www.neuron.yale.edu

It would be cleaner to have the Python function run at every timestep using a CVode.extra_scatter_gather and then just transfer values to NMODL (using pointers or directly; both should work.)

You could probably get the call from NMODL to work, but that would require a VERBATIM block.

From StackOverflow , it looks like that error could occur from XCode not matching the system version. Try the instructions in the first answer there to see if updating XCode resolves the issue. (The discussion at the link was for Catalina not Big Sur, but presumably the update Xcode advice should st...

Thank you for bringing this to our attention. This has now been fixed in the development version: https://github.com/neuronsimulator/nrn/commit/ec1d362eeaaf4fae4d59e1dd91a1872b12d87e53 The underlying issue was that 3D diameters are internally stored separately from the diameters reported at the cent...

When you change f_rate and b_rate , NEURON interprets that as changing the model, triggering a recompilation. If instead you used an rxd.Parameter , that just changes a parameter value, requiring no change to the model. See the bottom of this example which covers both changing initial conditions and...

As this is running on your own machine, consider updating your version of NEURON. The current release is 7.8.2.

You can get it from the NEURON website or directly from GitHub at https://github.com/neuronsimulator/nrn/ ... /tag/7.8.2

If you want to create a CellBuilder from a HOC morphology, you can load the HOC morphology, then open a CellBuilder, click the Management tab, then Import - top level. Confirm by clicking "go ahead and import" and then you can work with it in the CellBuilder.

Can you expand your comment? What do you get and how is it different from what you expected?

If there's a HOC file morphology, you can load it from the GUI or from e.g. `h.load_file("my_morphology.hoc")`

Vectors must be initialized after calling record before advancing . Your other code works with h.run() because a run is basically an h.finitialize(h.v_init) combined with an h.continuerun(h.tstop) . The solution is to declare your timeVector before the h.finitialize call, i.e. something like: timeV...

Hmmm... looks like that example depends on a change introduced about a month ago... so it's available in the "pip install" version for mac/linux or the windows nightly build . (Don't try to pip install on Windows, that will give a VERY old version of NEURON.) Sorry about that. So I guess t...

Unfortunately the .plot for both matplotlib and plotly (available in 8.0 development version) does not currently support the .color or .color_list values and instead always color based on the value of some variable (v, by default). (Note that you can use .mark as in the documentation to highlight sp...

Thanks for pointing this out.

The old link works now too.

Python provides a standard way of using a string to grab a property, namely the getattr function. e.g. if you have a section called soma and you wanted to get a pointer to a specific variable var from the 0.5 location, you could do ptr = getattr(soma(0.5).hh, f'_ref_{var}') Similarly, a second getat...

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 ...

Why did you compile NEURON from source?

Do you get this problem if you use the version from
How are you compiling the mod files? The x86_64 should appear in whatever folder you run nrnivmodl from.

You can't drop onto the main menu window directly, but I believe in Windows you can drop onto the icon . Three other options: (1) Select File - load hoc, change the filter from *.hoc to *.nrm, and then load your model that way. (2) type (using the correct filename): load_file("filename.nrm"...