 n_disp = 1
15 while True:
16 if os.path.isfile('POSCAR-%03d'% n_disp):
17 n_disp += 1
18 else:
19 break
20
21 if not os.path.isdir('disps'):
22 os.mkdir('disps')
23
24 for i in range(n_disp):
25 ''' disps-000 to store perfect supercell without perturbations'''
26 crt_dir = 'disps'+'/'+'disp-%03d'%i
27 if not os.path.isdir(crt_dir):
28 os.mkdir(crt_dir)
29 for _file in other_inp:
30 copy(_file, crt_dir)
31 if i != 0:
32 copy('POSCAR-%03d'%i, crt_dir+'/'+'POSCAR')
33 else:
34 copy('SPOSCAR', crt_dir+'/'+'POSCAR')INCAR：
!System settingsSYSTEM = AmmoniaPREC = normal low, normal, accurateISTART = 0 job : 0-new 1-cont 2-samecutICHARG = 2 charge: 0-INIWAV 1-CHGCAR 2-atom 10-nonselfISPIN = 1 spin polarized? 1:no 2:yesINIWAV = 1 0-jellium 1-rand!Electronic RelaxationENCUT = 200.0 eVNELM = 1000 max e SCNELMIN = 2 min e SCNELMDL = -5 non-SC +:every -:firstEDIFF = 1.0E-6 stopping-criterion for ELMLREAL = Auto real-space projectionALGO = 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 relaxationEDIFFG = -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-DOSCARIBRION = -1 ionic relax: 0-MD 1-static 2-CG 3-dampedMDISIF = 2POTIM = 1.0 time-step for ionic-motion!TEBEG = 600.0!TEEND = 600.0 temperature during runSMASS = -1 -3:micro -2:const -1:scaled >=0:Nose mass!DOS related values:!EMIN = 10.00!EMAX = -10.00 energy-range for DOS!NEDOS = 300ISMEAR = 0 1,2:metal -5,0:sem/insSIGMA = 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 1LWAVE = .FALSE. write WAVECARLCHARG = .FALSE. write CHGCARLVTOT = .FALSE. write LOCPOT, local potentialLELF = .FALSE. write electronic localiz. function (ELF)!LORBIT = 11!LAECHG = .TRUE.!LADDGRID = .TRUE.!Parallel flags!NPAR = 8 # of nodesLPLANE = .FALSE.LSCALU = .FALSE.LSCALAPACK = .FALSE.
KPOINTS:
Automatic mesh 0 MP1 1 10 0 0
4. 用VASP做超胞计算.
5. 计算Force Sets
1 #! /usr/bin/env python
2
3 # calculate force costant matrix
4
5 import os
6 import sys
7
8 i = 1
9 width = 3
10
11 if os.path.isfile('qe.in'):
12 mode = 'pwscf'
13 post_filename = '.00.out'
14 pre_pathname = "supercell"
15 supercell_dir = "supercells"
16 elif os.path.isfile('rmg.in'):
17 mode = 'rmg'
18 post_filename = '.in.00.log'
19 pre_pathname = "supercell"
20 supercell_dir = "supercells"
21 elif os.path.isfile('SPOSCAR'):
22 mode = 'vasp'
23 post_filename = 'vasprun.xml'
24 pre_pathname = "disp"
25 supercell_dir = "disps"
26 else:
27 print "Error: unitcell not found, exit."
28 sys.exit(1)
29
30 force_cmd = 'python /home/zjyx/softwares/phonopy-1.10.10/bin/phonopy --%s -f'% mode
31
32 while True:
33 path_tmp = '{pre_pathname}-{0:0{width}}'.format(i,
34 pre_pathname=pre_pathname,
35 width=width)
36 pathname = supercell_dir + ('/%s'% path_tmp)
37 if os.path.exists(pathname):
38 i += 1
39 force_cmd += ' %s/%s'%(pathname, post_filename)
40 else:
41 break
42
43 try:
44 os.system('%s'% force_cmd)
45 except:
46 print "Error: cannot operate command, exit."
47 sys.exit(1)
48 else:
49 print ('Force sets done!\n')
50 print (' total files: %d\n'%(i-1))这样当前目录下会出现FORCE_SETS文件。
6. 计算Band structure
1 #!/bin/bash 2 3 # plot band structure 4 5 if [ -e rmg.in ]; then 6 mode=rmg 7 input=rmg.in 8 elif [ -e qe.in ]; then 9 mode=pwscf 10 input=qe.in 11 elif [ -e POSCAR-unitcell ]; then 12 mode=vasp 13 input=POSCAR-unitcell 14 else 15 echo -e "No default unitcell file found.\n" 16 exit 1 17 fi 18 19 python /home/zjyx/softwares/phonopy-1.10.10/bin/phonopy --$mode -c $input -s -p band.conf 20 21 exit 0
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
转载于:https://www.cnblogs.com/zjyx/p/6614383.html
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