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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,67 +1,123 @@ | ||
| # Data sources | ||
| database( | ||
| thermoLibraries = ['primaryThermoLibrary'], | ||
| reactionLibraries = [], | ||
| thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo'], # 'surfaceThermoPt' is the default. Thermo data is derived using bindingEnergies for other metals | ||
| reactionLibraries = [('Surface/CPOX_Pt/Deutschmann2006_adjusted', False)], # when Ni is used change the library to Surface/Deutschmann_Ni | ||
| seedMechanisms = [], | ||
| kineticsDepositories = ['training'], | ||
| kineticsFamilies = 'default', | ||
| kineticsFamilies = ['surface', 'default'], | ||
| kineticsEstimator = 'rate rules', | ||
| ) | ||
|
|
||
| # List of species | ||
| catalystProperties( | ||
| bindingEnergies = { | ||
| 'H': (-2.75368,'eV/molecule'), | ||
| 'C': (-7.02516,'eV/molecule'), | ||
| 'N': (-4.63225,'eV/molecule'), | ||
| 'O': (-3.81153,'eV/molecule'), | ||
| }, | ||
| surfaceSiteDensity=(2.483e-9, 'mol/cm^2'), | ||
| coverageDependence=False | ||
| ) | ||
| species( | ||
| label='ethane', | ||
| label='CH4', | ||
| reactive=True, | ||
| structure=SMILES("CC"), | ||
| structure=SMILES("C"), | ||
| ) | ||
|
|
||
| # Reaction systems | ||
| simpleReactor( | ||
| temperature=(1350,'K'), | ||
| pressure=(1.0,'bar'), | ||
| initialMoleFractions={ | ||
| "ethane": 1.0, | ||
| }, | ||
| terminationConversion={ | ||
| 'ethane': 0.9, | ||
| }, | ||
| terminationTime=(1e6,'s'), | ||
| species( | ||
| label='O2', | ||
| reactive=True, | ||
| structure=adjacencyList( | ||
| """ | ||
| 1 O u1 p2 c0 {2,S} | ||
| 2 O u1 p2 c0 {1,S} | ||
| """), | ||
| ) | ||
|
|
||
| simpleReactor( | ||
| temperature=(1000,'K'), | ||
| pressure=(1.0,'bar'), | ||
| initialMoleFractions={ | ||
| "ethane": 1.0, | ||
| species( | ||
| label='N2', | ||
| reactive=False, | ||
| structure=SMILES("N#N"), | ||
| ) | ||
| species( | ||
| label='X', | ||
| reactive=True, | ||
| structure=adjacencyList("1 X u0"), | ||
| ) | ||
| # added for training | ||
| species( | ||
| label='CO2X', | ||
| reactive=True, | ||
| structure=adjacencyList( | ||
| """ | ||
| 1 O u0 p2 c0 {3,D} | ||
| 2 O u0 p2 c0 {3,D} | ||
| 3 C u0 p0 c0 {1,D} {2,D} | ||
| 4 X u0 p0 c0 | ||
| """), | ||
| ) | ||
| species( | ||
| label='COX', | ||
| reactive=True, | ||
| structure=adjacencyList( | ||
| """ | ||
| 1 O u0 p2 c0 {2,D} | ||
| 2 C u0 p0 c0 {1,D} {3,D} | ||
| 3 X u0 p0 c0 {2,D} | ||
| """), | ||
| ) | ||
| species( | ||
| label='OX', | ||
| reactive=True, | ||
| structure=adjacencyList( | ||
| """ | ||
| 1 O u0 p2 c0 {2,D} | ||
| 2 X u0 p0 c0 {1,D} | ||
| """), | ||
| ) | ||
| # If you would like to forbid the bidentate form of absorbed CO2 from your model, | ||
| # use the following `CO2_bidentate` forbidden structure | ||
| # forbidden( | ||
| # label='CO2_bidentate', | ||
| # structure=SMILES("O=C(*)O*"), | ||
| # ) | ||
| #---------- | ||
| # Reaction systems | ||
| surfaceReactor( | ||
| temperature=(1000, 'K'), | ||
| initialPressure=(1.0, 'bar'), | ||
| initialGasMoleFractions={ | ||
| "CH4": 0.15, | ||
| "O2": 0.15, | ||
| "N2": 0.7, | ||
| }, | ||
| terminationConversion={ | ||
| 'ethane': 0.9, | ||
| initialSurfaceCoverages={ | ||
| "X": 1.0, | ||
| }, | ||
| terminationTime=(1e6,'s'), | ||
| surfaceVolumeRatio=(1.e5, 'm^-1'), | ||
| terminationConversion = { "CH4": 0.95,}, | ||
| terminationTime=(0.1, 's'), | ||
| terminationRateRatio=0.01, | ||
| ) | ||
|
|
||
|
|
||
|
|
||
| simulator( | ||
| atol=1e-16, | ||
| rtol=1e-8, | ||
| atol=1e-18, | ||
| rtol=1e-12, | ||
| ) | ||
|
|
||
| model( | ||
| toleranceKeepInEdge=0.0, | ||
| toleranceMoveToCore=100.0, | ||
| toleranceInterruptSimulation=100.0, | ||
| toleranceMoveToCore=1e-1, | ||
| toleranceInterruptSimulation=0.1, | ||
| maximumEdgeSpecies=100000, | ||
| toleranceMoveEdgeReactionToSurface=1.0, | ||
| toleranceMoveSurfaceReactionToCore=2.0, | ||
| toleranceMoveSurfaceSpeciesToCore=.001, | ||
| dynamicsTimeScale=(1.0e-10,'sec'), | ||
| ) | ||
|
|
||
| options( | ||
| units='si', | ||
| generateOutputHTML=True, | ||
| generatePlots=False, | ||
| saveEdgeSpecies=True, | ||
| saveSimulationProfiles=True, | ||
| generateOutputHTML=False, | ||
| generatePlots=False, # Enable to make plots of core and edge size etc. But takes a lot of the total runtime! | ||
| saveEdgeSpecies=False, | ||
| saveSimulationProfiles=False, | ||
| ) | ||
| generatedSpeciesConstraints( | ||
| allowed=['input species','reaction libraries'], | ||
| maximumCarbonAtoms=2, | ||
| maximumOxygenAtoms=2, | ||
| maximumSurfaceSites=2, | ||
| ) | ||
|
|
||
|
|
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