add acetonitrile SEI chemistry example

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,
+)