rxd.plugins interface in Neuron 7.7

Extending NEURON to handle reaction-diffusion problems.

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davidsterratt
Posts: 28
Joined: Tue Jan 17, 2006 11:36 am

rxd.plugins interface in Neuron 7.7

Post by davidsterratt »

I have a student working on updating my KappaNEURON package (https://github.com/davidcsterratt/KappaNEURON) so that it works with Neuron 7.7 rather than 7.4. In 7.4, I overrode rxd callback functions, but in 7.7, it looks like I should create a SolverPlugin object and then set the solver using set_solver(). I've not found any documentation about this, and I was wondering if there is any around.
ramcdougal
Posts: 214
Joined: Fri Nov 28, 2008 3:38 pm
Location: Yale School of Public Health

Re: rxd.plugins interface in Neuron 7.7

Post by ramcdougal »

There was a significant revamp of the internals from 7.4 to 7.7 with the intent of speeding up calculations but it likely broke anything that depended on overriding internal functions.

What kind of connections do you need?
  • callbacks at each time step?
  • reading and writing concentrations?
  • do you need to write rates of change and Jacobian contributions?
We're hoping to release 8.0alpha soon, and if we haven't already stabilized the part of the interface you need, maybe we can have that stabilized for the entire 8.0 series.

(The plugin situation is more experimental than useful at the moment, to be honest. I wouldn't go down this path at this time.)

I'm happy to have a zoom call with you and/or your student to identify needs and solutions if that's better.
davidsterratt
Posts: 28
Joined: Tue Jan 17, 2006 11:36 am

Re: rxd.plugins interface in Neuron 7.7

Post by davidsterratt »

Thank-you. We need all items apart from the Jacobians. This page describes (rather roughly) how we interface with NEURON 7.4:
https://github.com/davidcsterratt/Kappa ... ron-7.4.md
A Zoom call would be great - I'll contact you about it by email.
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