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

# List of species
species(
    label='octane',
    reactive=True,
    structure=SMILES("C(CCCCC)CC"),
)

species(
    label='oxygen',
    reactive=True,
    structure=SMILES("[O][O]"),
)

# Reaction systems
liquidReactor(
    temperature=(500,'K'),
    initialConcentrations={
        "octane": (6.154e-3,'mol/cm^3'),
        "oxygen": (4.953e-6,'mol/cm^3')
    },
    terminationTime=(5,'s'),
)

solvation(
	solvent='octane'
)

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

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

options(
    units='si',
    saveRestartPeriod=None,
    drawMolecules=False,
    generatePlots=False,
    saveConcentrationProfiles=True,
)

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

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

# List of species
species(
    label='octane',
    multiplicity = 1,
    reactive=True,
    structure=SMILES("C(CCCCC)CC"),
)

species(
    label='oxygen',
    multiplicity = 3,
    reactive=True,
    structure=SMILES("[O][O]"),
)

# Reaction systems
liquidReactor(
    temperature=(500,'K'),
    initialConcentrations={
        "octane": (6.154e-3,'mol/cm^3'),
        "oxygen": (4.953e-6,'mol/cm^3')
    },
    terminationTime=(5,'s'),
)

solvation(
	solvent='octane'
)

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

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

options(
    units='si',
    saveRestartPeriod=None,
    drawMolecules=False,
    generatePlots=False,
    saveConcentrationProfiles=True,
)

Update RMG example liquid_phase with multiplicity label
Update RMG example liquid_phase with multiplicity label

  database(
      thermoLibraries = ['primaryThermoLibrary'],
      reactionLibraries = [],
      seedMechanisms = [],
      kineticsDepositories = ['training'],
      kineticsFamilies = 'default',
      kineticsEstimator = 'rate rules',
  )
  
+ # Constraints on generated species
+ generatedSpeciesConstraints(
+     maximumRadicalElectrons = 3,
+ )
+ 
  # List of species
  species(
      label='octane',
+     multiplicity = 1,
      reactive=True,
      structure=SMILES("C(CCCCC)CC"),
  )
  
  species(
      label='oxygen',
+     multiplicity = 3,
      reactive=True,
      structure=SMILES("[O][O]"),
  )
  
  # Reaction systems
  liquidReactor(
      temperature=(500,'K'),
      initialConcentrations={
          "octane": (6.154e-3,'mol/cm^3'),
          "oxygen": (4.953e-6,'mol/cm^3')
      },
      terminationTime=(5,'s'),
  )
  
  solvation(
  	solvent='octane'
  )
  
  simulator(
      atol=1e-16,
      rtol=1e-8,
  )
  
  model(
      toleranceKeepInEdge=1E-9,
      toleranceMoveToCore=0.001,
      toleranceInterruptSimulation=0.1,
      maximumEdgeSpecies=100000
  )
  
  options(
      units='si',
      saveRestartPeriod=None,
      drawMolecules=False,
      generatePlots=False,
      saveConcentrationProfiles=True,
  )
  
Update RMG example liquid_phase with multiplicity label
## Code Before:
database(
    thermoLibraries = ['primaryThermoLibrary'],
    reactionLibraries = [],
    seedMechanisms = [],
    kineticsDepositories = ['training'],
    kineticsFamilies = 'default',
    kineticsEstimator = 'rate rules',
)

# List of species
species(
    label='octane',
    reactive=True,
    structure=SMILES("C(CCCCC)CC"),
)

species(
    label='oxygen',
    reactive=True,
    structure=SMILES("[O][O]"),
)

# Reaction systems
liquidReactor(
    temperature=(500,'K'),
    initialConcentrations={
        "octane": (6.154e-3,'mol/cm^3'),
        "oxygen": (4.953e-6,'mol/cm^3')
    },
    terminationTime=(5,'s'),
)

solvation(
	solvent='octane'
)

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

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

options(
    units='si',
    saveRestartPeriod=None,
    drawMolecules=False,
    generatePlots=False,
    saveConcentrationProfiles=True,
)

## Instruction:
Update RMG example liquid_phase with multiplicity label
## Code After:
database(
    thermoLibraries = ['primaryThermoLibrary'],
    reactionLibraries = [],
    seedMechanisms = [],
    kineticsDepositories = ['training'],
    kineticsFamilies = 'default',
    kineticsEstimator = 'rate rules',
)

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

# List of species
species(
    label='octane',
    multiplicity = 1,
    reactive=True,
    structure=SMILES("C(CCCCC)CC"),
)

species(
    label='oxygen',
    multiplicity = 3,
    reactive=True,
    structure=SMILES("[O][O]"),
)

# Reaction systems
liquidReactor(
    temperature=(500,'K'),
    initialConcentrations={
        "octane": (6.154e-3,'mol/cm^3'),
        "oxygen": (4.953e-6,'mol/cm^3')
    },
    terminationTime=(5,'s'),
)

solvation(
	solvent='octane'
)

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

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

options(
    units='si',
    saveRestartPeriod=None,
    drawMolecules=False,
    generatePlots=False,
    saveConcentrationProfiles=True,
)
