stephan irle nagoya university tutorial: molecular structures and
TRANSCRIPT
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StephanIrleagoyaUniversity
Tutorial:MolecularstructuresandMDofsmallandlargermoleculesusingDFTB+
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HowtoconnecttoLired:1. [email protected]. Password:DFTBwork3. Youshouldseeprompt“[sirle@lired~]$4. Createyourowndirectory,e.g. mkdirjoe”wherejoeisthe
directoryyouwillruncalculaQonsin5. cd“joe”
Howtovisualize.xyzdatafiles:a) MOLDENb) JMOLc) …
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Shortinstruc8onsforimportantUNIXcommands(I):GeneralUNIXcommands:cd<dir> changedirectoryto<dir>cd.. Gobackonedirectoryls listfilesincurrentdirectoryvi <file> viewandeditfile<file>(geditisalsoavailable)cp<file><new> copyfile<file>tofile<new>mkdir<dir> createdirectory<dir>(askyourfriendsforhelpifyouarelostatany8me)
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Shortinstruc8onsforimportantUNIXcommands(II):Importantcommands:dJb+ (theDFTB+program) waveplot (ploPngmolecularorbitals,electrondensi8e ,etc.) gnuplot (thegnuplotprogram)VisualizaQon:DFTB+produces.xyzfileswhichcanbeviewedwithMOLDENorJMOLor…ToinstallMOLDENonyourcomputers,open:hbp://qc.chem.nagoya-u.ac.jpClickon“Teaching”
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Youwillsee:
Todownload,youareaskedtoprovideauseridandpassword.Userid:qcguestPassword:qcigf!(quantumchemistryisgreatfun!)
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For isualizaQonofmolecularorbitalsordensiQes, oucanuseVMDoranyothersofwarethatcanplotGaussian s“cube fileshbp://www.ks.uiuc.edu/Research/vmd/
Directoriesontheserver
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ThefollowingdirectorystructureexistswithcorrespondinginputsforDFTB+inourhomedirectory/gpfs/home/sirle:Directory Descrip8on H2O Watermoleculegeometryop8miza8onformamide inputforformamiderota8onalbarriercalcula8onbenzene benzenemoleculargeometryop8miza8onC60 C60geometryop8miza8onnanotube (5,5)nanotubegeometryop8miza8onFe38 Fe38geometryop8miza8onC82 singlepointcalcula8onforMOvisualiza8onSc2C2C82 singlepointcalcula8onforMOvisualiza8onMD waterNVE/NVTBOMDsimula8ons
Frequentlyoccurringproblems
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Theloca8onoftheDFTBparameterfileshastobespecifiedinthedftb_in.hsdinputfile.Ifthespecifieddirectorydoesnotexistortheparameterfilesdonotexist,theprogramwillstopwithanerrormessage.Theparameterfilesarestoredinthedirectorygpfs/home/sirle/SKfilesThedefaultmaximumnumberofgeometryupdatesduringgeometryop8miza8onis200.YoumayhavetochangethistoconvergeyourgeometriesbysePngMaxSteps=300(anumberlargerthan200)intheDriver{}Sec8onofdftb_in.hsd
1a)H2OsinglepointcalculaQon(input)
Geometryfile:
h2o.gen:3COH110.00.00.0221.00.00.0320.01.00.0
Geometry=GenFormat{<<<"h2o.gen"}Driver={}Hamiltonian=DFTB{Charge=0SpinPolarisa8on{}SCC=YesSCCTolerance=1e-6MaxSCCItera8ons=100Mixer=Broyden{}MaxAngularMomentum={O="p"H="s"}SlaterKosterFiles=Type2FileNames{Prefix="/gpfs/home/sirle/SKfiles/"Separator="-"Suffix=".skf"LowerCaseTypeName=No}}
dfb_in.hsd:
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Necessarycommands:cdjoecp–r/gpfs/home/sirle/H2O.cdH2OLsdJb+>dJb+.out&
**********************************************************************************Geometrystep:0********************************************************************************iSCCTotalelectronicDiffelectronicSCCerror1-0.41146057E+010.00000000E+000.77431585E+002-0.41189864E+01-0.43807053E-020.56529143E+003-0.41241083E+01-0.51219356E-020.62694765E-024-0.41241090E+01-0.64734819E-060.72216815E-045-0.41241090E+01-0.85880636E-100.52564193E-08>>Chargessavedforrestartincharges.binTotalEnergy:-4.0698274647HTotalMerminfreeenergy:-4.0698274647H
DFTBinThailand
dfbp.out:
detailed.out:
Netatomiccharges(e)AtomNetcharge1-0.5690887920.2845443930.28454439Eigenvalues/eV-23.02217599-10.69768502-9.04017641-7.065009977.8094676713.40675941Fillings2.000002.000002.000002.000000.000000.00000
1a)H2OsinglepointcalculaQon(output)
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1b)H2OgeometryopQmizaQon
OpQmizedgeometry,14geom.updates:TotalEnergy:-4.0779379339HTotalMerminfreeenergy:-4.0779379339HMaximalforcecomponent:0.873636E-06
IniQalgeometry:TotalEnergy:-4.0698274647HTotalMerminfreeenergy:-4.0698274647HMaximalforcecomponent:0.466498E-01
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Necessarycommands:vidJb_in.hsd(orgeditdJb_in.hsd)Jb+>dJb+.out&
Task:UseMOLDENtocheckbondlengthsandanglesbeforeandaJerop8miza8onCommand:moldengeo_end.xyz
EditthedJb_in.hsdfileusingthevicommand,andchangetheline:
Driver = {}To:
Driver = ConjugateGradient{}
DFTBinThailand 1c)rotaQonalbarrierinformamide
TransiQonstategeometry(TS):TotalEnergy:-8.5123283430HTotalMerminfreeenergy:-8.5123283430HMaximalforcecomponent:0.448038E-04Minimumgeometry(planar):
TotalEnergy:-8.5347931959HTotalMerminfreeenergy:-8.5347931959HMaximalforcecomponent:0.686719E-04
ΔE
ΔE=-8.5123283430--8.5347931959ha=-.0224648529ha=14.1kcal/mol 12
Necessarycommands:p-r/gpfs/home/sirle/formamide.lscdformamide/planardJb+>dJb+.out&<recordfinalenergy>moldengeo_end.xyzd../cdTSdJb+>dJb+.out&<recordfinalenergy>moldengeo_end.xyz
1d-1)waterdimergeometryopQmizaQon
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CCSD(T)/cc-pVQZop8mizedstructurefromHobzaetal.takenfromhwp://www.begdb.com
1.952Å
Task:MakeappropriateinputbyyourselfusingH2Oop8miza8on(task1b).ComputeSCC-DFTBbindingenergyBE=-[Edimer–2*Emonomer]Forthisconforma8on:Edimer=-8.1611635663haBE=-[-8.1611635663–2*(-4.0779379339)]ha=.0052876985=3.3kcal/mol
Slater-KirkwooddispersiontermforSCC-DFTB* *Elstner,M.etal.,J.Chem.Phys.,114,5149-5155,(2001).
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∑ −−=αβ
αβαβ
αβαβ6
6 )()()( RCRfREdis
470 )])(3exp(1[)( RRRf αβαβ −−=
ββ
αα
βαβα
αβ
62
62
666
2CpCpppCC
C+
=
36 75.0 ααα pNC =
R
f(R)
pα:polarizability(differentvaluesfordifferenthybridstatesofatoms)R0:cufoffdistance N α:effec8venumberofelectrons
Dampingfunc8on
~1/R6behavior Pauli repulsion AvailableforC,H,N,O,P(onlyPO4),andS(notSO2)
1d-2)DispersioninteracQon:benzenedimer
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Task1:op8mizebenzenemonomerwithandwithoutdispersioninterac8on;whatdifferencesdoyouobserve?Task2:Usingdispersioninterac8on,op8mizeS,PD,andTdimerstructuresandcompareyourenergieswithliteraturevalues:
S T PD BE 1.65 2.69 2.67[kcal/mol]NotethatDFTB-Dinterac8onsareintherange3-5kcal/mol.
benzene/inputs> lsbenzene-disp benzene-nodisp PD-disp S-disp T-disp
SandwichS
T-shapeT
Parallel-displacedPD
2a)C60geometryopQmizaQon
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OpQmizedgeometry,18geom.updates:TotalEnergy:-103.2321663552HTotalMerminfreeenergy:-103.2321663552HMaximalforcecomponent:0.693582E-04
IniQalgeometry:TotalEnergy:-103.1220165514HTotalMerminfreeenergy:-103.1220165514HMaximalforcecomponent:0.639238E-01
FromTn=2000KMDsimula8onDirectory:C60
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SCC-DFTBw/fracQonalorbitaloccupaQonnumbers
122tot i i rep
i
E f E q qαβ α βαβ
ε γ= + + Δ Δ∑ ∑
( ) 0vi iv
c H Sµν µνε− =∑
Frac8onaloccupa8onnumbersfiofKohn-Shameigenstatesreplaceintegerni
TB-eigenvalueequa8on
E
2fi012
µ
Finitetemperatureapproach(MerminfreeenergyEMermin)
( )1
exp / 1ii B e
fk Tε µ
=− +⎡ ⎤⎣ ⎦
( ) ( )2 ln 1 ln 1e B i i i ii
S k f f f f∞
= − + − −∑
Te: electronic temperature Se: electronic entropy
0 1
2N
repi i i i
i
EH H SF f c c q q
SR R R Rµν µν µν αξ
α µ ν α ξµν ξµνα α α α
γε
⎡ ⎤⎛ ⎞ ∂∂ ∂ ∂= − − − −Δ Δ −⎢ ⎥⎜ ⎟⎜ ⎟∂ ∂ ∂ ∂⎢ ⎥⎝ ⎠⎣ ⎦
∑ ∑ ∑r r r r r
0 1if≤ ≤
Atomicforce
M.Weinert,J.W.Davenport,Phys.Rev.B45,13709(1992)
EMermin=Etot-TeSe
2b)OxidaQonof(5,5)SWCNT
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Important:NeedtouseelectronictemperatureTe=1000KorsimilartoobtainSCCconvergenceOAtom:SCC-DFTBenergy:-3.0982859370haSWCNT:op8mizedSCC-DFTBenergy:-128.1960247645haOxidizedSWCNT:op8mizedSCC-DFTBenergy:-131.4584328407ha
+O
BindingenergyBE=-[E(SWCNT+O)–E(SWCNT)–E(O)]=103.0kcal/mol
SWCNTSWCNT+O
Directories:nanotube/inputs/pris8ne&oxidized&o_atom
OpQmizedgeometry,Te=1500K,144geom.updates:TotalEnergy:-55.6471927268HTotalMerminfreeenergy:-56.0689013490HMaximalforcecomponent:0.575369E-04
IniQalgeometry:TotalEnergy:-55.2723102833HTotalMerminfreeenergy:-55.7289532045HMaximalforcecomponent:0.736021E-01
2c)Fe38geometryopQmizaQon
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Directory:Fe38
2d)MOplotsofC82andSc2C2@C82
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Directories:C82andSc2C2C82,subdirectoriesinputandinput/orbitalinbothImportant:NeedtouseelectronictemperatureTe=1000KorsimilartoobtainSCCconvergenceWriteMO’sindJb_in.hsd:Op8ons={WriteDetailedXML=YesWriteEigenvectors=Yes}
C82 Sc2C2@C82
Bonus:CalculatebindingenergyofC2andScatoms:BE=-[E(Sc2C2@C82)–E(C82)–2E(Sc)–E(C2)]
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Sample“waveplot_in.hsd” #Generalop8onsOp8ons={TotalChargeDensity=Yes#Totaldensitybeplowed?TotalChargeDifference=Yes#Totaldensitydifferenceplowed?ChargeDensity=Yes#Chargedensityforeachstate?RealComponent=Yes#Plotrealcomponentofthewavefunc8onPlowedSpins={1-1}PlowedLevels={111415161718}#LevelstoplotPlowedRegion=Op8malCuboid{}#RegiontoplotNrOfPoints={505050}#Numberofgridpointsineachdirec8onNrOfCachedGrids=-1#Nrofcachedgrids(speedsupthings)Verbose=Yes#Wannaseealotofmessages?}DetailedXML="detailed.xml"#FilecontainingthedetailedxmloutputofDFTB+EigenvecBin="eigenvec.bin"#Filecointainingthebinaryeigenvecs#Defini8onofthebasisBasis={Resolu8on=0.01#Includingmio-0-1.hsd.(Ifyouuseaset,whichdependsonothersets,#thewfc.*.hsdfilesforeachrequiredsetmustbeincludedinasimilar#way.)<<+"wfc.mio-0-1.hsd"}
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VisualizetheMOswithVMD
• StartVMD:RunAllPrograms/University-of-Illinois/VMD/VMD1.8.7• File→NewMolecule,thenloadthethedesiredcubefilefrom(followtheprocedurebelow)-Browse-Mycomputer-Z:drive(longnamewithZ:attheend,double-click)-terminal_<color>_<M>(seelabelonyourterminal)-C82(orEr2C2C82)(double-click)-input(double-click)-orbital(double-click)-selectdesiredcubefile
Note:RunthesecommandsonyourTerminal!
Note:theloca8onofyourfileswilldependonthedirectoryinwhichyourantheDFTB+andwaveplotprograms
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VisualizetheMOswithVMD
• Graphics→Representa8ons,thenchoosethedrawingmethod(hereCPK)• Pushthe“CreateRep”buwon• Changethedrawingmethod“Isosurface”,thenchangethedrawtypefromPointstoSolidsurfacesandshowtypetoIsosurface• ChangethecoloringmethodfromNametoColorID(color0:blue)• SettheIsovalue(posi8venumber;forexample,0.01etc.)• Performthesamethingfornega8veIsovalue(forexample,-0.01,color1:red)
2d)MOplotsofC82andSc2C2@C82
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Energy[eV]
3a)H2ONVESCC-DFTB/MDsimulaQon
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dJb_in.hsd:
NVE
BOMD
e.dat:totalMDenergyv.dat:MDpoten8alenergy
Directory:MD/NVE
3a)H2ONVESCC-DFTB/MDsimulaQon
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dJb_in.hsd:
NVE
BOMD
T:grep"Kine8cEnergy:"md.out|awk'{print$4}'>t.datV:grep"Poten8alEnergy:"md.out|awk'{print$3}'>v.datE:grep"TotalMDEnergy:"md.out|awk'{print$4}'>e.datE=T+VEisconservedinNVE(microcanonical)simula8onsVisaliza8oningnuplot:Type“gnuplot”gnuplot> set style data linesplot ‘v.dat’,’e.dat’plot ‘t.dat’exitInterpretyourresults.HowareTandVrelated?
3b)H2ONVTSCC-DFTB/MDsimulaQon
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dJb_in.hsd:
NVT
BOMD
e.dat:totalMDenergyv.dat:MDpoten8alenergy
Geometry = GenFormat { <<< "h2o.gen" } Driver = VelocityVerlet{ Steps = 999 TimeStep [Femtosecond] = 0.10 Thermostat = Berendsen { Temperature [K] = 298.0 CouplingStrength = 0.1 } Velocities [AA/ps] = { <<< "VELOC.DAT" } OutputPrefix = "geo_stp" }
Hamiltonian = DFTB{ Charge = 0 SpinPolarisation{} SCC = Yes SCCTolerance = 1e-6 MaxSCCIterations = 100 Mixer = Broyden{} MaxAngularMomentum = { O = "p" H = "s" }SlaterKosterFiles = { O-O = "../SKfiles/O-O.skf" O-H = "../SKfiles/O-H.skf" H-O = "../SKfiles/H-O.skf" H-H = "../SKfiles/H-H.skf" } }
Directory:MD/NVT
3b)H2ONVTSCC-DFTB/MDsimulaQon
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dJb_in.hsd:
NVE
BOMD
EisNOTconservedinNVTsimula8ons,butTis:½mv2=3/2kbTIncaseofonewatermolecule,1au=105258.2Kawk'{print$1*105258.2}'t.dat>temp.datInterpretyourresults.TrydifferentvaluesofthecouplingconstantτT.WhatistheinfluenceofτT?
€
δ = 1+ΔtτT
T0T(t −Δt)
−1⎧ ⎨ ⎩
⎫ ⎬ ⎭
⎡
⎣ ⎢
⎤
⎦ ⎥
1/ 2
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vi = δvi,