有时我们在使用vasp计算声子谱时会出现虚频，这时可以换一种方法，用openmx结合alamode来计算
我们以Zn4C2这个结构为例，vasp优化好的POSCAR如下：
POSCAR\(1)
1.00000000000000
5.3030503048140787 0.0043751097418917 0.0000000000000000
-0.0044081956718473 5.3033109599103794 0.0000000000000000
0.0000000000000000 0.0000000000000000 33.4249000549000002
Zn C
4 2
Direct
0.4020481294372711 0.7814913255080578 0.5000117824032253
0.4020682568981326 0.2814685937223771 0.5000154217712736
0.9020980994915183 0.2815474588742708 0.5000123477693514
-0.0979667997484869 0.7815097457354251 0.5000092522639722
0.6520447475573569 0.5314929986752165 0.5000106003109016
0.1520475813642065 0.0314898574846514 0.5000106024812589
输入命令：phonopy -d --dim="3 3 1" -c POSCAR-unitcell 进行3*3的扩胞
准备文件alamode.sug.in，设置如下：
&general
PREFIX = Zn4C2
MODE = suggest
NAT = 54; NKD = 2
KD = Zn C
/
#&optimize
# DFSET = DFSET_harmonic
#/
&interaction
NORDER = 1 # 1: harmonic, 2: cubic, ..
/
&cell
1 # factor in Bohr unit 1 Bohr=0.529 Ang
8.4159408337399428969 0.0069432991603821279 0.0000000000000000
-0.0069958065312216651 8.4163544933777715788 0.0000000000000000
0.0000000000000000 0.0000000000000000 17.6817721290421001058
/
&cutoff
Zn-Zn None
Zn-C None
C-C None
/
&position
1 0.1340160431457570 0.2604971085026859 0.5000117824032253
1 0.4673493764790904 0.2604971085026859 0.5000117824032253
1 0.8006827098124237 0.2604971085026859 0.5000117824032253
1 0.1340160431457570 0.5938304418360192 0.5000117824032253
1 0.4673493764790904 0.5938304418360192 0.5000117824032253
1 0.8006827098124237 0.5938304418360192 0.5000117824032253
1 0.1340160431457570 0.9271637751693526 0.5000117824032253
1 0.4673493764790904 0.9271637751693526 0.5000117824032253
1 0.8006827098124237 0.9271637751693526 0.5000117824032253
1 0.1340227522993775 0.0938228645741257 0.5000154217712736
1 0.4673560856327109 0.0938228645741257 0.5000154217712736
1 0.8006894189660441 0.0938228645741257 0.5000154217712736
1 0.1340227522993775 0.4271561979074590 0.5000154217712736
1 0.4673560856327109 0.4271561979074590 0.5000154217712736
1 0.8006894189660441 0.4271561979074590 0.5000154217712736
1 0.1340227522993775 0.7604895312407924 0.5000154217712736
1 0.4673560856327109 0.7604895312407924 0.5000154217712736
1 0.8006894189660441 0.7604895312407924 0.5000154217712736
1 0.3006993664971728 0.0938491529580903 0.5000123477693514
1 0.6340326998305060 0.0938491529580903 0.5000123477693514
1 0.9673660331638394 0.0938491529580903 0.5000123477693514
1 0.3006993664971728 0.4271824862914236 0.5000123477693514
1 0.6340326998305060 0.4271824862914236 0.5000123477693514
1 0.9673660331638394 0.4271824862914236 0.5000123477693514
1 0.3006993664971728 0.7605158196247569 0.5000123477693514
1 0.6340326998305060 0.7605158196247569 0.5000123477693514
1 0.9673660331638394 0.7605158196247569 0.5000123477693514
1 0.9673444000838377 0.2605032485784750 0.5000092522639722
1 0.3006777334171710 0.2605032485784750 0.5000092522639722
1 0.6340110667505043 0.2605032485784750 0.5000092522639722
1 0.9673444000838377 0.5938365819118083 0.5000092522639722
1 0.3006777334171710 0.5938365819118083 0.5000092522639722
1 0.6340110667505043 0.5938365819118083 0.5000092522639722
1 0.9673444000838377 0.9271699152451417 0.5000092522639722
1 0.3006777334171710 0.9271699152451417 0.5000092522639722
1 0.6340110667505043 0.9271699152451417 0.5000092522639722
2 0.2173482491857856 0.1771643328917388 0.5000106003109016
2 0.5506815825191189 0.1771643328917388 0.5000106003109016
2 0.8840149158524523 0.1771643328917388 0.5000106003109016
2 0.2173482491857856 0.5104976662250721 0.5000106003109016
2 0.5506815825191189 0.5104976662250721 0.5000106003109016
2 0.8840149158524523 0.5104976662250721 0.5000106003109016
2 0.2173482491857856 0.8438309995584055 0.5000106003109016
2 0.5506815825191189 0.8438309995584055 0.5000106003109016
2 0.8840149158524523 0.8438309995584055 0.5000106003109016
2 0.0506825271214022 0.0104966191615505 0.5000106024812589
2 0.3840158604547355 0.0104966191615505 0.5000106024812589
2 0.7173491937880688 0.0104966191615505 0.5000106024812589
2 0.0506825271214022 0.3438299524948838 0.5000106024812589
2 0.3840158604547355 0.3438299524948838 0.5000106024812589
2 0.7173491937880688 0.3438299524948838 0.5000106024812589
2 0.0506825271214022 0.6771632858282171 0.5000106024812589
2 0.3840158604547355 0.6771632858282171 0.5000106024812589
2 0.7173491937880688 0.6771632858282171 0.5000106024812589
/
输入命令：alm alamode.sug.in > alm.log1，产生以下文件：
准备openmx的输入文件，格式如下，注意原子位置用的是分数坐标：
# # This was generated by OpenMX Viewer System.CurrrentDirectory ./ System.Name abc level.of.stdout 1 level.of.fileout 1 DATA.PATH /public/sourcecode/openmx_DATA19 Species.Number 2 <Definition.of.Atomic.Species C C6.0-s2p2d1 C_PBE19 Zn Zn6.0H-s3p2d1 Zn_PBE19H Definition.of.Atomic.Species> Atoms.Number 54 Atoms.SpeciesAndCoordinates.Unit FRAC <Atoms.SpeciesAndCoordinates 1 Zn 0.1340160 0.2604970 0.5000120 10.0 10.0 2 Zn 0.4673490 0.2604970 0.5000120 10.0 10.0 3 Zn 0.8006830 0.2604970 0.5000120 10.0 10.0 4 Zn 0.1340160 0.5938300 0.5000120 10.0 10.0 5 Zn 0.4673490 0.5938300 0.5000120 10.0 10.0 6 Zn 0.8006830 0.5938300 0.5000120 10.0 10.0 7 Zn 0.1340160 0.9271640 0.5000120 10.0 10.0 8 Zn 0.4673490 0.9271640 0.5000120 10.0 10.0 9 Zn 0.8006830 0.9271640 0.5000120 10.0 10.0 10 Zn 0.1340230 0.0938230 0.5000150 10.0 10.0 11 Zn 0.4673560 0.0938230 0.5000150 10.0 10.0 12 Zn 0.8006890 0.0938230 0.5000150 10.0 10.0 13 Zn 0.1340230 0.4271560 0.5000150 10.0 10.0 14 Zn 0.4673560 0.4271560 0.5000150 10.0 10.0 15 Zn 0.8006890 0.4271560 0.5000150 10.0 10.0 16 Zn 0.1340230 0.7604900 0.5000150 10.0 10.0 17 Zn 0.4673560 0.7604900 0.5000150 10.0 10.0 18 Zn 0.8006890 0.7604900 0.5000150 10.0 10.0 19 Zn 0.3006990 0.0938490 0.5000120 10.0 10.0 20 Zn 0.6340330 0.0938490 0.5000120 10.0 10.0 21 Zn 0.9673660 0.0938490 0.5000120 10.0 10.0 22 Zn 0.3006990 0.4271820 0.5000120 10.0 10.0 23 Zn 0.6340330 0.4271820 0.5000120 10.0 10.0 24 Zn 0.9673660 0.4271820 0.5000120 10.0 10.0 25 Zn 0.3006990 0.7605160 0.5000120 10.0 10.0 26 Zn 0.6340330 0.7605160 0.5000120 10.0 10.0 27 Zn 0.9673660 0.7605160 0.5000120 10.0 10.0 28 Zn 0.9673440 0.2605030 0.5000090 10.0 10.0 29 Zn 0.3006780 0.2605030 0.5000090 10.0 10.0 30 Zn 0.6340110 0.2605030 0.5000090 10.0 10.0 31 Zn 0.9673440 0.5938370 0.5000090 10.0 10.0 32 Zn 0.3006780 0.5938370 0.5000090 10.0 10.0 33 Zn 0.6340110 0.5938370 0.5000090 10.0 10.0 34 Zn 0.9673440 0.9271700 0.5000090 10.0 10.0 35 Zn 0.3006780 0.9271700 0.5000090 10.0 10.0 36 Zn 0.6340110 0.9271700 0.5000090 10.0 10.0 37 C 0.2173480 0.1771640 0.5000110 2.0 2.0 38 C 0.5506820 0.1771640 0.5000110 2.0 2.0 39 C 0.8840150 0.1771640 0.5000110 2.0 2.0 40 C 0.2173480 0.5104980 0.5000110 2.0 2.0 41 C 0.5506820 0.5104980 0.5000110 2.0 2.0 42 C 0.8840150 0.5104980 0.5000110 2.0 2.0 43 C 0.2173480 0.8438310 0.5000110 2.0 2.0 44 C 0.5506820 0.8438310 0.5000110 2.0 2.0 45 C 0.8840150 0.8438310 0.5000110 2.0 2.0 46 C 0.0506830 0.0104970 0.5000110 2.0 2.0 47 C 0.3840160 0.0104970 0.5000110 2.0 2.0 48 C 0.7173490 0.0104970 0.5000110 2.0 2.0 49 C 0.0506830 0.3438300 0.5000110 2.0 2.0 50 C 0.3840160 0.3438300 0.5000110 2.0 2.0 51 C 0.7173490 0.3438300 0.5000110 2.0 2.0 52 C 0.0506830 0.6771630 0.5000110 2.0 2.0 53 C 0.3840160 0.6771630 0.5000110 2.0 2.0 54 C 0.7173490 0.6771630 0.5000110 2.0 2.0 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang <Atoms.UnitVectors 15.9091570 0.0000000 0.0000000 -0.0000997 15.9099390 0.0000000 0.0000000 0.0000000 33.4249000 Atoms.UnitVectors> scf.XcType GGA-PBE scf.SpinPolarization off scf.ElectronicTemperature 300.0 scf.energycutoff 220.0 scf.maxIter 100 scf.EigenvalueSolver band scf.Kgrid 8 8 1 scf.Mixing.Type rmm-diisk scf.Init.Mixing.Weight 0.05 scf.Min.Mixing.Weight 0.01 scf.Max.Mixing.Weight 0.30 scf.Mixing.History 25 scf.Mixing.StartPulay 15 scf.criterion 1.0e-7 MD.Type nomd MD.maxIter 1 MD.TimeStep 1.0 MD.Opt.criterion 0.0003
输入命令：python /public/sourcecode/alamode/displace.py --OpenMX=open.in --mag=0.01 -pf Zn4C2.pattern_HARMONIC，这时会自动产生移动过原子位置的openmx的输入文件，如下图所示：
在不同的文件夹里分别计算openmx，提交任务：
提取力常数，使用命令python /public/sourcecode/alamode/extract.py --OpenMX=open.in 1/*.out 2/*.out 3/*.out 4/*.out > DFSET_harmonic
修改alamode.in,修改MODE = optimize，添加&fitting
DFSET = DFSET_harmonic
/
如下所示：
&general
PREFIX = Zn4C2
MODE = optimize
NAT = 54; NKD = 2
KD = Zn C
/
&optimize
DFSET = DFSET_harmonic
/
&interaction
NORDER = 1 # 1: harmonic, 2: cubic, ..
/
&cell
1 # factor in Bohr unit 1 Bohr=0.529 Ang
8.4159408337399428969 0.0069432991603821279 0.0000000000000000
-0.0069958065312216651 8.4163544933777715788 0.0000000000000000
0.0000000000000000 0.0000000000000000 17.6817721290421001058
/
&cutoff
Zn-Zn None
Zn-C None
C-C None
/
&position
1 0.1340160431457570 0.2604971085026859 0.5000117824032253
1 0.4673493764790904 0.2604971085026859 0.5000117824032253
1 0.8006827098124237 0.2604971085026859 0.5000117824032253
1 0.1340160431457570 0.5938304418360192 0.5000117824032253
1 0.4673493764790904 0.5938304418360192 0.5000117824032253
1 0.8006827098124237 0.5938304418360192 0.5000117824032253
1 0.1340160431457570 0.9271637751693526 0.5000117824032253
1 0.4673493764790904 0.9271637751693526 0.5000117824032253
1 0.8006827098124237 0.9271637751693526 0.5000117824032253
1 0.1340227522993775 0.0938228645741257 0.5000154217712736
1 0.4673560856327109 0.0938228645741257 0.5000154217712736
1 0.8006894189660441 0.0938228645741257 0.5000154217712736
1 0.1340227522993775 0.4271561979074590 0.5000154217712736
1 0.4673560856327109 0.4271561979074590 0.5000154217712736
1 0.8006894189660441 0.4271561979074590 0.5000154217712736
1 0.1340227522993775 0.7604895312407924 0.5000154217712736
1 0.4673560856327109 0.7604895312407924 0.5000154217712736
1 0.8006894189660441 0.7604895312407924 0.5000154217712736
1 0.3006993664971728 0.0938491529580903 0.5000123477693514
1 0.6340326998305060 0.0938491529580903 0.5000123477693514
1 0.9673660331638394 0.0938491529580903 0.5000123477693514
1 0.3006993664971728 0.4271824862914236 0.5000123477693514
1 0.6340326998305060 0.4271824862914236 0.5000123477693514
1 0.9673660331638394 0.4271824862914236 0.5000123477693514
1 0.3006993664971728 0.7605158196247569 0.5000123477693514
1 0.6340326998305060 0.7605158196247569 0.5000123477693514
1 0.9673660331638394 0.7605158196247569 0.5000123477693514
1 0.9673444000838377 0.2605032485784750 0.5000092522639722
1 0.3006777334171710 0.2605032485784750 0.5000092522639722
1 0.6340110667505043 0.2605032485784750 0.5000092522639722
1 0.9673444000838377 0.5938365819118083 0.5000092522639722
1 0.3006777334171710 0.5938365819118083 0.5000092522639722
1 0.6340110667505043 0.5938365819118083 0.5000092522639722
1 0.9673444000838377 0.9271699152451417 0.5000092522639722
1 0.3006777334171710 0.9271699152451417 0.5000092522639722
1 0.6340110667505043 0.9271699152451417 0.5000092522639722
2 0.2173482491857856 0.1771643328917388 0.5000106003109016
2 0.5506815825191189 0.1771643328917388 0.5000106003109016
2 0.8840149158524523 0.1771643328917388 0.5000106003109016
2 0.2173482491857856 0.5104976662250721 0.5000106003109016
2 0.5506815825191189 0.5104976662250721 0.5000106003109016
2 0.8840149158524523 0.5104976662250721 0.5000106003109016
2 0.2173482491857856 0.8438309995584055 0.5000106003109016
2 0.5506815825191189 0.8438309995584055 0.5000106003109016
2 0.8840149158524523 0.8438309995584055 0.5000106003109016
2 0.0506825271214022 0.0104966191615505 0.5000106024812589
2 0.3840158604547355 0.0104966191615505 0.5000106024812589
2 0.7173491937880688 0.0104966191615505 0.5000106024812589
2 0.0506825271214022 0.3438299524948838 0.5000106024812589
2 0.3840158604547355 0.3438299524948838 0.5000106024812589
2 0.7173491937880688 0.3438299524948838 0.5000106024812589
2 0.0506825271214022 0.6771632858282171 0.5000106024812589
2 0.3840158604547355 0.6771632858282171 0.5000106024812589
2 0.7173491937880688 0.6771632858282171 0.5000106024812589
/
输入命令：alm alamode.in > alm.log2，产生.xml文件
准备官网第四步文件phband.in，主要是晶格常数，这里是没有扩胞的，添加k点路径，如下，之后执行命令anphon phband.in > phband.log，
&general
PREFIX = omx
MODE = phonons
FCSXML = Zn4C2.xml
NKD = 2
KD = Zn C
/
&cell # in Bohr, 1 Bohr=0.529 Ang
1.0
2.8053136112466476323 0.0023144330534607093 0.0000000000000000
-0.0023319355104072217 2.8054514977925907026 0.0000000000000000
0.0000000000000000 0.0000000000000000 17.6817721290421001058
/
&kpoint
1 # KPMODE = 1: line mode
G 0.00000 0.00000 0.00000 R 0.50000 0.50000 0.00000 101
R 0.50000 0.50000 0.00000 Y 0.00000 0.50000 0.00000 101
Y 0.00000 0.50000 0.00000 G 0.00000 0.00000 0.00000 101
G 0.00000 0.00000 0.00000 X 0.50000 0.00000 0.00000 101
/
产生了omx.band文件，即为声子谱
详细可见alamode官网：
No Comments
Leave a comment Cancel