Search found 30 matches
- Wed May 29, 2024 12:22 pm
- Forum: NEURON + Python
- Topic: Setting and Confirming NEURON's Solver
- Replies: 1
- Views: 157
Re: Setting and Confirming NEURON's Solver
Update: I ran a percent error calculation comparing the results of all the solver settings in the post above. For all conditions except Crank-Nicholson, the error between any two solver settings is 0%. I interpret this to mean I have failed to actually change the solver, since I would expect at leas...
- Fri May 24, 2024 12:11 pm
- Forum: NEURON + Python
- Topic: Setting and Confirming NEURON's Solver
- Replies: 1
- Views: 157
Setting and Confirming NEURON's Solver
I'm trying to compare the results of different solvers offered in NEURON. My strategy goes something like this: moi_switch = 1 match moi_switch: case 0: h.CVode().use_daspk() self.cell.integration_method = 'SUNDIALS - DASPK' case 1: h.secondorder = 2 self.cell.integration_method = 'Crank-Nicholson' ...
- Fri Apr 12, 2024 12:47 pm
- Forum: NEURON + Python
- Topic: NetStim causes SaveState crash
- Replies: 6
- Views: 1490
Re: NetStim causes SaveState crash
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...
- Mon Apr 08, 2024 4:23 pm
- Forum: NEURON + Python
- Topic: NetStim causes SaveState crash
- Replies: 6
- Views: 1490
Re: NetStim causes SaveState crash
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() ...
- Fri Apr 05, 2024 11:00 am
- Forum: NEURON + Python
- Topic: NetStim causes SaveState crash
- Replies: 6
- Views: 1490
Re: NetStim causes SaveState crash
I haven't yet been able to resolve this issue
- Fri Mar 22, 2024 7:11 pm
- Forum: NEURON + Python
- Topic: NetStim causes SaveState crash
- Replies: 6
- Views: 1490
NetStim causes SaveState crash
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...
- Thu Mar 21, 2024 6:33 pm
- Forum: Other questions
- Topic: Results Don't Converge with Decreasing Time Step
- Replies: 3
- Views: 750
Re: Results Don't Converge with Decreasing Time Step
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...
- Mon Mar 18, 2024 12:58 pm
- Forum: Other questions
- Topic: Results Don't Converge with Decreasing Time Step
- Replies: 3
- Views: 750
Results Don't Converge with Decreasing Time Step
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 ...
- Tue Oct 24, 2023 2:22 pm
- Forum: Other questions
- Topic: CTNG Support
- Replies: 0
- Views: 31316
CTNG Support
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...
- Thu Aug 17, 2023 10:06 am
- Forum: NEURON + Python
- Topic: Play Stimulus Vectors Sequentially During Run-time
- Replies: 2
- Views: 16945
Re: Play Stimulus Vectors Sequentially During Run-time
Done - thanks so much
- Tue Aug 15, 2023 3:28 pm
- Forum: NEURON + Python
- Topic: Play Stimulus Vectors Sequentially During Run-time
- Replies: 2
- Views: 16945
Play Stimulus Vectors Sequentially During Run-time
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...
- Fri Aug 11, 2023 10:26 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Stimulus Activation/Deactivation in NMODL
- Replies: 3
- Views: 17381
Re: Stimulus Activation/Deactivation in NMODL
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...
- Sat Aug 05, 2023 5:04 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Stimulus Activation/Deactivation in NMODL
- Replies: 3
- Views: 17381
Stimulus Activation/Deactivation in NMODL
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...
- Thu Jul 27, 2023 2:46 pm
- Forum: NEURON + Python
- Topic: Play a Unique Vector to Each Model Segment
- Replies: 1
- Views: 15339
Play a Unique Vector to Each Model Segment
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 ...
- Fri Jul 21, 2023 10:20 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Extracellular Mechanism and Hodgkin-Huxley
- Replies: 10
- Views: 26285
Re: Extracellular Mechanism and Hodgkin-Huxley
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--