Re: [moose-generic] shape of the compartment

[Niraj D. <ni...@nc...>]

Dear Ekaterina,

Your email to the list had got stuck in the list's filter.

As I mentioned earlier (in person), the length and diameter do not hold much numerical
importance. They are mainly there to hold structural information, that can be used for
displaying the cell. When one reads in a model (NeuroML or ReadCell), the import code
usually assumes cylindrical compartments, and calculates the passive parameters
accordingly. However, you are free to change the Ra, Rm and Cm yourself afterwards. The
numerical implementations (EE and HSolve) do not care about the length/diameter, and
instead just look at the Ra, Rm and Cm values for each compartment.

Best,
Niraj


> Dear All,
>
> could you make it clear regarding the shape of the compartment ?
> For example, if I want to create a rectangular shape and then I set length
> and diameter fields. How then other parameters (for instance Ra) will be
> recalculated?
> Or, shall I calculate the values by myself and then set the parameters
> manually according to my shape? If it's so, will that work correctly during
> the simulation, I mean where else the shape of the compartment can be used?
>
> P.S. I'm using buildQ branch.
>
> thank you
> kind regards,
> Katja
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