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Using simFunction Object in Simbiology when my stoichiometry depends on a model parameter

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Prevusly asked this question and my problem was solved. Now I have another question:
I am working on a SimBiology code with Stochiometry depending on a parameter (DAR). The specise are calculated based on their concentrations (nmol/liter). The size of the component changes too which is based on repeated rules. I use SimFunction for paarmetrization, therefor as we discussed, I use rate rules for the specieses in which their concentration depends on DAR. The method was explained before in this thread. But I get the follwoing error. Is their any way to fix this error?
Rate rule for species 'PL_ext' is invalid. Species 'PL_ext' is in concentration and in a compartment with varying capacity. For this to be valid, the compartment capacity
must be varied by a rate rule.

Accepted Answer

Arthur Goldsipe
Arthur Goldsipe on 21 Mar 2024
The error you report is intended to communicate that SimBiology does not allow the following the following combination of conditions:
  • A species is in concentration.
  • The concentration of that species is determined by a rate rule.
  • The compartment (that the species is in) is determined by a repeated assignment rule or an algebraic rule.
One fix would be the one mentioned at the end of the error message: Replace the repeated assignment rule or algebraic rule with a rate rule that gives equivalent behavior.
Another option would be to change the species units to amount instead of concentration and use (species amount)/(compartment volume) anywhere you need to reference the concentration.

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