原子分子物理中用高斯画态密度图的方法.docx

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）