9.7. Thermo Estimation Module

The thermo estimation module can be run stand-alone. An example input file for this module is shown below:

database(
    thermoLibraries = ['primaryThermoLibrary', 'GRI-Mech3.0']
)

species(
    label='Cineole',
    structure=SMILES('CC12CCC(CC1)C(C)(C)O2'),
)

quantumMechanics(
    software='mopac',#mopac or gaussian
    method='pm3',#pm3, pm6, pm7
    fileStore='QMfiles', # defaults to inside the output folder.
    onlyCyclics = True,#True, False
    maxRadicalNumber = 0, # 0, 1
)

The database block is used to specify species thermochemistry libraries. Multiple libraries may be created, if so desired. The order in which the thermo libraries are specified is important: If a species appears in multiple thermo libraries, the first instance will be used.

Please see Section Thermo Database for details on editing the thermo library. In general, it is best to leave the ThermoLibrary set to its default value. In particular, the thermodynamic properties for H and H2 must be specified in one of the primary thermo libraries as they cannot be estimated by Benson’s method.

For example, if you wish to use the GRI-Mech 3.0 mechanism [GRIMech3.0] as a ThermoLibrary in your model, the syntax will be:

thermoLibraries = ['primaryThermoLibrary','GRI-Mech3.0']

This library is located in the RMG-database/input/thermo/libraries directory. All “Locations” for the ThermoLibrary field must be with respect to the RMG-database/input/thermo/libraries directory.

The optional quantumMechanics block is used when quantum mechanical calculations are desired to determine thermodynamic parameters. These calculations are only run if the molecule is not included in a specified thermo library. The software option accepts either the mopac or gaussian string. The method option refers to the level-of-theory, which can either be pm3,``pm6``, or pm7. A folder can be specified to store the files used in these calculations, however if not specified this defaults to a QMfiles folder in the output folder. The onlyCyclics option, if True, only runs these calculations for cyclic species. In this case, group contribution estimates are used for all other species. The calculations are also only run on species with a maximum radical number set by the user. If a molecule has a higher radical number, the molecule is saturated with hydrogen atoms, then quantum mechanical calculations with subsequent hydrogen bond incrementation is used to determine the thermodynamic parameters.

Submitting a job is easy:

python thermoEstimator.py input.py

We recommend you make a job-specific directory for each thermoEstimator simulation.

You can also specify that an RMG-style thermo library be saved upon completion:

python thermoEstimator.py -l input.py

Note that the RMG website also provides thermo estimation through the Molecule Search.