#Git Commit
#RMG-Py:670e781c961166271c9ea7e605de45cb8bf8d383
#RMG-Database:efa658f48e6698ea48fb102fdfc2db3eafb37daf
 
# Data sources
database(
    thermoLibraries = ['primaryThermoLibrary','SulfurLibrary'],
    reactionLibraries = [],
    seedMechanisms = ['Sulfur/DTBS'],
    kineticsDepositories = ['training'],
    kineticsFamilies = 'default', 
    kineticsEstimator = 'rate rules',
)

# List of species
species(
    label='DTBS',
    reactive=True,
    structure=adjacencyList(
    """
    1  C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
    2  C u0 p0 c0 {1,S} {10,S} {11,S} {12,S}
    3  C u0 p0 c0 {1,S} {13,S} {14,S} {15,S}
    4  C u0 p0 c0 {1,S} {16,S} {17,S} {18,S}
    5  S u0 p2 c0 {1,S} {6,S}
    6  C u0 p0 c0 {5,S} {7,S} {8,S} {9,S}
    7  C u0 p0 c0 {6,S} {19,S} {20,S} {21,S}
    8  C u0 p0 c0 {6,S} {22,S} {23,S} {24,S}
    9  C u0 p0 c0 {6,S} {25,S} {26,S} {27,S}
    10 H u0 p0 c0 {2,S}
    11 H u0 p0 c0 {2,S}
    12 H u0 p0 c0 {2,S}
    13 H u0 p0 c0 {3,S}
    14 H u0 p0 c0 {3,S}
    15 H u0 p0 c0 {3,S}
    16 H u0 p0 c0 {4,S}
    17 H u0 p0 c0 {4,S}
    18 H u0 p0 c0 {4,S}
    19 H u0 p0 c0 {7,S}
    20 H u0 p0 c0 {7,S}
    21 H u0 p0 c0 {7,S}
    22 H u0 p0 c0 {8,S}
    23 H u0 p0 c0 {8,S}
    24 H u0 p0 c0 {8,S}
    25 H u0 p0 c0 {9,S}
    26 H u0 p0 c0 {9,S}
    27 H u0 p0 c0 {9,S}
    """
    ),
)

species(
    label='H2S',
    reactive=True,
    structure=adjacencyList(
    """
    1 S u0 p2 c0 {2,S} {3,S}
    2 H u0 p0 c0 {1,S}
    3 H u0 p0 c0 {1,S}
    """
    ),
)

species(
    label='C4H8',
    reactive=True,
    structure=adjacencyList(
    """
    1 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S}
    2 C u0 p0 c0 {3,S} {8,S} {9,S} {10,S}
    3 C u0 p0 c0 {1,S} {2,S} {4,D}
    4 C u0 p0 c0 {3,D} {11,S} {12,S}
    5 H u0 p0 c0 {1,S}
    6 H u0 p0 c0 {1,S}
    7 H u0 p0 c0 {1,S}
    8 H u0 p0 c0 {2,S}
    9 H u0 p0 c0 {2,S}
    10 H u0 p0 c0 {2,S}
    11 H u0 p0 c0 {4,S}
    12 H u0 p0 c0 {4,S}
    """
    ),
)

species(
    label='C4H9SH',
    reactive=True,
    structure=adjacencyList(
    """
    1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
    2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
    3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
    4 C u0 p0 c0 {1,S} {12,S} {13,S} {14,S}
    5 S u0 p2 c0 {1,S} {15,S}
    6 H u0 p0 c0 {2,S}
    7 H u0 p0 c0 {2,S}
    8 H u0 p0 c0 {2,S}
    9 H u0 p0 c0 {3,S}
    10 H u0 p0 c0 {3,S}
    11 H u0 p0 c0 {3,S}
    12 H u0 p0 c0 {4,S}
    13 H u0 p0 c0 {4,S}
    14 H u0 p0 c0 {4,S}
    15 H u0 p0 c0 {5,S}
    """
    ),
)

species(
    label='C4H10',
    reactive=True,
    structure=adjacencyList(
    """
    1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
    2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
    3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
    4 C u0 p0 c0 {1,S} {12,S} {13,S} {14,S}
    5 H u0 p0 c0 {1,S}
    6 H u0 p0 c0 {2,S}
    7 H u0 p0 c0 {2,S}
    8 H u0 p0 c0 {2,S}
    9 H u0 p0 c0 {3,S}
    10 H u0 p0 c0 {3,S}
    11 H u0 p0 c0 {3,S}
    12 H u0 p0 c0 {4,S}
    13 H u0 p0 c0 {4,S}
    14 H u0 p0 c0 {4,S}
    """
    ),
)

species(
    label='C6H10',
    reactive=True,
    structure=adjacencyList(
    """
    1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
    2 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
    3 C u0 p0 c0 {1,S} {6,S} {11,S} {12,S}
    4 C u0 p0 c0 {2,S} {5,S} {13,S} {14,S}
    5 C u0 p0 c0 {4,S} {6,D} {15,S}
    6 C u0 p0 c0 {3,S} {5,D} {16,S}
    7 H u0 p0 c0 {1,S}
    8 H u0 p0 c0 {1,S}
    9 H u0 p0 c0 {2,S}
    10 H u0 p0 c0 {2,S}
    11 H u0 p0 c0 {3,S}
    12 H u0 p0 c0 {3,S}
    13 H u0 p0 c0 {4,S}
    14 H u0 p0 c0 {4,S}
    15 H u0 p0 c0 {5,S}
    16 H u0 p0 c0 {6,S}
    """
    ),
)

# Reaction systems
simpleReactor(
    temperature=(653,'K'),
    pressure=(15,'torr'),
    initialMoleFractions={
        "DTBS": 0.4,
        "H2S": 0,
        "C4H8": 0,
        "C4H9SH": 0,
        "C4H10": 0,
        "C6H10": 0.6,
    },
    terminationConversion={
        'DTBS': 0.6,
    },
    terminationTime=(1e12,'s'),
)
simpleReactor(
    temperature=(653,'K'),
    pressure=(116,'torr'),
    initialMoleFractions={
        "DTBS": 0.4,
        "H2S": 0,
        "C4H8": 0,
        "C4H9SH": 0,
        "C4H10": 0,
        "C6H10": 0.6,
    },
    terminationConversion={
        'DTBS': 0.6,
    },
    terminationTime=(1e12,'s'),
)
simpleReactor(
    temperature=(653,'K'),
    pressure=(217,'torr'),
    initialMoleFractions={
        "DTBS": 0.4,
        "H2S": 0,
        "C4H8": 0,
        "C4H9SH": 0,
        "C4H10": 0,
        "C6H10": 0.6,
    },
    terminationConversion={
        'DTBS': 0.6,
    },
    terminationTime=(1e12,'s'),
)

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

model(
    toleranceKeepInEdge=0.0,
    toleranceMoveToCore=0.01,
    toleranceInterruptSimulation=0.01,
    maximumEdgeSpecies=100000
)

options(
    units='si',
    saveRestartPeriod=None,
    generateOutputHTML=True,
    generatePlots=False,
    saveEdgeSpecies=False,
    saveSimulationProfiles=False,
)

generatedSpeciesConstraints(
    allowed=['input species','seed mechanisms','reaction libraries'],
    maximumCarbonAtoms=12,
    maximumSulfurAtoms=2,
    #maximumHeavyAtoms=10,
    #maximumRadicalElectrons=10,
)