-
Notifications
You must be signed in to change notification settings - Fork 228
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'main' into wsl_docs_addition
- Loading branch information
Showing
18 changed files
with
606 additions
and
134 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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, | ||
| ) | ||
|
|
||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.