原子分子物理中用高斯畫態(tài)密度圖方法計(jì)劃

1、用GaussSum用高斯畫態(tài)密度圖的方法1、用實(shí)驗(yàn)室現(xiàn)成的GaussSum做DOS圖時(shí)，發(fā)現(xiàn)log文件過大解析不了，下載到最新版本的問題就解決了。2、經(jīng)常出現(xiàn)cclibhasproblemsparsing*.log問題，檢查自己的log文件可否完滿。3、關(guān)于做PDOS（重點(diǎn)哈），做單點(diǎn)能計(jì)算時(shí)必定要有pop=fulliop(3/33=1,3/36=-1),關(guān)鍵字，這在GaussSum幫助文件和例子里面寫得很詳細(xì)。至于做PDOS的時(shí)候，需要有g(shù)roup.txt文件，選擇做atoms時(shí)，詳細(xì)的兩個(gè)要求是每個(gè)原子要列出以及所列原子不能夠重復(fù)，這里我還得補(bǔ)充一點(diǎn)group.txt格式，atomspar

2、t1（你所想要解析的某個(gè)分子部分）1-5,8-20,30（該部分原子序號(hào)）part26-7,21-29,31-33（注意了，直接保存就可以，下面不能夠有空行，我被這個(gè)給整慘了）在選擇用orbitals時(shí)，大體相同，唯一不相同就是不用列出所有的軌道。4、就以上例子解析，我要的結(jié)果是part1和part2的PDOS,但GaussSum做出來的和part2的圖的結(jié)果是part1和total（圖上顯示的是part2，經(jīng)過數(shù)據(jù)比較很明顯就是part1total）也許part2和total（同理），估計(jì)是我下載的軟件bug，但能夠從它產(chǎn)生的DOSSpectrum.txt文件（里面有你想要的part1，pa

3、rt2，total）提取數(shù)據(jù)在origin里面作圖，結(jié)果就很好了。5、在做COOP時(shí)，和做PDOS一個(gè)樣。關(guān)于做其他圖，遇到的問題就沒什么了，只要你的log文件沒錯(cuò)，基本就okay！WorkedExampleDescriptionAstudyoftheelectronicstructureandvibrationalspectrumof1,4-divinyl-benzene(attheB3LYP/STO-3Gleveloftheory)usingGaussian03W.ConfiguringGaussSumIopenedtheSettingsdialogbox,byclickingon,and

4、verifiedthatthelocationoftheGnuplotexecutablewascorrectbyclickingontheTestbutton.GeometryoptimisationInputfile:PhCCCC_gopt.gjfPartialoutputfile:PhCCCC_gopt_partial.outCompleteoutputfile:PhCCCC_gopt.outDuringtheinitialSCFcalculation,IranGaussSum(MonitorSCF;defaults;PhCCCC_gopt_partial.out)toseewhethe

5、rthecalculationwasconverging.Theresultisshownbelow.Thelineisheadingtowardszero,whichindicatesthattheSCFisconverging.Theprogressofthegeometryoptimisationwasalsomonitoredduringthecalculation.Thegeometryoptimisationproceededsmoothlytoanenergyminimumasshownbythegraphbelow(MonitorGeoOpt;defaults;PhCCCC_g

6、opt.out).MolecularorbitalinformationInputfile:PhCCCC_gopt.gjfOutputfile:PhCCCC_gopt.outGaussSumoutputs:gausssum2.1/orbital_data.txtgausssum2.1/DOS_spectrum.txtIextractedthemolecularorbitalinformationfromtheoutputthegeometryoptimisation(Orbitals;defaults;PhCCCC_gopt.out).Molecularorbitalinformationwa

7、swrittentotheorbital_data.txtasubdirectorycalledgausssum2.1.Informationonthefrontierorbitalsisshownbelow.MOeVSymmetry40L+47.42BG39L+34.96AU38L+23.01BG37L+12.46AU36LUMO1.02AU35HOMO-4.17BG34H-1-5.31BG33H-2-5.78AU32H-3-7.17BG31H-4-7.82AGAdensityofstatesdiagramwasconvolutedfromthemolecularorbitaldata(Or

8、bitals;DOS,start=-15,end=8,FWHM=0.3;PhCCCC_gopt.out).Itisshownbelow.Thedatausedtodrawthisgraphiscontainedingausssum2.1/DOS_spectrum.txt.Input:PhCCCC_pop.gjfOutput:PhCCCC_pop.outGaussSuminput:gausssum2.1/groups.txtGaussSumoutputs:gausssum2.1/orbital_data.txtgausssum2.1/DOS_spectrum.txtgausssum2.1/ori

9、gin_orbs.txtIwantedtodescribeeachmolecularorbitalintermsofapercentcontributionfromthebenzeneportion,andapercentcontributionfromthedivinylportion.GaussSumcanuseMullikenpopulationanalysistodothis(pleasebeawarethatMullikenpopulationanalysishassomesevereshortcomings).Firstofall,IneededtomakeGaussianoutp

10、utorbitaloverlapinformationandinformationonthemolecularorbitalcoefficients.ThisrequiredasinglepointenergycalculationwiththekeywordsPOP=FULLIOP(9/33=1,9/36=-1).Next,Icreatedagroups.txtinthegausssum2.1subdirectory,whichcontainedthefollowinglines:atomsC6H41-8,19-20C=C9-18Finally,IusedGaussSumtocalculat

11、ethemolecularorbitalcontributionsagain(Orbitals;defaults;PhCCCC_pop.out,gausssum2.1/groups.txt).Thistime,orbital_data.txtcontainedmoreinformation(seebelowforinformationonthefrontierorbitals).TheHOMOisabout50/50C6H4anddivinyl.Theso-calledaccuratevaluesshouldbeignored,althoughtheyarerequiredfortheElec

12、tronictransitionsoptiontocalculatechangesinelectrondensity.(Notethatthesecolumnsaretab-separatedandsocanbeimportedeasilyintospreadsheetsoftware.)MOeVSymmetryC6H4C=CAccuratevalues(fortheElectronictransitionsmodule)38L+23.01BG17830.8315700245237L+12.46AU10000.9998186530490.061336LUMO1.02AU54460.543282

13、1273180.45672539915335HOMO-4.17BG54460.5417785039970.45822859435434H-1-5.31BG10000.9998774411720.335933H-2-5.78AU15850.845103027118TheinitialDOSspectrumcreatedbyGaussSumdidnotincludeanyofthevirtualorbitals.Asaresult,Iwantedtochangethestartandendpointofthespectrum,butIdidnotwanttorecalculateallofthec

14、ontributionsofthegroups.IsetUseexistingorbital_data.txt?toTRUE,andalteredthevaluesofstartandenduntilIwashappy(Orbitals;start=-15,end=8,FWHM=0.3,Useexistingorbital_data.txt?=TRUE;PhCCCC_pop.out):Anicerimagecanbecreatedusingspreadsheetsoftware,oraprogramsuchasMicrocalOrigin,andthe.Theimagebelowwascrea

15、tedusingMicrocalOrigin(forLinux,tryScigraphicaorGrace).InsteadofdrawingaDOScurve,youmayprefertouseamorestraightforwarddepictionofthebreakdownofmolecularorbitalsbetweenvariousgroupsinamolecule.Todoso,setCreateoriginorbs.txttoTRUE,andrerunGaussSum(Orbitals;start=-15,end=8,FWHM=0.3,Useexistingorbital_d

16、ata.txt?=TRUE,Createoriginorbs.txt?=TRUE;PhCCCC_pop.out).OriginorGracemaythenbeusedtocreatetheimageshownbelowusingthedataingausssum2.1/origin_orbs.txt(itmaytakesomepractice-inOriginyouneedtosetthecolumnsXYXY,andplotthefourcolumnsusing2-pointsegments).Input:PhCCCC_pop.gjfOutput:PhCCCC_pop.outGaussSum

17、input:gausssum2.1/groups.txtGaussSumoutputs:gausssum2.1/COOP_data.txtgausssum2.1/COOP_spectrum.txtTheinteractionbetweenthetwogroupscanbevisualisedusingaCOOP(CrystalOrbitalOverlapPopulation)diagram.Thisinteractionismeasuredbythedegreeofpositive/negativeoverlapforaparticularmolecularorbital.Formoreinf

18、ormationonitsuse,seethepaperofHerlemandLakardlistedinthebibliography.ThediagrambelowwascreatedfromPhCCCC_pop.outusingGaussSum(Orbitals;COOP,start=-15,end=8,FWHM=0.3;PhCCCC_pop.out,gausssum2.1/groups.txt).VibrationalspectrumInput:PhCCCC_IR.gjfOutput:PhCCCC_IR.outGaussSumoutputs:gausssum2.1/IRSpectrum

19、.txtgausssum2.1/IRSpectrum.txt(afterscaling)IcalculatedthevibrationalfrequenciesofdivinylbenzeneandtheirassociatedIRintensities.GaussSumextractsthisinformationfromtheloggausssum/IRSpectrum.txt(Frequencies;start=0,end=1000,numpts=500,FWHM=3,Scalingfactors=(General,1.00);PhCCCC_IR.out):NormalModesMode

20、LabelFreq(cm-1)IRact1AU52.78810.03232BG83.93680.03AU148.15710.38264BU178.67270.2686Iwantedtoscaleallnormalmodesgreaterthan1000cm-1by0.5(thisisnotarealexample!:-).IopenedIRSpectrum.txtinExcel,andchangedthevaluesforthescalingfactorsfrom1.00to0.5forthosenormalmodesgreaterthan1000cm-1.IresavedIRSpectrum

21、.txtinthesameformat(Tab-separated)andlocation.AfterchoosingtheFrequenciesoptionIchoseIndividualscalingfactorsandranGaussSumagain(Frequencies;start=0,end=1000,numpts=500,FWHM=3,scalingfactors=Individual;PhCCCC_IR.out,gausssum2.1/IRSpectrum.txt).Theresultisshownbelow.UV-VisibleSpectrumInput:PhCCCC_TD.

22、gjfOutput:PhCCCC_TD.outGaussSumoutputs:gausssum2.1/UVSpectrum.txtgausssum2.1/UVData.txtIwantedtocalculatetheUV-Visabsorptionspectrumofdivinylbenzene.IaddedthekeywordIOP(9/40=2)totheTD-DFTcommand,tooutputinformationonsmallercontributionstoeachelectronictransition.IrantheElectronictransitionsoptionwit

23、hthedefaultsettings(Electronictransitions;start=300,end=800,numpts=500,fwhm=3000;PhCCCC_TD.out)butnographwasdrawn,andtherewasamessageTherearenopeaksinthiswavelengthrange!.Ilookedatgausssum2.1/UVData.txtandsawthatthelowestenergypeakwasatabout230nm.IrantheElectronictransitionsoptionagain,thistimeusingmoreappropriatevaluesforthestartandendofthediagram(Electronictransitions;start=170,end=270,numpts=500,