www.neuron.yale.edu

Another way of putting it: the description specified in nmodl400.pdf is still pretty accurate. The text you found refers to something very specific to xtra.mod... most models will still use BREAKPOINT instead. See hh.mod for how NEURON implemented Hodgkin-Huxley itself. A few suggestions for modern ...

Sounds like NEURON might have been built without dynamic MPI, in which case it'll try to use whichever version of MPI was picked at compile time. Before we try debugging the compilation instructions for 7.6, have you tested to see if the current release (8.2.1) binary works? Even if you want the old...

Not sure why it doesn't like nrniv -python , but launching nrniv when you really want to run python complicates things unnecessarily. As long as your script initializes MPI before setting up the model, either via mpi4py or via: h.nrnmpi_init() it suffices to just: mpiexec -n 2 python run_model_to_st...

Unfortunately, the []s will cause problems for trying to read/write them from mod files.

specs0, specs1, ... specs19 would work for names (and then you could have e.g. specs0i, ispecs0, etc)

setpointer literally sets a double* that's allocated inside of the MOD file. Once the assignment has been made, there is no explicit semantic information obtainable from the pointer. That is, h.setpointer(secA(0.5)._ref_v, 'V_pre', synAB) is 100% equivalent to: synAB._ref_V_pre = secA(0.5)._ref_v Bo...

The binaries for NEURON 7.7 would not work with Python 3.8, which did not exist at the time 7.7 was released. I imagine it would work if it was compiled specifically for 3.8, but I would strongly suggest using a more recent version of NEURON. My guess is that it's saying there's a folder called &quo...

Here's a possible clue... it's looking for a .so file. Usually on Windows, the equivalent is a .dll Are you using the regular Windows version of NEURON or a version the windows subsystem for linux (WSL)? Either way, if you try running with python -i myprogram.py (that is, add the -i flag so it doesn...

Try putting the Shell next to the dendrite... i.e. you want lo = 1
The numbers here are in fractions of a radius not µm.

We'll look into this. What you describe sounds like it should have worked.

Fixed. Thanks.

For what it's worth, the tutorials at https://nrn.readthedocs.io are generally more up-to-date than the ones on the NEURON yale site (but we haven't moved all of them over yet).

If you're using NEURON 8.1+, the pure-NEURON solution is to either use h.SaveState (which saves ~everything) or rxd.save_state() and rxd.restore_state(), where the rxd-specific solutions represent state using byte-strings. See the (admittedly brief) discussion at https://nrn.readthedocs.io/en/latest...

Unfortunately rxd doesn't directly support expressions that depend on time.

Algebraic expressions should just work. (There's an example of this in the documentation linked below.)

For math functions, you'll want to use rxdmath see the rxdmath discussion in the documentation

Roughly speaking the HOC code would look exactly like the Python, but drop the h. part. That said, HOC and Python are just two different interfaces to the same simulator. You can mix and match. e.g. from Python, you can run a HOC script called my_script.hoc via: h.load_file("my_script.hoc"...

This looks like an install from the PKG installer?

In particular, you'll find you have a NEURON folder in Applications. Remove that, and then enter the following into the terminal:

Glu.nodes is a list of all Glu nodes. If there is only one, then it is unambiguously safe to use Glu.nodes[0] . Otherwise, you'll want to filter down to a specific node by specifying e.g. segment, possibly region if there are multiple by using () for the filtering... So something like Glu.nodes(som...