www.neuron.yale.edu

Similarly, NEURON automatically updates Nernst potentials for species defined using rxd. For more on the math governing Nernst Potentials, see this entry on Wikipedia. Ion current through a channel is typically proportional to the difference between the membrane potential and the corresponding Nerns...

The first issue should go away when you upgrade to 7.7. As far as tolerance goes: if you're using variable step, you can specify an atolscale when you declare the Species... I don't know that that's related, but I'm mentioning it just in case. As of this time, we have no automatic advice for automat...

It looks like when going from 7.6.x to 7.7.x we lost the ability to have non-uniform diffusion constants in 3D. Sorry about that; we're working on a fix. I'm not sure I fully understand your other observations; could you explain more? With 7.7.x, crxd and rxd are now the same thing... that is, rxd g...

The above code requires NEURON 7.7.2 or newer.

Older versions won't recognize _ref_foo, and instead need to have the pointer set using h.setpointer; i.e. replace the for loop in the above with:

You can assign your data to a numpy array, get a pointer to the numpy array using neuron.numpy_element_ref, send that pointer to all point processes (this is fast... there's no copying of data), and then have the point process read from the array using a single VERBATIM line. Our driving Python prog...

Sounds like the PATH and PYTHONPATH environment variables didn't get set correctly somehow. Please try reinstalling to see if this fixes the problem. During installation, it should prompt you for permission to let it modify your paths. Be sure to agree to this. Changes won't be effective in existing...

As long as you're using NEURON 7.7+, mod file code is available for introspection from Python, so it can be parsed manually with a handful of lines of Python. Here's a function that seems to work to get parameters: from neuron import h import re def get_parameters(mech_name): mech = h.MechanismType(...

We've started a process of redoing those tutorials, which are pretty old. The new versions use more modern idioms and come as Jupyter notebooks. We haven't moved these to the website because we don't have a full replacement, but here's a few: https://neuron.yale.edu/ftp/ramcdougal/pythontutorial.ipy...

Are you trying to debug NEURON itself or a NEURON simulation? For debugging NEURON simulations written in Python, you can use pdb as with any other Python code. A quick search will lead you to many pdb tutorials. For debugging NEURON simulations written in HOC... there's no equivalent. Going forward...

Calling h.fadvance() advances the simulation by one timestep. When using fixed-step integration, the time step size is controllable by setting h.dt ; by default it is 1/40 ms. When controlling a simulation in this way, before beginning your advances, you must explicitly initialize the simulation wit...

Internally, the Sections are stored in a linked list. There is thus no direct, consistent-across-runs section indexing scheme... but as you've observed, there's no advantage for NEURON storing such a list since you can create it quickly in the non-parallel case : seclist = list(h.allsec()) Once you ...

Unfortunately, this isn't in 7.7; we considered it an internal class and didn't realize people were using it otherwise. The general workaround is to use the corresponding section method trueparentseg (there's also a parentseg); e.g. >>> from neuron import h >>> soma = h.Section(name='soma') >>> dend...

Are you trying to simulate ephaptic coupling or extracellular diffusion of ion concentrations in the extracellular space? There are currently at least two models in ModelDB that use NEURON for ephaptic coupling: http://identifiers.org/modeldb/3676 and http://identifiers.org/modeldb/240957 (The rxd m...

The literal translation is adapex=h.ADEX(0.5) Since this is technically a point process, the 0.5 means it gets associated with the middle of some section, the so called currently accessed section. This is fine, but in Python we can be more explicit about which section, here mysec: adapex=h.ADEX(myse...

I've added a full working code (and the associated image output) to the calcium wave rxd tutorial page: https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave There's not much in the way of explanation yet, but hopefully after working through the rest of the existing tutorials ( https:/...