原子分子物理中用高斯画态密度图的方法

1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，atomspart1（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）part26-7,21-29,31-33（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！WorkedExampleDescriptionAstudyoftheelectronicstructureandvibrationalspectrumof1,4-divinyl-benzene(attheB3LYP/STO-3Gleveloftheory)usingGaussian03W.2ConfiguringGaussSumIopenedtheSettingsdialogbox,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).3Molecularorbitalinformation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.MOeVSymmetry40L+47.42BG39L+34.96AU38L+23.01BG37L+12.46AU36LUMO1.02AU35HOMO-4.17BG34H-1-5.31BG33H-2-5.78AU32H-3-7.17BG31H-4-7.82AG4Adensityofstatesdiagramwasconvolutedfromthemolecularorbitaldata(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:atomsC6H41-8,19-205C=C9-18Finally,IusedGaussSumtocalculatethemolecularorbitalcontributionsagain(Orbitals;defaults;PhCCCC_pop.out,gausssum2.1/groups.txt).Thistime,orbital_data.txtcontainedmoreinformation(seebelowforinformationonthefrontierorbitals).TheHOMOisabout50/50C6H4anddivinyl.Theso-called'accuratevalues'shouldbeignored,althoughtheyarerequiredfortheElectronictransitionsoptiontocalculatechangesinelectrondensity.(Notethatthesecolumnsaretab-separatedandsocanbeimportedeasilyintospreadsheetsoftware.)MOeVSymmetryC6H4C=CAccuratevalues(fortheElectronictransitionsmodule)38L+23.01BG17830.1684302093240.8315700245237L+12.46AU10000.9998186530490.00018185951061336LUMO1.02AU54460.5432821273180.45672539915335HOMO-4.17BG54460.5417785039970.45822859435434H-1-5.31BG10000.9998774411720.00014157036335933H-2-5.78AU15850.1548993041330.845103027118TheinitialDOSspectrumcreatedbyGaussSumdidnotincludeanyofthevirtualorbitals.Asaresult,Iwantedtochangethestartandendpointofthespectrum,butIdidnotwanttorecalculateallofthecontributionsofthegroups.IsetUseexistingorbital_data.txt?toTRUE,andalteredthevaluesofstartandenduntilIwashappy(Orbitals;start=-15,end=8,FWHM=0.3,Useexistingorbital_data.txt?=TRUE;PhCCCC_pop.out):6Anicerimagecanbecreatedusingspreadsheetsoftware,oraprogramsuchasMicrocalOrigin,andthefilegausssum2.1/DOS_spectrum.txt.TheimagebelowwascreatedusingMicrocalOrigin(forLinux,tryScigraphicaorGrace).7InsteadofdrawingaDOScurve,youmayprefertouseamorestraightforwarddepictionofthebreakdownofmolecularorbitalsbetweenvariousgroupsinamolecule.Todoso,setCreateoriginorbs.txttoTRUE,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]G