課件教案成果gulp qm mm calculation of the sw1 defect formation energy carbon nanotube

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QM/MMcalculationoftheSW1defectformationenergyforacarbonnanotube

Purpose:IntroduceshowtousetheQMERAmoduleinMaterialsStudio.Specialattentionispaidtopreparingthesystemandwhichtypeofembeddingschemetouse.

Modules:MaterialsVisualizer,QMERA

Time:Prerequisites:None

Background

TheStone-Wales(SW)defectisacommondefectoncarbonnanotubesthatisthoughttohaveimportantimplicationsfortheirmechanicalproperties(seeAndzelmetal.,2006).The90°rotationoftwocarbonatomsaroundthemidpointoftheC-Cbondtransformsfourhexagonsintotwopentagonsandtwoheptagons.ThissubstructureisknownasStone-Walesdefect.InthistutorialwewillcalculatetheformationenergyofanonchiralSWdefect(SW1).

Thefollowingstepswillbecoveredhere:

Structurepreparation

QMregiondefinition

QMERAcalculation

ysisofresults

Tip.Thistutorialisbestcarriedoutwiththefileextensionsforeachdisyed.IfthefileextensionsarenotdisyedinyourProjectExplorer,refertotheProjectExplorertopicforinstructionsonhowtoreconfigure.

Note.Inordertoensurethatyoucanfollowthistutorialexactlyasintended,youshouldusetheSettingsOrganizerdialogtoensurethatallyourprojectsettingsaresettotheirAccelrysdefaultvalues.SeetheCreatingaprojecttutorialforinstructionsonhowtorestoredefaultprojectsettings.

Structurepreparation

Thefirstthingyouneedtospreparethestructureofthesingle-wallednanotube(SWNT).

SelectBuild|BuildNanostructure|Single-WallNanotubefromthe bar.ChangetheNandM

indicesto8and0respectively.

Thiscorrespondstoananotubeof6.26?diameter.

UncheckthePeriodicnanotubeboxandchangethenumberofRepeatunitsto7,thisgivesananotubelengthof29.82?.SelectBothendsfromtheHydrogenterminationdropdownlist.ClickontheBuildbuttonandclosethedialog.

Nowyouhavetocreatethedefectinthemiddleofthenanotube.

Right-clickinthe3DViewerandselectDisyStylefromtheshortcut toopentheDisyStyledialog.ClickontheStickradiobuttonandclosethedialog.

Presstheleftarrowkeyonthekeyboardtwicetorotatethenanotubesothatyoucanseeitsfulllengthhorizontally.

TheZaxisshouldbepointingtotheleftandtheYaxisshouldbepointingup,ontheaxisorientationdisy,seeFigure1.

Selecttwocarbonatomswhicharenearthecenterofthenanotubewallandwhichareconnectedbyahorizontalbondandthenselecttheremainderofbenzeneringsateachendofthebond.

Figure1.SWNTwithtwocentralcarbonatomsandtheirpendantbenzeneringsselected.

Clickonthearrowforthe3DViewerRecenterfromthetoolbarandselectViewOntofromthedropdownlist.Clickanywhereinthe3DViewertodeselecteverythingandreselectthecentraltwocarbonatoms.

Figure2.SWNTviewedfromabove,withtwocentralcarbonatomsselected.

SelecttheMovementtoolsfromthetoolbar,changetheAngleto90.0andclicktheMoveAroundZ

button.

Thiscreatesthedefectbyrotatingthetwocarbonatoms90°aroundthescreenZaxis.

ToviewtheappropriateconnectivityselectBuild|Bondsfromthe bartoopentheBondCalculationdialog.UncheckCalculatebondtype,settheConvertrepresentationtooptiontoResonant.ClickontheCalculatebutton.

RenametheSWNT.xsd toSW1.xsd.

Figure3.SW1defect(highlightedhereinblue)onaSWNT.

Tip.TheinputfilescsobefoundintheExamplesfolderinthefollowinglocationExamples/Projects/QMERA/Stone-WalesFiles/ s.TheSW1.xsdfilecontainsthedefectstructureandSWNT.xsdcontainsthedefect- nanotube.

QMregiondefinition

ThenextstepistodefinetheQMregionthatyouwanttouseinthesimulation.Itisnecessarytoincludefullringsinthecalculationtoavoidpossibleclashesbetweenhydrogenlinkatoms,andtoleaveenoughspacebetweenthedefectandtheboundaryQM-MMatoms.InthiscaseyouwillincludethedefectplusacrownoffullringsarounditintheQMregion(seeFigure4).

Withthetwocarbonatomscentraltothedefectstillselected,chooseEdit|AtomSelectionfromthe

bartoopentheSelectiondialog.SelectConnectedfromtheSelectbyPropertydropdownlistandchoosetheAddtotheexistingselectionradiobutton.ClicktheSelectbuttonfourtimesandclosethedialog.HolddowntheSHIFTkeyandselectthefourcarbonsneededtocompletethecrownofsix-memberedrings.

Select|CalculationfromthemodulestoolbartoopentheQMERACalculationdialog.ClickontheAdd

buttontoaddtheselectedatomstotheQuantumAtomsset.

Clickanywhereinthe3DViewer,theatomsinthesetwillbehighlightedinpurple.

Figure4.SW1defectwiththeQuantumAtomssetdefined.

Ifyouwanttovisualizethehydrogenlinkatomstobesurethattherearenoproblemsrelatedtotheirposition,youcanusetheViewbuttonontheQMERACalculationdialog.

OntheSetuptaboftheQMERACalculationdialogclickontheViewbutton.Anewwindowwillopen,double-clickontheLinkAtomslabel.Checkthatthepositionofthehydrogenlinkatomsmakessenseandclosethewindow.

QMERAcalculation

YouarenowreadytoruntheQMERAcalculation.Inthiscasethepolarizationeffectsarenegligibleandthechargesofallatomswillbeleftaszero,whichiscompatiblewiththeDreidingfield.ItisalsosufficienttochooseamechanicalembeddingapproachfortheQM/MMcalculation.

Note.Byassigningchargestoallatoms(forexampleusingachargeequilibrationmethodorusingthechargesfroma field)forthiskindofembedding,theQM/MMelectrostaticin ctionisaccountedforbytheclassicalCoulombin ctionbetweenallatoms.SotheMMregionchargesdonotentertheQMcalculation.Whennon-zerochargesareused,thenetchargesoftheQMandMMregionsmustbeintegervalues.

Therearetwodifferentmodelsavailableformechanicalembedding:QM-Potandadditive.WewillusetheQM-Potmodelwhichusesasubtractiveexpressiontocalculatethetotalenergy. fieldparametersarethereforerequiredforallatomsofthesystem.

OntheSetuptaboftheQMERACalculationdialogselectGeometryOptimizationastheTaskandensurethattheQualityofthecalculationissettoMedium.

Inordertocompletethetutorialmorequickly,youcouldusetheCoarsequalitysetting.

ClickontheMore...buttonassociatedwiththetask,toopentheQMERAGeometryOptimizationdialog.SelectHDLCastheMethodandclosethedialog.

TheHDLCminimizercombinestheuseofhighlydecoupleddelocalizedinternalcoordinateswiththelinearscalingBFGSupdateoftheHessian(L-BFGS)method.ThisusuallyachievesfasterconvergencethannormalBFGSorconjugategradientmethodsforcovalentsystemsofthissize.

ClickontheMore...buttonfortheQMservertoopentheQMERADMol3Parametersdialog.SelectGGA

andPBEforthefunctionalandclosethedialog.

ClickontheMore...buttonfortheMMservertoopentheQMERAGULPParametersdialog.Select

Dreidingasthe fieldandUsecurrentfortheCharges,closethedialog.

SelecttheOptionstaboftheQMERACalculationdialog,andselectMechanicalastheEmbedding

scheme,asModelselectQM-Pot.ClickontheRunbutton.

GGAfunctionalsprovideagooddescriptionoftheelectronicsubsystemandthePBEexchange-correlationfunctionalhaspreviouslybeenidentifiedasefficientforQM/MMcalculationsonnanotubes,seeAndzelmetal.,2006forsimilarcalculations.

Dependingonyourhardware,thiscalculationmaytakeseveralhourstocomplete.IfyouwishtoexamineandyzetheresultsdirectlytheoutputfilesareprovidedintheExamples/Projects/QMERA/Stone-Wales

Files/ s/directoryintheSW1QMERAGeomOptandSWNTQMERAGeomOptfolders.

ysisofresults

TheresultsofthecalculationwillbereturnedinanewfoldercalledSW1QMERAGeomOpt.OpentheSW1.xsdfileintheSW1QMERAGeomOptfoldertoseetheoptimizedgeometry.

ThefinalenergyforthisstructurecanbefoundintheSW1.csoutfile,theQM/MMEnergyheadingreportsthecorrespondingenergyina.u.,whichareHartreesinthiscase.

Double-clickonSW1.csouttoopentheenergyfile,presstheCTRL+FkeyandenterEnergy(subtractive)

intotheFinddialog.

ofthefileisdisyed.ScrollupalittleandexaminetheQM/MMEnergy.

Toexaminetherelationshipbetweentheenergyandthestructureyoucancomparetheenergychartwiththetrajectory.Youwillneedtoyzetheresultstoobtainthetrajectoryandcharts,evenifyoualreadyhavesomechartswithintermediateupdates.

SelectModules|QMERA|ysisfromthe bartoopentheQMERA ysisdialog.SelectEnergyevolutionandclickontheViewbutton.ThenselectStructureandclickViewagain.Closethedialog.

Theenergyevolutioneithercreatesoropenstwochart s,calledSW1Energies.xcdandSW1Convergence.xcd.Thestructure ysiscreatesoropensatrajectoryoftheoptimizationcalculation,calledSW1.xtd.

MakeSW1.xtdtheactive and,ontheanimationtoolbar,clickonthe ybutton.Astheanimationproceedstheseven-memberedringswiden.

StoptheanimationandopenSW1Energies.xcd.

Clickonapointonthegraphnearthebeginningoftheoptimization.

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