原子分子物理中用高斯画态密度图的方法.docx
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原子分子物理中用高斯画态密度图的方法
原子分子物理中用高斯画态密度图的方法
用GaussSum用高斯画态密度图的方法
1、用实验室现成的GaussSum做DOS图时,发现log文件过大分析不了,下载到最新版本的问题就解决了。
2、经常出现cclibhasproblemsparsing***.log问题,检查自己的log文件是否完整。
3、关于做PDOS(重点哈),做单点能计算时必须要有pop=fulliop(3/33=1,3/36=-1),关键字,这在GaussSum帮助文件和例子里面写得很详细。
至于做PDOS的时候,需要有group.txt文件,选择做atoms时,具体的两个要求是每个原子要列出以及所列原子不能重复,这里我还得补充一点group.txt格式,
atoms
part1(你所想要分析的某个分子部分)
1-5,8-20,30(该部分原子序号)
part2
6-7,21-29,31-33(注意了,直接保存就可以,下面不能有空行,我被这个给整惨了)
在选择用orbitals时,大致一样,唯一不同就是不必列出所有的轨道。
4、就以上例子分析,我要的结果是part1和part2的PDOS,但GaussSum做出来的part1和part2的图的结果是part1和total(图上显示的是part2,经过数据对比很明显就是total)或者part2和total(同理),估计是我下载的软件bug,但可以从它产生的DOSSpectrum.txt文件(里面有你想要的part1,part2,total)提取数据在origin里面作图,结果就很好了。
5、在做COOP时,和做PDOS一个样。
关于做其他图,遇到的问题就没什么了,只要你的log文件没错,基本就okay!
WorkedExample
Description
Astudyoftheelectronicstructureandvibrationalspectrumof1,4-divinyl-benzene(attheB3LYP/STO-3Gleveloftheory)usingGaussian03W.
ConfiguringGaussSum
IopenedtheSettingsdialogbox,byclickingonFile/Settings,andverifiedthatthelocationoftheGnuplotexecutablewascorrectbyclickingontheTestbutton.
Geometryoptimisation
∙Inputfile:
[PhCCCC_gopt.gjf]
∙Partialoutputfile:
[PhCCCC_gopt_partial.out]
∙Completeoutputfile:
[PhCCCC_gopt.out]
DuringtheinitialSCFcalculation,IranGaussSum("MonitorSCF";defaults;PhCCCC_gopt_partial.out)toseewhetherthecalculationwasconverging.Theresultisshownbelow.Thelineisheadingtowardszero,whichindicatesthattheSCFisconverging.
Theprogressofthegeometryoptimisationwasalsomonitoredduringthecalculation.Thegeometryoptimisationproceededsmoothlytoanenergyminimumasshownbythegraphbelow("MonitorGeoOpt";defaults;PhCCCC_gopt.out).
Molecularorbitalinformation
∙Inputfile:
[PhCCCC_gopt.gjf]
∙Outputfile:
[PhCCCC_gopt.out]
∙GaussSumoutputs:
[gausssum2.1/orbital_data.txt] [gausssum2.1/DOS_spectrum.txt]
Iextractedthemolecularorbitalinformationfromtheoutputfileofthegeometryoptimisation("Orbitals";defaults;PhCCCC_gopt.out).Molecularorbitalinformationwaswrittentotheorbital_data.txtfileinasubdirectorycalledgausssum2.1.Informationonthefrontierorbitalsisshownbelow.
MOeVSymmetry
40L+47.42BG
39L+34.96AU
38L+23.01BG
37L+12.46AU
36LUMO1.02AU
35HOMO-4.17BG
34H-1-5.31BG
33H-2-5.78AU
32H-3-7.17BG
31H-4-7.82AG
Adensityofstatesdiagramwasconvolutedfromthemolecularorbitaldata("Orbitals";DOS,start=-15,end=8,FWHM=0.3;PhCCCC_gopt.out).Itisshownbelow.Thedatausedtodrawthisgraphiscontainedingausssum2.1/DOS_spectrum.txt.
∙Input:
[PhCCCC_pop.gjf]
∙Output:
[PhCCCC_pop.out]
∙GaussSuminput:
[gausssum2.1/groups.txt]
∙GaussSumoutputs:
[gausssum2.1/orbital_data.txt] [gausssum2.1/DOS_spectrum.txt] [gausssum2.1/origin_orbs.txt]
Iwantedtodescribeeachmolecularorbitalintermsofapercentcontributionfromthebenzeneportion,andapercentcontributionfromthedivinylportion.GaussSumcanuseMullikenpopulationanalysistodothis(pleasebeawarethatMullikenpopulationanalysishassomesevereshortcomings).Firstofall,IneededtomakeGaussianoutputorbitaloverlapinformationandinformationonthemolecularorbitalcoefficients.ThisrequiredasinglepointenergycalculationwiththekeywordsPOP=FULLIOP(9/33=1,9/36=-1).
Next,Icreatedafilecalledgroups.txtinthegausssum2.1subdirectory,whichcontainedthefollowinglines:
atoms
C6H4
1-8,19-20
C=C
9-18
Finally,IusedGaussSumtocalculatethemolecularorbitalcontributionsagain("Orbitals";defaults;PhCCCC_pop.out,gausssum2.1/groups.txt).Thistime,orbital_data.txtcontainedmoreinformation(seebelowforinformationonthefrontierorbitals).TheHOMOisabout50/50C6H4 anddivinyl.Theso-called'accuratevalues'shouldbeignored,althoughtheyarerequiredforthe"Electronictransitions"optiontocalculatechangesinelectrondensity.(Notethatthesecolumnsaretab-separatedandsocanbeimportedeasilyintospreadsheetsoftware.)
MOeVSymmetryC6H4C=CAccuratevalues(fortheElectronictransitionsmodule)
38L+23.01BG17830.1684302093240.83157002452
37L+12.46AU10000.9998186530490.000181859510613
36LUMO1.02AU54460.5432821273180.456725399153
35HOMO-4.17BG54460.5417785039970.458228594354
34H-1-5.31BG10000.9998774411720.000141570363359
33H-2-5.78AU15850.1548993041330.845103027118
TheinitialDOSspectrumcreatedbyGaussSumdidnotincludeanyofthevirtualorbitals.Asaresult,Iwantedtochangethestartandendpointofthespectrum,butIdidnotwanttorecalculateallofthecontributionsofthegroups.Iset"Useexistingorbital_data.txt?
"toTRUE,andalteredthevaluesofstartandenduntilIwashappy("Orbitals";start=-15,end=8,FWHM=0.3,"Useexistingorbital_data.txt?
"=TRUE;PhCCCC_pop.out):
Anicerimagecanbecreatedusingspreadsheetsoftware,oraprogramsuchasMicrocalOrigin,andthefilegausssum2.1/DOS_spectrum.txt.TheimagebelowwascreatedusingMicrocalOrigin(forLinux,tryScigraphicaorGrace).
InsteadofdrawingaDOScurve,youmayprefertouseamorestraightforwarddepictionofthebreakdownofmolecularorbitalsbetweenvariousgroupsinamolecule.Todoso,set"Createoriginorbs.txt"toTRUE,andrerunGaussSum("Orbitals";start=-15,end=8,FWHM=0.3,"Useexistingorbital_data.txt?
"=TRUE,"Createoriginorbs.txt?
"=TRUE;PhCCCC_pop.out).OriginorGracemaythenbeusedtocreatetheimageshownbelowusingthedataingausssum2.1/origin_orbs.txt(itmaytakesomepractice-inOriginyouneedtosetthecolumnsXYXY,andplotthefourcolumnsusing2-pointsegments).
∙Input:
[PhCCCC_pop.gjf]
∙Output:
[PhCCCC_pop.out]
∙GaussSuminput:
[gausssum2.1/groups.txt]
∙GaussSumoutputs:
[gausssum2.1/COOP_data.txt] [gausssum2.1/COOP_spectrum.txt]
TheinteractionbetweenthetwogroupscanbevisualisedusingaCOOP(CrystalOrbitalOverlapPopulation)diagram.Thisinteractionismeasuredbythedegreeofpositive/negativeoverlapforaparticularmolecularorbital.Formoreinformationonitsuse,seethepaperofHerlemandLakardlistedinthebibliography.ThediagrambelowwascreatedfromPhCCCC_pop.outusingGaussSum("Orbitals";COOP,start=-15,end=8,FWHM=0.3;PhCCCC_pop.out,gausssum2.1/groups.txt).
Vibrationalspectrum
∙Input:
[PhCCCC_IR.gjf]
∙Output:
[PhCCCC_IR.out]
∙GaussSumoutputs:
[gausssum2.1/IRSpectrum.txt] [gausssum2.1/IRSpectrum.txt(afterscaling)]
IcalculatedthevibrationalfrequenciesofdivinylbenzeneandtheirassociatedIRintensities.GaussSumextractsthisinformationfromthelogfileintogausssum/IRSpectrum.txt("Frequencies";start=0,end=1000,numpts="500",FWHM=3,Scalingfactors=(General,1.00);PhCCCC_IR.out):
NormalModes
ModeLabelFreq(cm-1)IRact
1AU52.78810.0323
2BG83.93680.0
3AU148.15710.3826
4BU178.67270.2686
Iwantedtoscaleallnormalmodesgreaterthan1000cm-1 by0.5(thisisnotarealexample!
:
-).IopenedIRSpectrum.txtinExcel,andchangedthevaluesforthescalingfactorsfrom1.00to0.5forthosenormalmodesgreaterthan1000cm-1.IresavedIRSpectrum.txtinthesameformat(Tab-separated)andlocation.Afterchoosingthe"Frequencies"optionIchose"Individualscalingfactors"andranGaussSumagain("Frequencies";start=0,end=1000,numpts=500,FWHM=3,scalingfactors=Individual;PhCCCC_IR.out,gausssum2.1/IRSpectrum.txt).Theresultisshownbelow.
UV-VisibleSpectrum
∙Input:
[PhCCCC_TD.gjf]
∙Output:
[PhCCCC_TD.out]
∙GaussSumoutputs:
[gausssum2.1/UVSpectrum.txt] [gausssum2.1/UVData.txt]
IwantedtocalculatetheUV-Visabsorptionspectrumofdivinylbenzene.IaddedthekeywordIOP(9/40=2)totheTD-DFTcommand,tooutputinformationonsmallercontributionstoeachelectronictransition.
Iranthe"Electronictransitions"optionwiththedefaultsettings("Electronictransitions";start=300,end=800,numpts=500,fwhm=3000;PhCCCC_TD.out)butnographwasdrawn,andtherewasamessage"Therearenopeaksinthiswavelengthrange!
".Ilookedatgausssum2.1/UVData.txtandsawthatthelowestenergypeakwasatabout230nm.Iranthe"Electronictransitions"optionagain,thistimeusingmoreappropriatevaluesforthestartandendofthediagram("Electronictransitions";start=170,end=270,numpts=500,fwhm=3000;PhCCCC_TD.out)andtheresultisshownbelow(thisinformationiswrittentogausssum2.1/UVSpectrum.txt).
Thefilegausssum2.1/UVData.txtiscreatedcontainingthefollowinginformation:
No.eVnmOsc.Str.Symmetry
15.3351232.390.1695Singlet-BU
25.3747230.680.6789Singlet-BU
36.2152199.480.0Singlet-AG
BecauseIranthe"Orbitals"moduleearlierusingagroups.txt,informationaboutthechangeintheelectrondensityofvariousgroupsinthemoleculeisalsoprintedingausssum2.1/UVData.txt.Notethatthisinformationisveryapproximate,asitiscalculatedonthebasisthatthesquaresofthecontributionsofthevariousone-electrontransitionsequalsone,whichis*not*true,butmaybealmosttrue:
-).
No.MajorcontribsMinorcontribsC6H4C=C
1H-1->L(47%),H->L(-15%),H->L+1(36%)76-->71(-5)24-->29(5)
2H-1->L(13%),H->L(61%)H->L+1(6%)62-->58(-4)38-->42(4)
3H-2->LUMO(62%),H->L+2(-38%)30-->40(10)70-->60(-10)