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I think I need help understanding the relationship of h.run(), h.continuerun(), and h.tstop. Below is a snippet of your code containing calls for all three. def erun(): # prepdatastores() h.tstop = EPOCHDUR h.tstop_changed() myinit() # model-specific initialization for ii in range(NUM): h.continueru...

I've avoided hoc as much as I could thus far, so let me check that I understand what's happening between the .py and .ses files. pyrig.ses recreates the h.IClamp() instance (which can also be created in Python), the RunControl window, and the h.Graph() object. pysyndrive.ses creates the h.NetStim() ...

I haven't yet been able to resolve this issue

The code below is meant to run a simulation in small chunks (basically useless for the toy script here, but useful to control RAM consumption for very large datasets). The h.ExpSyn() / h.NetStim() / h.NetCon() trio causes NEURON to deliver the error message NEURON: ExpSyn[0] :Event arrived out of or...

zip up just enough code to reproduce what you describe Will do, I thought it may have more to do with NEURON than any specific code chunk. If you're really concerned about numerical accuracy, use secondorder and a dt of 0.001 ms, or use adaptive integration (but make sure that the various states' e...

Why would NEURON give different results when I vary the time step outside the stimulus period? Below, I contextualize this question in the abstract, but I can provide a code example if necessary. My situation: I have an extremely short-duration E-field pulse I'm applying to a neuron model to assess ...

The CTNG Python tool to convert .swc data to watertight 3D models (introduced in 2013 here: https://www.sciencedirect.com/science/article/abs/pii/S0165027013003221) appears not to have been updated in some time. On my machine, I seem to be required to roll a few packages back to much earlier version...

Done - thanks so much

This code is a proof-of-principle experiment in playing a vector into a point process/distributed mechanism during run-time. (Reason: for extremely complex stimuli, the entire stimulus cannot be contained in memory at once. To circumvent this limitation, the stimulus will be calculated in chunks pas...

From https://nrn.readthedocs.io/en/latest/python/modelspec/programmatic/network/netcon.html#NetCon , I see The target must be a POINT_PROCESS or ARTIFICIAL_CELL that defines a NET_RECEIVE procedure. From the NMODL reference book*, I see An onset event, generated by the system when the connecting Net...

I made the following NMODL file to deliver a transmembrane current injection into a cell. The RANGE variable amp receives a played-in vector from a Python script. Below, I show the original method (which doesn't work quite right) and the second method (which does). The difference between them is onl...

How can I play a unique vector into an arbitrary variable in each of an arbitrary number of cell segments? For example, in this NMODL file NEURON { SUFFIX playtest :RANGE xx : doesn't work :NONSPECIFIC_CURRENT xx : doesn't work :GLOBAL xx : works, but inflexible :ELECTRODE_CURRENT xx : doesn't work ...

Wow, that's incredible - thank you! I've been working to meet a deadline this week, but hoping to return to this issue first thing next week--

v is not the sum of e_extracellular and anything else This was my deduction both from the documentation at https://nrn.readthedocs.io/en/latest/hoc/modelspec/programmatic/mechanisms/mech.html -- Vext is solved simultaneously with the v. When the extracellular mechanism is present, v refers to the m...

I'd like to avoid having to look at any of your hoc or Python code, if possible. Totally understand - my original question was just about the mechanics of how NEURON handles e_extracellular in a custom Hodgkin-Huxley-style .mod file, specifically, about the use of the NMODL 'v'. Is e_extracellular ...