# Data sources
database(
    thermoLibraries = ['primaryThermoLibrary'],
    reactionLibraries = [],
    seedMechanisms = [],
    kineticsDepositories = ['training'],
    kineticsFamilies = 'default',
    kineticsEstimator = 'rate rules',
)

# Constraints on generated species
generatedSpeciesConstraints(
    maximumRadicalElectrons = 3,
)

# List of species
species(
    label='reactant1',
    reactive=True,
    structure=SMILES("Cc1cc(O)cc(=O)o1"),
)

species(
    label='reactant2',
    reactive=True,
    structure=SMILES("CC(C)SCl"),
)
species(
    label='methanol',
    reactive=True,
    structure=InChI("InChI=1S/CH4O/c1-2/h2H,1H3"),
)
# Reaction systems
liquidReactor(
    temperature=(300,'K'),
    initialConcentrations={
        "reactant1": (6.154e-3,'mol/cm^3'),
        "reactant2": (6.154e-3,'mol/cm^3'),
        "methanol": (12.154e-3,'mol/cm^3')
    },
    terminationTime=(5,'s'),
)

solvation(
	solvent='methanol'
)

simulator(
    atol=1e-16,
    rtol=1e-8,
)

model(
    toleranceKeepInEdge=1E-9,
    toleranceMoveToCore=0.001,
    toleranceInterruptSimulation=0.1,
    maximumEdgeSpecies=100000
)

options(
    units='si',
    generateOutputHTML=True,
    generatePlots=True,
    saveEdgeSpecies=True,
    saveSimulationProfiles=True,
)