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Use diam3d instead of diam, and forall sections adjust indices from 0 to n3d -1, inclusive. EDIT: The idea is right but this code is wrong. diam3d is read only and diameters most he changed with pt3dchange. See my next post. forall { for (j = 0; j < n3d(); j+=1) { diam3d(j) = diam3d(j)*1.0 } } There...

Not exactly what you're looking for, but check out Rempe and Chopp 2006, A Predictor‐Corrector Algorithm for Reaction‐Diffusion Equations Associated with Neural Activity on Branched Structures. In particular, section 8 is entitled "spatial adaptivity." They demonstrate this on a morphologically deta...

Every segment corresponds to a location where membrane potential is computed. In particular, this is a distinct concept from the 3D shape of the cell. Segments can contain arbitrarily many 3D points and the surface area, etc for that segment will be computed correctly. In Python with NEURON 7.5+, yo...

In addition to the text editors that ted mentioned, consider Visual Studio Code. It's free and runs on all platforms. More importantly for NEURON: the first time you open a HOC or MOD file, it will prompt you to install an extension that provides NEURON syntax highlighting.

Ion channel genealogy lists 524 NEURON calcium channel models, not all distinct. If you click that link, you'll see them grouped by similarity. Clicking on an individual model (dot) in the figure will load it in the channel details pane on the bottom right. The info tab (opened by default) contains ...

Note that Hodgkin and Huxley considered only the role of sodium, potassium, and leak currents. In particular, it follows that the hh mechanism does not generate a calcium current.

If you want to customize the dynamics to be (potentially) not-mass-action, use the custom_dynamics=True keyword argument: reaction = rxd.Reaction(2 * hydrogen + oxygen > water, reac_speed, custom_dynamics=True) (What you were getting was mass action where the "constant" part of the mass action was r...

Not having seen your nadifl.mod, it's impossible to say for certain, but if we consider this file of the same name, the interesting part is the KINETIC block: KINETIC conc { COMPARTMENT PI*diam*diam/4 {nai} LONGITUDINAL_DIFFUSION D {nai} ~ nai << (-ina/(FARADAY)*PI*diam*(1e4)) } The COMPARTMENT line...

The equations for nadifl and kdifl are in the mod files that you're using; they're not part of NEURON itself. Without seeing them, they are likely to just be LONGITUDINAL_DIFFUSION based mechanisms, possibly with radial diffusion as well. If by "small dimension" you're talking about the 0.1 microns ...

This is probably not doing what you meant to do, although I'm not entirely sure what your question is. The following HOC code (did you want to use Python instead of HOC?) soma { nseg = 10000 L = 1// [µm] length diam = 0.1 // [µm] diameter creates a single section called soma with total length of jus...

Minor comments: the inside of proc advance should invoke fadvance not advance. Also note you can get slightly more readable code by using a multiline string: h(r""" proc advance() { fadvance() m1 = IntFire1[0].M() }""") The r in front of the multi-line string opening is not needed here, but allows y...

I second Ted's point about the need for state-specific error tolerance scale multipliers. Unfortunately, the rxd state variables are not integrated into the VariableStepControl GUI's analysis at this time. You can, however, specify a species-specific atolscale. The rxd.Species constructor prototype ...

This is still a bit of a hack, but it should keep the GUI responsive and avoid the memory issue.

Before you do your h.run() (or equivalent), do:

Also: do the concentrations go negative with fixed-step integration?

Not directly. If you're not using mass-action, it's possible to write reactions that mathematically demand concentrations go negative. Can you tell us more about your reaction specification? Assuming some are not mass action, have you checked to make sure the reaction rates are not such that the con...