diff --git a/examples/rmg/SEI_pure_ACN/input.py b/examples/rmg/SEI_pure_ACN/input.py new file mode 100644 index 0000000000..22891fd91f --- /dev/null +++ b/examples/rmg/SEI_pure_ACN/input.py @@ -0,0 +1,173 @@ +# Data sources +database( + thermoLibraries=['LithiumSurface','electrocatLiThermo','primaryThermoLibrary', 'LithiumPrimaryThermo', 'LithiumAdditionalThermo', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo'], # 'surfaceThermoPt' is the default. Thermo data is derived using bindingEnergies for other metals + reactionLibraries = ['LithiumPrimaryKinetics',"LithiumSurface"], # when Ni is used change the library to Surface/Deutschmann_Ni + seedMechanisms = [], + kineticsDepositories = ['training'], + kineticsFamilies = ['surface', + '1+2_Cycloaddition', + 'Surface_Carbonate_Deposition', + 'Surface_Carbonate_F_CO_Decomposition', + 'Surface_Carbonate_2F_Decomposition', + 'Surface_Carbonate_CO_Decomposition', + '1,2_Elimination_LiR', + '1,2_Intra_Elimination_LiR', + 'Li_Addition_MultipleBond', + 'Li_NO_Substitution', + 'Li_NO_Ring_Opening', + 'Li_Abstraction', + 'R_Addition_MultipleBond_Disprop', + 'Cation_R_Recombination', + 'Cation_Addition_Multiple_Bond', + '1,2-Birad_to_alkene', + '1,2_Insertion_CO', + '1,2_Insertion_carbene', + '1,2_shiftS', + '1,3_Insertion_CO2', + '1,3_Insertion_ROR', + '1,3_Insertion_RSR', + '1,4_Cyclic_birad_scission', + '1,4_Linear_birad_scission', + '2+2_cycloaddition', + 'Birad_recombination', + 'CO_Disproportionation', + 'Birad_R_Recombination', + 'Cyclic_Ether_Formation', + 'Cyclic_Thioether_Formation', + 'Diels_alder_addition', + 'Diels_alder_addition_Aromatic', + #'Disproportionation', + 'HO2_Elimination_from_PeroxyRadical', + 'H_Abstraction', + 'Intra_Retro_Diels_alder_bicyclic', + 'Intra_Disproportionation', + 'Intra_R_Add_Endocyclic', + 'Intra_R_Add_Exocyclic', + 'R_Addition_COm', + 'R_Addition_MultipleBond', + 'R_Recombination', + 'intra_H_migration', + 'intra_NO2_ONO_conversion', + 'intra_OH_migration', + 'intra_substitutionCS_cyclization', + 'intra_substitutionCS_isomerization', + 'intra_substitutionS_cyclization', + 'intra_substitutionS_isomerization', + #'ketoenol', + 'Singlet_Carbene_Intra_Disproportionation', + 'Singlet_Val6_to_triplet', + 'Intra_5_membered_conjugated_C=C_C=C_addition', + 'Intra_Diels_alder_monocyclic', + 'Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH', + 'Intra_2+2_cycloaddition_Cd', + 'Intra_ene_reaction', + 'Cyclopentadiene_scission', + '6_membered_central_C-C_shift', + 'Intra_R_Add_Exo_scission', + '1,2_shiftC', + '1,2_NH3_elimination', + '1,3_NH3_elimination', + 'Retroene',], + kineticsEstimator = 'rate rules', + adsorptionGroups='adsorptionLi', +) + +catalystProperties( + metal = 'Li110', +) + +# List of species +species( + label="Lip", + reactive=True, + structure=SMILES("[Li+]"), +) + +species( + label='ACN', + reactive=True, + structure=SMILES("CC#N"), +) + +species( + label='vacantX', + reactive=True, + structure=adjacencyList("1 X u0"), +) + +liquidSurfaceReactor( + temperature=(298.15,'K'), + distance=(10.0e-10,"m"), + viscosity=(5e7,"Pa*s"), + liqPotential=(0.3,'V'), + surfPotential=(0.0,'V'), + initialConcentrations={ + "ACN": (0.019146,'mol/cm^3'), + "Lip": (15.0,'mol/m^3'), + }, + initialSurfaceCoverages={ + "vacantX": 1.0, + }, + surfaceVolumeRatio=(1.0e-5, 'm^-1'), + terminationTime=(1e3,'sec'), + constantSpecies=["ACN","Lip"], +) + +liquidSurfaceReactor( + temperature=(298.15,'K'), + distance=(0.0,"m"), + liqPotential=(0.0,'V'), + surfPotential=(0.0,'V'), + initialConcentrations={ + "ACN": (0.019146,'mol/cm^3'), + "Lip": (15.0,'mol/m^3'), + }, + initialSurfaceCoverages={ + "vacantX": 1.0, + }, + surfaceVolumeRatio=(1.0e5, 'm^-1'), + terminationTime=(1e3,'sec'), + constantSpecies=["ACN","Lip"], +) + +solvation( + solvent='acetonitrile' +) + +simulator( + atol=1e-16, + rtol=1e-6, +) + +model( + toleranceKeepInEdge=1E-20, + toleranceMoveToCore=0.1, + toleranceRadMoveToCore=0.1, + toleranceInterruptSimulation=1e10, + maximumEdgeSpecies=100000, + filterReactions=False, + maxNumObjsPerIter=1, + terminateAtMaxObjects=True, + toleranceBranchReactionToCore=0.001, + branchingIndex=0.5, + branchingRatioMax=1.0, +) + +options( + units='si', + saveEdgeSpecies=False, +) + +generatedSpeciesConstraints( + allowed=['input species','reaction libraries'], + maximumSurfaceSites=1, + explicitlyForbiddenGroups=[groupAdjacencyList(""" +1 Xv u0 p0 c0 +""")], + explicitlyForbiddenMolecules=[adjacencyList(""" +1 Li u0 p0 c0 {2,S} +2 Li u0 p0 c0 {1,S}""")], + maximumCarbonAtoms=7, + maximumNitrogenAtoms=4, + maximumRadicalElectrons=1, +)