Pressure dependence (rmgpy.pdep)

The rmgpy.pdep subpackage provides functionality for calcuating the pressure-dependent rate coefficients \(k(T,P)\) for unimolecular reaction networks.

A unimolecular reaction network is defined by a set of chemically reactive molecular configurations - local minima on a potential energy surface - divided into unimolecular isomers and bimolecular reactants or products. In our vernacular, reactants can associate to form an isomer, while such association is neglected for products. These configurations are connected by chemical reactions to form a network; these are referred to as path reactions. The system also consists of an excess of inert gas M, representing a thermal bath; this allows for neglecting all collisions other than those between an isomer and the bath gas.

An isomer molecule at sufficiently high internal energy can be transformed by a number of possible events:

  • The isomer molecule can collide with any other molecule, resulting in an increase or decrease in energy
  • The isomer molecule can isomerize to an adjacent isomer at the same energy
  • The isomer molecule can dissociate into any directly connected bimolecular reactant or product channel

It is this competition between collision and reaction events that gives rise to pressure-dependent kinetics.

Collision events

Class Description
SingleExponentialDown A collisional energy transfer model based on the single exponential down model

Reaction events

Function Description
calculateMicrocanonicalRateCoefficient() Return the microcanonical rate coefficient \(k(E)\) for a reaction
applyRRKMTheory() Use RRKM theory to compute \(k(E)\) for a reaction
applyInverseLaplaceTransformMethod() Use the inverse Laplace transform method to compute \(k(E)\) for a reaction

Pressure-dependent reaction networks

Class Description
Configuration A molecular configuration on a potential energy surface
Network A collisional energy transfer model based on the single exponential down model

The master equation

Function Description
generateFullMEMatrix() Return the full master equation matrix for a network

Master equation reduction methods

Function Description
msc.applyModifiedStrongCollisionMethod() Reduce the master equation to phenomenological rate coefficients \(k(T,P)\) using the modified strong collision method
rs.applyReservoirStateMethod() Reduce the master equation to phenomenological rate coefficients \(k(T,P)\) using the reservoir state method
cse.applyChemicallySignificantEigenvaluesMethod() Reduce the master equation to phenomenological rate coefficients \(k(T,P)\) using the chemically-significant eigenvalues method

Exceptions

Exception Description
NetworkError Raised when an error occurs while working with a pressure-dependent reaction network
InvalidMicrocanonicalRateError Raised when the \(k(E)\) is not consistent with the high pressure-limit kinetics or thermodynamics