Module mass_action 

Mass-action ODE analysis of models.

Such ODEs are based on the law of mass action familiar from chemistry and mathematical epidemiology. Here, however, we also consider a generalised version where we do not require that mass be preserved. This allows the construction of systems of arbitrary polynomial (first-order) ODEs.

Structs

MassActionProblemData

Data defining an unbalanced mass-action ODE problem for a model.

PetriNetMassActionAnalysis

Mass-action ODE analysis for Petri nets.

StockFlowMassActionAnalysis

Mass-action ODE analysis for stock-flow models.

Enums

Direction

The associated direction of a “flow” term. Note that this is opposite from the terminology of “input” and “output”, i.e. a flow A=>B gives rise to an incoming flow to B and an outgoing flow from A.

FlowParameter

Parameters in the generated polynomial equations are undirected in the balanced case and directed in the unbalanced case.

MassConservationType

There are three types of mass-action semantics, each more expressive than the previous:

RateGranularity

When mass is not necessarily conserved, consumption/production rate parameters can be set either per transition or per place.

RateParameter

Depending on the rate granularity, the parameters are specified by different structures.

Functions

extend_mass_action_scalars

Substitutes numerical rate coefficients into a symbolic mass-action system.

into_mass_action_analysis

Builds the numerical ODE analysis for a mass-action system whose scalars have been substituted.