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add ethylene carbonate example
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‎examples/rmg/SEI_pure_EC/input.py‎

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# Data sources
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database(
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thermoLibraries=['electrocatLiThermo','primaryThermoLibrary', 'LithiumPrimaryThermo', 'LithiumAdditionalThermo', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo'], # 'surfaceThermoPt' is the default. Thermo data is derived using bindingEnergies for other metals
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reactionLibraries = ['LithiumPrimaryKinetics','LithiumAnalogyKinetics'], # when Ni is used change the library to Surface/Deutschmann_Ni
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seedMechanisms = [],
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kineticsDepositories = ['training'],
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kineticsFamilies = ['surface','electrochem',
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'1+2_Cycloaddition',
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'1,2-Birad_to_alkene',
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'1,2_Insertion_CO',
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'1,2_Insertion_carbene',
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'1,2_shiftS',
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'1,3_Insertion_CO2',
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'1,3_Insertion_ROR',
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'1,3_Insertion_RSR',
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'1,4_Cyclic_birad_scission',
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'1,4_Linear_birad_scission',
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'2+2_cycloaddition',
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'Birad_recombination',
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'CO_Disproportionation',
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'Birad_R_Recombination',
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'Cyclic_Ether_Formation',
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'Cyclic_Thioether_Formation',
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'Diels_alder_addition',
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'Diels_alder_addition_Aromatic',
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#'Disproportionation',
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'HO2_Elimination_from_PeroxyRadical',
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'H_Abstraction',
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'Intra_Retro_Diels_alder_bicyclic',
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'Intra_Disproportionation',
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'Intra_R_Add_Endocyclic',
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'Intra_R_Add_Exocyclic',
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'R_Addition_COm',
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'R_Addition_MultipleBond',
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'R_Recombination',
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'intra_H_migration',
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'intra_NO2_ONO_conversion',
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'intra_OH_migration',
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'intra_substitutionCS_cyclization',
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'intra_substitutionCS_isomerization',
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'intra_substitutionS_cyclization',
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'intra_substitutionS_isomerization',
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#'ketoenol',
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'Singlet_Carbene_Intra_Disproportionation',
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'Singlet_Val6_to_triplet',
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'Intra_5_membered_conjugated_C=C_C=C_addition',
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'Intra_Diels_alder_monocyclic',
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'Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH',
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'Intra_2+2_cycloaddition_Cd',
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'Intra_ene_reaction',
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'Cyclopentadiene_scission',
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'6_membered_central_C-C_shift',
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'Intra_R_Add_Exo_scission',
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'1,2_shiftC',
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'1,2_NH3_elimination',
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'1,3_NH3_elimination',
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'Retroene',],
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kineticsEstimator = 'rate rules',
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adsorptionGroups='adsorptionLi',
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)
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catalystProperties(
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metal = 'Li110'
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)
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# List of species
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species(
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label="Lip",
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reactive=True,
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structure=SMILES("[Li+]"),
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)
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species(
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label='ethylene-carbonate',
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reactive=True,
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structure=SMILES("C1COC(=O)O1"),
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)
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species(
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label='vacantX',
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reactive=True,
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structure=adjacencyList("1 X u0"),
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)
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species(
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label="Li",
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reactive=True,
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structure=SMILES("[Li]"),
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)
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species(
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label='[Li]O[C]1OCCO1',
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reactive=True,
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structure=SMILES("[Li]O[C]1OCCO1"),
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)
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species(
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label='[Li]OC(=O)OC[CH2]',
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reactive=True,
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structure=SMILES("[Li]OC(=O)OC[CH2]"),
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)
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#species(
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# label='[Li]OC(=O)O[Li]',
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# reactive=True,
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# structure=SMILES("[Li]OC(=O)O[Li]"),
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# )
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#species(
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# label='[Li]OC(=O)OCCOC(=O)OC[CH2]',
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# reactive=True,
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# structure=SMILES("[Li]OC(=O)OCCOC(=O)OC[CH2]"),
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# )
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#species(
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# label='[Li]OC(=O)OCCOC(=O)O[Li]',
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# reactive=True,
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# structure=SMILES("[Li]OC(=O)OCCOC(=O)O[Li]"),
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# )
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#species(
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# label='[Li]OC(=O)OCCCCOC(=O)O[Li]',
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# reactive=True,
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# structure=SMILES("[Li]OC(=O)OCCCCOC(=O)O[Li]"),)
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#species(
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# label='[Li]OCCOC(=O)CCOC(=O)O[Li]',
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# reactive=True,
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# structure=SMILES("[Li]OCCOC(=O)CCOC(=O)O[Li]"),
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# )
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#species(
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# label='[Li]OCCOC(=O)OC(=O)O[Li]',
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# reactive=True,
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# structure=SMILES("[Li]OCCOC(=O)OC(=O)O[Li]"),
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#)
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#species(
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# label='C2H4',
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# reactive=True,
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# structure=SMILES("C=C"),
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#)
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#species(
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# label='O=[C]OCCO[Li]',
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# reactive=True,
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# structure=SMILES("O=[C]OCCO[Li]"),
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#)
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#species(
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# label='CO2',
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# reactive=True,
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# structure=SMILES("O=C=O"),
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#)
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#species(
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# label='[Li]OC[CH2]',
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# reactive=True,
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# structure=SMILES("[Li]OC[CH2]"),
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#)
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#species(
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# label='O1CCO[C]1OC2(O[Li])OCCO2',
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# reactive=True,
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# structure=SMILES("O1CCO[C]1OC2(O[Li])OCCO2"),
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#)
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#species(
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# label='O1CCOC1(O[Li])OC(=O)OC[CH2]',
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# reactive=True,
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# structure=SMILES("O1CCOC1(O[Li])OC(=O)OC[CH2]"),
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#)
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#species(
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# label='O1CCOC1(O[Li])OC(=O)OCCOC(=O)O[Li]',
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# reactive=True,
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# structure=SMILES("O1CCOC1(O[Li])OC(=O)OCCOC(=O)O[Li]"),
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#)
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species(
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label='CO3X2',
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reactive=True,
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structure=adjacencyList("""1 O u0 p2 {2,D}
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2 C u0 p0 {1,D} {3,S} {4,S}
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3 O u0 p2 {2,S} {5,S}
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4 O u0 p2 {2,S} {6,S}
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5 X u0 p0 c0 {3,S}
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6 X u0 p0 c0 {4,S}
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"""),
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)
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#species(
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# label="CO",
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# reactive=True,
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# structure=SMILES("[C-]#[O+]"),
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#)
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#species(
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# label='[Li]OC(=O)OCCX',
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# reactive=True,
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# structure=adjacencyList("""1 O u0 p2 c0 {2,S} {7,S}
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# 2 C u0 p0 c0 {1,S} {3,D} {4,S}
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# 3 O u0 p2 c0 {2,D}
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# 4 O u0 p2 c0 {2,S} {5,S}
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# 5 C u0 p0 c0 {4,S} {6,S} {8,S} {9,S}
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# 6 C u0 p0 c0 {5,S} {10,S} {11,S} {12,S}
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# 7 Li u0 p0 c0 {1,S}
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# 8 H u0 p0 c0 {5,S}
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# 9 H u0 p0 c0 {5,S}
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# 10 H u0 p0 c0 {6,S}
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# 11 H u0 p0 c0 {6,S}
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# 12 X u0 p0 c0 {6,S}
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# """),
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#)
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#species(
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# label='O=C(X)OCCO[Li]',
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# reactive=True,
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# structure=adjacencyList("""1 O u0 p2 c0 {2,D}
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# 2 C u0 p0 c0 {1,D} {3,S} {12,S}
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# 3 O u0 p2 c0 {2,S} {4,S}
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# 4 C u0 p0 c0 {3,S} {5,S} {7,S} {8,S}
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# 5 C u0 p0 c0 {4,S} {6,S} {9,S} {10,S}
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# 6 O u0 p2 c0 {5,S} {11,S}
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# 7 H u0 p0 c0 {4,S}
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# 8 H u0 p0 c0 {4,S}
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# 9 H u0 p0 c0 {5,S}
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# 10 H u0 p0 c0 {5,S}
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# 11 Li u0 p0 c0 {6,S}
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# 12 X u0 p0 c0 {2,S}
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# """),
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#)
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liquidSurfaceReactor(
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temperature=(298.15,'K'),
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liqPotential=(-1.0,'V'),
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surfPotential=(0.0,'V'),
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initialConcentrations={
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"ethylene-carbonate": (7.585e-3*2.0,'mol/cm^3'),
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"Lip": (15.0,'mol/m^3'),
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},
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initialSurfaceCoverages={
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"vacantX": 1.0,
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},
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surfaceVolumeRatio=(1.0e5, 'm^-1'),
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terminationTime=(1.0e3,'sec'),
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constantSpecies=["ethylene-carbonate","Lip"],
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)
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solvation(
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solvent='ethylene carbonate'
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)
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simulator(
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atol=1e-16,
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rtol=1e-6,
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)
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model(
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toleranceKeepInEdge=1E-20,
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toleranceMoveToCore=0.000001,
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toleranceRadMoveToCore=0.00000000001,
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toleranceInterruptSimulation=1e10,
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maximumEdgeSpecies=100000,
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filterReactions=False,
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maxNumObjsPerIter=1,
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terminateAtMaxObjects=True,
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toleranceBranchReactionToCore=0.000001,
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branchingIndex=0.3,
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branchingRatioMax=1.0,
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)
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options(
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units='si',
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saveEdgeSpecies=False,
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)
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generatedSpeciesConstraints(
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allowed=['input species','reaction libraries'],
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maximumSurfaceSites=1,
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explicitlyForbiddenGroups=[groupAdjacencyList("""
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1 Xv u0 p0 c0
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""")],
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maximumCarbonAtoms=8,
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maximumOxygenAtoms=8,
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maximumRadicalElectrons=1,
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)
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