set third dimension size

[lkeegan]

Currently the geometry in third dimension is implicitly of length 1 in model units of length.

It would be nice to allow the user to set it to some other value, especially when the total compartment volume is relevant, e.g. when importing an ODE model with inter-compartment reactions (thanks @baronvonderheyden)

Need to work out what the implications are of changing this, for model/sbml/GUI/simulation.

Ideally would also offer to rescale parameters in the model automatically when changing this length such that current model behaviour is preserved.

[lkeegan]

• for a PDE model, changing this doesn't actually change anything observable (in terms of species concenrtrations) in the model
  • the PDE (in terms of concentrations) does not depend on the depth
  • we are simulating a 2d slice of a 3d model assuming no variation in the z-direction
• what it does change is the area of the membranes / volume of compartments, & hence the total species amount in the compartments
  • typically not relevant for compartment reactions when importing an ODE model
    • if they are in the initial form of COMPARTMENT_VOLUME * dc/dt (this is what COPASI provides)
    • since we symbolically divide by this volume factor, its actual value doesn't affect the imported reaction rate in terms of concentrations
  • but very relevant when importing an ODE with membrane reactions
    • they are divided by the membrane area, which does depend on the depth
    • if the ODE was constructed with realistic volumes, the depth should match the one in the ODE to roughly reproduce the dynamics on import
• to represent this properly in SBML, I guess we need to write 3d models instead of 2d models? (with XxYx1 sampled field? with 2d mesh?)