This is an old question but an answer could still benefit others who bumped into the same issue.
The key piece of the error message is: This object is being used in a reaction or in another rule
Indeed, the ODE driving the dynamics of a species can only be defined by EITHER a set of reactions OR a rate rule. But not both.
For the code above to work, 3 options can be considered:
- remove the reactions from the model and only keep the rate rules
- remove the rate rule and only keep the reactions. There one can use a built-in kinetic law or type in a custom reaction rate.
- one could keep the reactions for visualization purposes and the rate rules. but for this to work, the species property BoundaryCondition must be set to true.
Side note:
There is no need to add the parameters to the kinetic laws (lines of code with addparameter(kx,...) ). The forward rate parameters can be the model-scoped parameters.
The code above creates two independent k2_2 parameters: one scoped to the model (accessible by all reactions), one scoped to the reaction (only accessible by this reaction). Changing one does not change the other.
Here, both lines of code with addparameter(kx,...) can be removed.
