9.4. Generate Reactions

The script generateReactions.py generates reactions between all species mentioned in an input file. To call this method type:

python generateReactions.py Input_File

where Input_File is a file similar to a general RMG input file which contains all the species for RMG to generate reactions between. An example file is placed in $RMGPy/examples/generateReactions/input.py

# Data sources for kinetics
database(
    thermoLibraries = ['BurkeH2O2','primaryThermoLibrary','DFT_QCI_thermo','CBS_QB3_1dHR'],
    reactionLibraries = [],  
    seedMechanisms = [],
    kineticsDepositories = 'default', 
    #this section lists possible reaction families to find reactioons with
    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
    kineticsEstimator = 'rate rules',
)

# List all species you want reactions between
species(
    label='ethane',
    reactive=True,
    structure=SMILES("CC"),
)

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

species(
    label='butane',
    reactive=True,
    structure=SMILES("CCCC"),
)


# you must list reactor conditions (though this may not effect the output)
simpleReactor(
    temperature=(650,'K'),
    pressure=(10.0,'bar'),
    initialMoleFractions={
        "ethane": 1,
    },
    terminationConversion={
        'butane': .99,
    },
    terminationTime=(40,'s'),
)

#optional module if you want to get pressure dependent kinetics. 

#pressureDependence(
#     method='modified strong collision',
#     maximumGrainSize=(0.5,'kcal/mol'),
#     minimumNumberOfGrains=250,
#     temperatures=(300,2200,'K',2),
#     pressures=(0.01,100,'bar',3),
#     interpolation=('Chebyshev', 6, 4),
#     maximumAtoms=15,
#)

#optional module if you want to limit species produced in reactions. 

#generatedSpeciesConstraints(
#    allowed=['input species','seed mechanisms','reaction libraries'],
#    maximumCarbonAtoms=4,
#    maximumOxygenAtoms=7,
#    maximumNitrogenAtoms=0,
#    maximumSiliconAtoms=0,
#    maximumSulfurAtoms=0,
#    maximumHeavyAtoms=20,
#    maximumRadicalElectrons=1,
#)

This method will produce an output.html file in the directory of input.py which contains the all the reactions produced between the species.

This method is also available to use with a web browser from the RMG website: Populate Reactions.