5. measure.reaction - Working with reaction rate coefficients

Contains functions for working with reaction rate coefficients. The calculateMicrocanonicalRateCoefficients() function is used to calculate the forward and reverse microcanonical rate coefficients for each path reaction. The fitInterpolationModel() function is used to fit an interpolation model to a phenomenological rate coefficient k(T,P)() for each net reaction.

5.1. Microcanonical Rate Coefficients

measure.reaction.calculateMicrocanonicalRateCoefficient()

Calculate the microcanonical rate coefficient for the reaction reaction at the energies Elist in J/mol. reacDensStates and prodDensStates are the densities of states of the reactant and product configurations for this reaction. If the reaction is irreversible, only the reactant density of states is required; if the reaction is reversible, then both are required. This function will try to use the best method that it can based on the input data available:

• If detailed information has been provided for the transition state (i.e. the molecular degrees of freedom), then RRKM theory will be used.
• If the above is not possible but high-pressure limit kinetics have been provided, then the inverse Laplace transform method will be used.

The density of states for the product prodDensStates and the temperature of interest T in K can also be provided. For isomerization and association reactions prodDensStates is required; for dissociation reactions it is optional. The temperature is used if provided in the detailed balance expression to determine the reverse kinetics, and in certain cases in the inverse Laplace transform method.

measure.reaction.applyRRKMTheory()

Calculate the microcanonical rate coefficient for a reaction using RRKM theory, where transitionState is the transition state of the reaction, Elist is the array of energies in J/mol at which to evaluate the microcanonial rate, and densStates is the density of states of the reactant.

measure.reaction.applyInverseLaplaceTransformMethod()

Calculate the microcanonical rate coefficient for a reaction using the inverse Laplace transform method, where kinetics is the high pressure limit rate coefficient, E0 is the ground-state energy of the transition state, Elist is the array of energies in J/mol at which to evaluate the microcanonial rate, and densStates is the density of states of the reactant. The temperature T in K is not required, and is only used when the temperature exponent of the Arrhenius expression is negative (for which the inverse transform is undefined).

5.2. Interpolation Models for Phenomenological Rate Coefficients

measure.reaction.fitInterpolationModel()

For a set of phenomenological rate coefficients K computed at a grid of temperatures Tlist in K and pressures Plist in Pa, fit a interpolation model, a tuple where the first item is a string describing the type of model - either 'chebyshev' or 'pdeparrhenius' - and the remaining elements contain parameters for that model. For Chebyshev polynomials, the parameters are the number of terms to use in each of the temperature and pressure dimensions. For pressure-dependent Arrhenius models there are no additional parameters. Tmin, Tmax, Pmin, and Pmax specify the temperature and pressure ranges in K and Pa, respectively, over which the interpolation model is valid. If errorCheck is True, a check will be performed to ensure that the interpolation model does not deviate too much from the data; as this is not necessarily a fast process, it is optional.