#Data sources
database(
    thermoLibraries =['BurkeH2O2','FFCM1(-)','thermo_DFT_CCSDTF12_BAC','CBS_QB3_1dHR','DFT_QCI_thermo','primaryThermoLibrary'], # 'FFCM1(-)','primaryThermoLibrary', 'BurkeH2O2','DFT_QCI_thermo','CBS_QB3_1dHR'
    reactionLibraries = [('2005_Senosiain_OH_C2H2',False),('Glarborg/C3', False)], # 
    seedMechanisms = ['BurkeH2O2inN2','FFCM1(-)',], #
    kineticsDepositories = ['training'], 
    kineticsFamilies = ['default'],
    kineticsEstimator = 'rate rules',
)

#Constraints on generated species
generatedSpeciesConstraints(
    maximumRadicalElectrons = 2,
    allowed=['input species','seed mechanisms','reaction libraries'],
    maximumCarbonAtoms=9,
    maximumOxygenAtoms=4,
)

#List of species
species(
    label='C7H16',
    reactive=True,
    structure=SMILES("CCCCCCC"),
)
species(
    label='O2',
    reactive=True,
        structure=adjacencyList(
        """
        1 O u1 p2 {2,S}
        2 O u1 p2 {1,S}
        """),
)
species(
    label='N2',
    reactive=False,
    structure=SMILES("N#N")
)





#Reaction systems
simpleReactor(
    temperature=[(600,'K'),(1500,'K')],
    pressure=[(10.0,'bar'),(40.0,'bar')],
    nSims=8,
    initialMoleFractions={
        #"C7H10": 1,
        "O2":   0.10885, # phi=1 means 9.5 O2 per C7H10
        "N2":   0.881684808, # 8.1 times as much N2 as O2
        "C7H16":0.00946, #  
           
    },
    terminationTime = (1.0, 's'),
    terminationRateRatio = 0.01,
    terminationConversion={
                'C7H16': 0.99,
        },
)

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


model(
    toleranceKeepInEdge=0, # No pruning to start
    toleranceMoveToCore=0.4,
    toleranceInterruptSimulation=1,
    maxNumObjsPerIter=3, 
    terminateAtMaxObjects=True,
    maxNumSpecies=200, # first stage is until core reaches 100 species
    filterReactions=True, # should speed up model generation
)

model(
    toleranceMoveToCore=0.25,
    toleranceInterruptSimulation=1e8,
    toleranceKeepInEdge=0.01, # Pruning enabled for stage 2
    maximumEdgeSpecies=200000,
    minCoreSizeForPrune=100,
    minSpeciesExistIterationsForPrune=2,
    filterReactions=True,
    )

options(
    units='si',
    # saveRestartPeriod=(1,'hour'),
    generateOutputHTML=False,
    generatePlots=True,
    saveSimulationProfiles=True,
    saveEdgeSpecies=False,
)