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9.ChemicalPhysicsBasicTAMkinrecipes
Inthischapter,wediscussafewexamplescriptsforTAMkinindetail.Theycanbeusedasatemplatefor
writingnewscripts,whichismucheasierthanstartingfromscratch.Therearemoreexamplesinthe
examples/directorythanthosediscussedhere.AssumingTAMkinisdownloadedinadirectory~/code/,
thenonewillfindtheexamplesonthefollowinglocation:
toon@poony~>cd~/code/tamkin/examples
toon@poony~/code/tamkin/examples>ls
001_ethane
002_linear_co2
003_pentane
004_alkanes
005_acrylamide_reaction
006_5T_ethene_reaction
007_mfi_propene_reaction
...

9.1.Thermodynamicpropertiesofamolecule
TODO:seeexamples/001_ethanefornow.

9.2.ConformationalEquilibrium
Wewillstudythethermodynamicequilibriumbetweenthetwobutaneconformers:transandgauche.The
balanceisasfollows:

BothbutanegeometriesareoptimizedusingtheB3LYP/631G(d)leveloftheory,andconsequently
frequencycomputationsarecarriedoutusingGaussian03.Theformattedcheckpointfilesofthefrequency
jobsaretrans.fchkandgauche.fchkrespectively.Thisisatrivialexample,butonemustnotforgettotake
intoaccountthedegeneracyofthegauchegroundstate,i.e.thereasalefthandedandarighthanded
gauchestate.
Thescriptbelowcomputestheequilibriumconstantoftheconformationalequilibriumconstantatdifferent
temperatures:300K,400K,500Kand600K.Themultiplicityoptionoftheelectroniccontributionis
(ab)usedtotakeintoaccountthegeometricalgauchemultiplicity.
File:examples/020_butane_conformers/equilibrium.py
#Importlibraries.
fromtamkinimport*#TheTAMkinlibrary
#Loadthemolecules(includingtheHessianetc.)
mol_trans=load_molecule_g03fchk("trans.fchk")
mol_gauche=load_molecule_g03fchk("gauche.fchk")
#Performnormalmodeanalysisonthemolecules
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nma_trans=NMA(mol_trans,ConstrainExt())
nma_gauche=NMA(mol_gauche,ConstrainExt())
#Constructthepartitionfunctions.
pf_trans=PartFun(nma_trans,[ExtTrans(),ExtRot()])
pf_gauche=PartFun(nma_gauche,[ExtTrans(),ExtRot(),Electronic(multiplicity=2)])
#Defineakineticmodelforthechemicalreaction.
tm=ThermodynamicModel([pf_trans],[pf_gauche])
#Writetableswiththeprincipalenergiesat300K,400K,500Kand600K
tm.write_table(300,"equilibrium300.csv")
tm.write_table(400,"equilibrium400.csv")
tm.write_table(500,"equilibrium500.csv")
tm.write_table(600,"equilibrium600.csv")
#Writeanoverviewofthethermodynamicmodeltoafile
tm.write_to_file("equilibrium.txt")

Thescriptswritesseveraloutputfilesdiscussedinthesubsectionsbelow.

9.2.1.CSVFileswiththeenergeticanalysis
Thefileconformation_energies300.csvContainsthefollowinginformation.
Temperature[K]

Quantity

300

Trans

Gauche

Signedstoichiometry
Valuesina.u.
Electronicenergy
Zeropointenergy
Internalheat(300.00K)
Chemicalpotential
(300.00K)
CorrectionsinkJ/mol
Zeropointenergy
Internalheat(300.00K)
Chemicalpotential
(300.00K)

Otherquantities
Equilibriumconstant

158.4581
158.3252
158.3184
158.3528

158.4567
158.3237
158.3170
158.3520

Linearcombination
(alwaysinkJ/mol)

3.5
3.8
3.7
2.0

348.8
366.6
276.5

349.1
366.7
274.9

0.3
0.1
1.5

Unit
1

Value
0.450

Thenumbersinthistableareroundedtoimprovethereadability,buttheactualCSVfilecontainsall
numbersinfullmachineprecision.Thelinearcombinationofthechemicalpotentialsisalsoknownasthe
changeinfreeenergyassociatedwiththereaction.
Fromtheequilibriumconstantonecanderivetheprobabilityoffindingatransoragaucheconformerat
300K:

Giventhattheprobabilitiessumtounity,onegets:

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9.2.2.Alogfilewithandescriptionoftheequilibrium
Thefileequilibrium.txtcontainsthefollowingdata:
Electronicenergydifference[kJ/mol]=3.5
Zeropointenergydifference[kJ/mol]=3.8
Thechemicalbalance:
1.0*("Trans")<>1.0*("Gauche")
Partitionfunction0
Signedstoichiometry:1
Title:Trans
Electronicenergy[au]:158.45806
Zeropointcontribution[kJ/mol]:348.7969543
Zeropointenergy[au]:158.32521
Contributionstothepartitionfunction:
ELECTRONIC
Multiplicity:1
Electronicenergy:158.4580557
ROTATIONAL
Rotationalsymmetrynumber:2
Momentsofinertia[amu*bohr**2]:77.114693501.601343533.985400
Thresholdfornonzeromomentsofinertia[amu*bohr**2]:5.485799e04
Nonzeromomentsofinertia:3
TRANSLATIONAL
Dimension:3
Constantpressure:True
Pressure[bar]:1.01325
BIGFATWARNING!!!
ThisisanNpTpartitionfunction.
InternalheatcontainsaPVterm(andisthereforetheenthalpy).
FreeenergycontainsaPVterm(andisthereforetheGibbsfreeenergy).
Theheatcapacityiscomputedatconstantpressure.
Mass[amu]:58.078250
VIBRATIONAL
Numberofzerowavenumbers:0
Numberofrealwavenumbers:36
Numberofimaginarywavenumbers:0
Frequencyscalingfactor:1.0000
Zeropointscalingfactor:1.0000
RealWavenumbers[1/cm]:
126.0221.0257.8260.9424.2744.3821.0847.3
973.7988.51027.21072.51180.51225.41306.71340.8
1348.91418.71439.61442.01517.41522.01528.81530.0
1536.21543.73020.43028.13041.03041.73042.33064.3
3103.43107.53110.03110.8
Zeropointcontribution[kJ/mol]:348.7969543
Partitionfunction1
Signedstoichiometry:1
Title:Gauche
Electronicenergy[au]:158.45671
Zeropointcontribution[kJ/mol]:349.0988179
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Zeropointenergy[au]:158.32375
Contributionstothepartitionfunction:
ELECTRONIC
Multiplicity:2
Electronicenergy:158.4567137
ROTATIONAL
Rotationalsymmetrynumber:2
Momentsofinertia[amu*bohr**2]:135.679032386.092746451.000474
Thresholdfornonzeromomentsofinertia[amu*bohr**2]:5.485799e04
Nonzeromomentsofinertia:3
TRANSLATIONAL
Dimension:3
Constantpressure:True
Pressure[bar]:1.01325
BIGFATWARNING!!!
ThisisanNpTpartitionfunction.
InternalheatcontainsaPVterm(andisthereforetheenthalpy).
FreeenergycontainsaPVterm(andisthereforetheGibbsfreeenergy).
Theheatcapacityiscomputedatconstantpressure.
Mass[amu]:58.078250
VIBRATIONAL
Numberofzerowavenumbers:0
Numberofrealwavenumbers:36
Numberofimaginarywavenumbers:0
Frequencyscalingfactor:1.0000
Zeropointscalingfactor:1.0000
RealWavenumbers[1/cm]:
112.6216.7266.5324.1433.1756.2799.6840.7
972.6979.81003.41093.91166.11209.41305.11328.6
1391.41397.91442.21443.21514.01517.01528.11536.6
1537.11542.63024.43024.93043.43045.63058.13062.0
3106.43107.73113.63120.2
Zeropointcontribution[kJ/mol]:349.0988179

9.3.ChemicalEquilibrium
TODO

9.4.Heatofformation
Inthisexamplewecomputetheheatofformationofthewatermolecule(ingasphase).Thiscomesdown
tothecomputationofthechemicalequilibriumpropertiesofthefollowingreaction:

Aswewillseebelow,thisisnotanequilibriumreaction,sothetermchemicalequilibriumissomewhat
misleading.Thepointisthattheunderlyingcomputationisexactlythatofanyotherthermodynamic
equilibriumwithTAMkin.
WepreparedoptimizedgeometriesandfrequencycomputationsforthethreecomponentsattheB3LYP/6
31G(d)levelusingGaussian03.Theformattedcheckpointfilesofthefrequencyjobsareoxygen.fchk,
hydrogen.fchkandwater.fchk.
Thefollowingscriptcomputestheheatofformationat298.15K.
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File:examples/021_water_formation/formation.py
#Importlibraries.
fromtamkinimport*#TheTAMkinlibrary
#Loadthemolecules(includingtheHessianetc.)
mol_oxygen=load_molecule_g03fchk("oxygen.fchk")
mol_hydrogen=load_molecule_g03fchk("hydrogen.fchk")
mol_water=load_molecule_g03fchk("water.fchk")
#Performnormalmodeanalysisonthemolecules
nma_oxygen=NMA(mol_oxygen,ConstrainExt())
nma_hydrogen=NMA(mol_hydrogen,ConstrainExt())
nma_water=NMA(mol_water,ConstrainExt())
#Constructthepartitionfunctions.
pf_oxygen=PartFun(nma_oxygen,[ExtTrans(),ExtRot()])
pf_hydrogen=PartFun(nma_hydrogen,[ExtTrans(),ExtRot()])
pf_water=PartFun(nma_water,[ExtTrans(),ExtRot()])
#Defineakineticmodelforthechemicalreaction.
tm=ThermodynamicModel([pf_oxygen,(pf_hydrogen,2)],[(pf_water,2)])
#Writetableswiththeprincipalenergiesat298.15K
tm.write_table(298.15,"formation.csv")
#Writeanoverviewofthethermodynamicmodeltoafile
tm.write_to_file("formation.txt")

PayspecialattentiontothewaythestoichiometryofthebalanceispassedtotheThermodynamicModel
constructor.Onecanalwaysreplaceapartitionfunction,pf,withatuple(pf,st)wherestisthe
stoichiometry,whichdoesnothavetobeaninteger.ThesamecanbedonewiththeKineticModel
constructor.

9.4.1.CSVFileswiththeenergeticanalysis
Thethermodynamicequilibriumpropertiesat298.15Karesummarizedinthefileformation.csv.
Temperature[K]

Quantity

298.15

Oxygen

Hydrogen

Water

Signed
stoichiometry
Valuesina.u.
Electronicenergy
Zeropointenergy
Internalheat
(298.15K)
Chemicalpotential
(298.15K)
Correctionsin
kJ/mol
Zeropointenergy
Internalheat
(298.15K)
Chemicalpotential
(298.15K)

Linear
combination
(alwaysinkJ/mol)

150.2574
150.2537
150.2504

1.1755
1.1653
1.1620

76.4090
76.3878
76.3840

550
502
508

150.2726

1.1768

76.4055

485

10
19

27
35

56
65

48
42

40

65

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Otherquantities
Equilibrium
constant

9.ChemicalPhysicsBasicTAMkinrecipesTAMkin1.0.9documentation

Unit
m**3*mol**1

Value
2.068e+83

Thelinearcombinationofinternalheatsistheheatofformationoftwowatermolecules(duetothe
stoichiometry).Forasinglewatermolecule,onegetsabout254kJ/mol.Theexperimentalvaluereported
ontheNISTChemistrywebbookisabout242kJ/mol.

9.4.2.Alogfilewithandescriptionoftheequilibrium
Thefileformation.txtcontainsthefollowingdata:
Electronicenergydifference[kJ/mol]=550.1
Zeropointenergydifference[kJ/mol]=502.1
Thechemicalbalance:
1.0*("Oxygen")+2.0*("Hydrogen")<>2.0*("Water")
Partitionfunction0
Signedstoichiometry:1
Title:Oxygen
Electronicenergy[au]:150.25743
Zeropointcontribution[kJ/mol]:9.8303186
Zeropointenergy[au]:150.25368
Contributionstothepartitionfunction:
ELECTRONIC
Multiplicity:1
Electronicenergy:150.2574266
ROTATIONAL
Rotationalsymmetrynumber:2
Momentsofinertia[amu*bohr**2]:0.00000042.22454142.224541
Thresholdfornonzeromomentsofinertia[amu*bohr**2]:5.485799e04
Nonzeromomentsofinertia:2
TRANSLATIONAL
Dimension:3
Constantpressure:True
Pressure[bar]:1.01325
BIGFATWARNING!!!
ThisisanNpTpartitionfunction.
InternalheatcontainsaPVterm(andisthereforetheenthalpy).
FreeenergycontainsaPVterm(andisthereforetheGibbsfreeenergy).
Theheatcapacityiscomputedatconstantpressure.
Mass[amu]:31.989829
VIBRATIONAL
Numberofzerowavenumbers:0
Numberofrealwavenumbers:1
Numberofimaginarywavenumbers:0
Frequencyscalingfactor:1.0000
Zeropointscalingfactor:1.0000
RealWavenumbers[1/cm]:
1643.5
Zeropointcontribution[kJ/mol]:9.8303186
Partitionfunction1
Signedstoichiometry:2
Title:Hydrogen
Electronicenergy[au]:1.17548
Zeropointcontribution[kJ/mol]:26.6354070
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Zeropointenergy[au]:1.16534
Contributionstothepartitionfunction:
ELECTRONIC
Multiplicity:1
Electronicenergy:1.1754824
ROTATIONAL
Rotationalsymmetrynumber:2
Momentsofinertia[amu*bohr**2]:0.0000000.9928480.992848
Thresholdfornonzeromomentsofinertia[amu*bohr**2]:5.485799e04
Nonzeromomentsofinertia:2
TRANSLATIONAL
Dimension:3
Constantpressure:True
Pressure[bar]:1.01325
BIGFATWARNING!!!
ThisisanNpTpartitionfunction.
InternalheatcontainsaPVterm(andisthereforetheenthalpy).
FreeenergycontainsaPVterm(andisthereforetheGibbsfreeenergy).
Theheatcapacityiscomputedatconstantpressure.
Mass[amu]:2.015650
VIBRATIONAL
Numberofzerowavenumbers:0
Numberofrealwavenumbers:1
Numberofimaginarywavenumbers:0
Frequencyscalingfactor:1.0000
Zeropointscalingfactor:1.0000
RealWavenumbers[1/cm]:
4453.1
Zeropointcontribution[kJ/mol]:26.6354070
Partitionfunction2
Signedstoichiometry:2
Title:Water
Electronicenergy[au]:76.40895
Zeropointcontribution[kJ/mol]:55.5664022
Zeropointenergy[au]:76.38779
Contributionstothepartitionfunction:
ELECTRONIC
Multiplicity:1
Electronicenergy:76.4089533
ROTATIONAL
Rotationalsymmetrynumber:2
Momentsofinertia[amu*bohr**2]:2.2917744.1744636.466237
Thresholdfornonzeromomentsofinertia[amu*bohr**2]:5.485799e04
Nonzeromomentsofinertia:3
TRANSLATIONAL
Dimension:3
Constantpressure:True
Pressure[bar]:1.01325
BIGFATWARNING!!!
ThisisanNpTpartitionfunction.
InternalheatcontainsaPVterm(andisthereforetheenthalpy).
FreeenergycontainsaPVterm(andisthereforetheGibbsfreeenergy).
Theheatcapacityiscomputedatconstantpressure.
Mass[amu]:18.010565
VIBRATIONAL
Numberofzerowavenumbers:0
Numberofrealwavenumbers:3
Numberofimaginarywavenumbers:0
Frequencyscalingfactor:1.0000
Zeropointscalingfactor:1.0000
RealWavenumbers[1/cm]:
1713.13727.43849.4
Zeropointcontribution[kJ/mol]:55.5664022
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NotehowTAMkinpicksuptherightrotationalsymmetrynumbersandthenonzeromomentsofinertia.

9.5.ReactionKinetics(unimolecular)
TODO

9.6.ReactionKinetics(bimolecular)
Inthisexampleweshowhowoneestimateskineticparametersfortheadditionofethenetoethylinthegas
phaseatconstantpressure.Thereactionbalanceis

Forthisexamplewepreparedthreefrequencycomputations:
Oneforeachgroundstategeometryofthereactants(etheneandethyl).Theformattedcheckpoint
filesofthefrequencyjobsareethene.fchkandethyl.fchk.
Oneforthetransitionstatewhereetheneperformsatransattackonethyl.Thegeometryofthe
transitionstateisoptimizedtowardsthesaddlepointinthepotentialenergysurface.Theformatted
checkpointfileofthefrequencyjobists_trans.fchk.
ThefrequencycomputationsarecarriedoutwithGaussian03.TheleveloftheoryisB3LYP/631G(d).The
followingscriptcomputesthekineticparameters(AandEa)throughalinearfitof
versus inthe
temperaturerange300K600K.
File:examples/019_ethyl_ethene_simple/kinetic.py

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#Importlibraries.
fromtamkinimport*#TheTAMkinlibrary

#Loadthemolecules(includingtheHessianetc.)
mol_ethyl=load_molecule_g03fchk("ethyl.fchk")
mol_ethene=load_molecule_g03fchk("ethene.fchk")
mol_ts_trans=load_molecule_g03fchk("ts_trans.fchk")
#Performnormalmodeanalysisonthemolecules
nma_ethyl=NMA(mol_ethyl,ConstrainExt())
nma_ethene=NMA(mol_ethene,ConstrainExt())
nma_ts_trans=NMA(mol_ts_trans,ConstrainExt())
#Constructthepartitionfunctions.
pf_ethyl=PartFun(nma_ethyl,[ExtTrans(),ExtRot()])
pf_ethene=PartFun(nma_ethene,[ExtTrans(),ExtRot()])
pf_ts_trans=PartFun(nma_ts_trans,[ExtTrans(),ExtRot()])
#Defineakineticmodelforthechemicalreaction.
km_trans=KineticModel([pf_ethyl,pf_ethene],pf_ts_trans)
#Writetableswiththeprincipalenergiesat300K,400K,500Kand600K
km_trans.write_table(300,"kinetic300.csv")
km_trans.write_table(400,"kinetic400.csv")
km_trans.write_table(500,"kinetic500.csv")
km_trans.write_table(600,"kinetic600.csv")
#Analyzethechemicalreactions.
ra_trans=ReactionAnalysis(km_trans,300,600)
#MaketheArrheniusplot

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27
28
29

ra_trans.plot_arrhenius("arrhenius.png")
#Writetheanalysistoafile
ra_trans.write_to_file("kinetic.txt")

Thescriptswritesseveraloutputfilesdiscussedinthesubsectionsbelow.

9.6.1.CSVFileswiththeenergeticanalysis
CSVfilesarecreatedfordifferenttemperatures:300K,400K,500Kand600K.Thefileat300Kcontains
thefollowingdata:
Temperature[K]

Quantity

300

Ethyl

Ethene

Transitionstate

Signed
stoichiometry
Valuesina.u.
Electronicenergy
Zeropointenergy
Internalheat
(300.00K)
Chemicalpotential
(300.00K)
Correctionsin
kJ/mol
Zeropointenergy
Internalheat
(300.00K)
Chemicalpotential
(300.00K)

Otherquantities
Rateconstant

Linear
combination
(alwaysinkJ/mol)

79.1579
79.0982
79.0933

78.5875
78.5362
78.5322

157.7371
157.6231
157.6157

22
30
26

79.1225

78.5573

157.6536

69

157
170

134
145

299
319

8
4

93

79

219

47

Unit
Value
m**3*mol**1/second 0.167

Thenumbersinthistableareroundedtoimprovethereadability,buttheactualCSVfilecontainsall
numbersinfullmachineprecision.Thelinearcombinationofthechemicalpotentialsisalsoknownasthe
changeinfreeenergyassociatedwiththereaction.

9.6.2.Arrheniusplot
Thefilearrhenius.pngcontainstheArrheniusplot.Thisplotcanbeusedforavisualcheckofthelinear
regressionanalysistoestimatethekineticparameters.

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9.6.3.Alogfilewithananalysisofthekineticparameters
Thisfileiswrittentothefilekinetic.txt.Itcontainsthefollowingdata:
Summary
A[m**3*mol**1/second]=8.93643e+04
ln(A[a.u.])=10.63
Ea[kJ/mol]=33.16
R2(Pearson)=99.94%
Temperaturegrid
T_low[K]=300.0
T_high[K]=600.0
T_step[K]=10.0
Numberoftemperatures=31
Reactionrateconstants
T[K]Delta_rF[kJ/mol]k(T)[m**3*mol**1/second]
300.0068.71.66848e01
310.0070.12.48896e01
320.0071.63.62870e01
330.0073.05.18109e01
340.0074.47.25806e01
350.0075.99.99197e01
360.0077.31.35374e+00
370.0078.71.80731e+00
380.0080.12.38032e+00
390.0081.63.09593e+00
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400.0083.03.98015e+00
410.0084.45.06200e+00
420.0085.86.37365e+00
430.0087.37.95046e+00
440.0088.79.83115e+00
450.0090.11.20579e+01
460.0091.51.46762e+01
470.0092.91.77354e+01
480.0094.42.12883e+01
490.0095.82.53912e+01
500.0097.23.01043e+01
510.0098.63.54916e+01
520.00100.04.16205e+01
530.00101.44.85623e+01
540.00102.85.63922e+01
550.00104.26.51888e+01
560.00105.67.50346e+01
570.00107.18.60158e+01
580.00108.59.82222e+01
590.00109.91.11747e+02
600.00111.31.26688e+02
Electronicenergybarrier[kJ/mol]=21.6
Zeropointenergybarrier[kJ/mol]=29.7
Reactant0partitionfunction
Title:Ethyl
Electronicenergy[au]:79.15787
Zeropointcontribution[kJ/mol]:156.6101213
Zeropointenergy[au]:79.09822
Contributionstothepartitionfunction:
ELECTRONIC
Multiplicity:2
Electronicenergy:79.1578683
ROTATIONAL
Rotationalsymmetrynumber:1
Momentsofinertia[amu*bohr**2]:17.46847479.68486885.942337
Thresholdfornonzeromomentsofinertia[amu*bohr**2]:5.485799e04
Nonzeromomentsofinertia:3
TRANSLATIONAL
Dimension:3
Constantpressure:True
Pressure[bar]:1.01325
BIGFATWARNING!!!
ThisisanNpTpartitionfunction.
InternalenergycontainsaPVterm(andisthereforetheenthalpy).
FreeenergycontainsaPVterm(andisthereforetheGibbsfreeenergy).
Theheatcapacityiscomputedatconstantpressure.
Mass[amu]:29.039125
VIBRATIONAL
Numberofzerowavenumbers:0
Numberofrealwavenumbers:15
Numberofimaginarywavenumbers:0
Frequencyscalingfactor:1.0000
Zeropointscalingfactor:1.0000
RealWavenumbers[1/cm]:
123.7457.5817.9995.01074.21207.61430.11492.4
1510.81514.82965.53058.33102.33168.13264.7
Zeropointcontribution[kJ/mol]:156.6101213
Reactant1partitionfunction
Title:Ethene
Electronicenergy[au]:78.58746
Zeropointcontribution[kJ/mol]:134.4868825
Zeropointenergy[au]:78.53624
Contributionstothepartitionfunction:
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Contributionstothepartitionfunction:
ELECTRONIC
Multiplicity:1
Electronicenergy:78.5874587
ROTATIONAL
Rotationalsymmetrynumber:4
Momentsofinertia[amu*bohr**2]:12.28007660.07555272.355628
Thresholdfornonzeromomentsofinertia[amu*bohr**2]:5.485799e04
Nonzeromomentsofinertia:3
TRANSLATIONAL
Dimension:3
Constantpressure:True
Pressure[bar]:1.01325
BIGFATWARNING!!!
ThisisanNpTpartitionfunction.
InternalenergycontainsaPVterm(andisthereforetheenthalpy).
FreeenergycontainsaPVterm(andisthereforetheGibbsfreeenergy).
Theheatcapacityiscomputedatconstantpressure.
Mass[amu]:28.031300
VIBRATIONAL
Numberofzerowavenumbers:0
Numberofrealwavenumbers:12
Numberofimaginarywavenumbers:0
Frequencyscalingfactor:1.0000
Zeropointscalingfactor:1.0000
RealWavenumbers[1/cm]:
834.8956.1976.11070.11248.01395.81494.31720.2
3151.93167.33222.23247.7
Zeropointcontribution[kJ/mol]:134.4868825
Transitionstatepartitionfunction
Title:Transitionstate
Electronicenergy[au]:157.73711
Zeropointcontribution[kJ/mol]:299.2533370
Zeropointenergy[au]:157.62313
Contributionstothepartitionfunction:
ELECTRONIC
Multiplicity:2
Electronicenergy:157.7371095
ROTATIONAL
Rotationalsymmetrynumber:1
Momentsofinertia[amu*bohr**2]:92.846631597.569081642.613097
Thresholdfornonzeromomentsofinertia[amu*bohr**2]:5.485799e04
Nonzeromomentsofinertia:3
TRANSLATIONAL
Dimension:3
Constantpressure:True
Pressure[bar]:1.01325
BIGFATWARNING!!!
ThisisanNpTpartitionfunction.
InternalenergycontainsaPVterm(andisthereforetheenthalpy).
FreeenergycontainsaPVterm(andisthereforetheGibbsfreeenergy).
Theheatcapacityiscomputedatconstantpressure.
Mass[amu]:57.070425
VIBRATIONAL
Numberofzerowavenumbers:0
Numberofrealwavenumbers:32
Numberofimaginarywavenumbers:1
Frequencyscalingfactor:1.0000
Zeropointscalingfactor:1.0000
RealWavenumbers[1/cm]:
48.5154.6157.1247.0370.8547.0765.2823.5
831.9848.8917.81024.81035.81075.21228.41247.8
1317.91432.11487.21498.51514.51518.41609.42985.9
3061.73100.73149.13153.73163.83225.63237.23251.4
ImaginaryWavenumbers[1/cm]:
http://molmod.github.io/tamkin/tutorial/chemphys_examples.html

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9.ChemicalPhysicsBasicTAMkinrecipesTAMkin1.0.9documentation

ImaginaryWavenumbers[1/cm]:
383.6
Zeropointcontribution[kJ/mol]:299.2533370

9.7.ReactionKineticswithBSSEcorrections(bimolecular)
ThereislittlespecialrequiredtoincludeBSSEcorrectedenergiesfortransitionstatesorcomplexes.In
additiontothefrequencycomputationoutput,TAMkinalsorequiresanoutputfilefromaBSSE
computation.
InthecaseofaGaussiancomputation,onejustsreplacesthenormalwaytoloadthemolecule,
mol=load_molecule_g03fchk("freq.fchk")

by
mol=load_molecule_g03fchk("freq.fchk","bsse.fchk")

OnemaycomputetheBSSEcorrectedenergyatarefinedleveloftheory.

9.8.ReactionKineticswithinternalrotors(bimolecular)
TODO

9.9.Thermodynamicisotopeeffects
TODO

9.10.Kineticisotopeeffects
TODO:seeexamples/015_kiefornow.

9.11.Physisorption
TODO:seeexamples/018_physisorptionfornow.

9.12.Chemisorption
TODO

http://molmod.github.io/tamkin/tutorial/chemphys_examples.html

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9.13.Reactionkineticsonasurface
TODO

9.14.Reactionswithaprereactivecomplex
TODO:seeexamples/017_activationkineticmodelfornow.

http://molmod.github.io/tamkin/tutorial/chemphys_examples.html

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