Search found 5334 matches

by ted
Thu Oct 18, 2018 10:18 am
Forum: Modeling networks
Topic: A question about "proc init()"
Replies: 1
Views: 13

Re: A question about "proc init()"

when I type "proc init ()", the system displays “c:\nrn\bin\nrniv.exe: Segmentation violation” You mean you entered proc init() at NEURON's oc> prompt? Suggestion: use the Forum's formatting options to make your posts more readable. For example, to preserve indentation of source code, select the en...
by ted
Thu Oct 18, 2018 9:57 am
Forum: The GUI
Topic: Plot vector_y vs vector_x
Replies: 3
Views: 73

Re: Plot vector_y vs vector_x

NEURON's "phase plane graphs" are not used for plotting vectors. They're just ordinary instances of the Graph class configured to plot traces defined by points at (x,y) coordinates in which the x value comes from an expression that is updated at every advance of a simulation. If you create one with ...
by ted
Tue Oct 16, 2018 10:20 am
Forum: Suggestions and Feedback
Topic: Search in forum not usable
Replies: 1
Views: 76

Re: Search in forum not usable

Thanks for pointing this out. Search customization settings appear to have been lost during a recent software update.
by ted
Tue Oct 16, 2018 10:18 am
Forum: The GUI
Topic: Plot vector_y vs vector_x
Replies: 3
Views: 73

Re: Plot vector_y vs vector_x

If the x and y values are updated in the course of a simulation, use NEURON Main Menu / Graph / Phase plane If you want to plot data that have been recorded to a pair of Vectors in the course of a simulation, you'll need to do that the Vector class's plot method is what you want, and you'll need to ...
by ted
Tue Oct 16, 2018 12:16 am
Forum: Other questions
Topic: Using event delivery system with fixed time step method.
Replies: 7
Views: 254

Re: Using event delivery system with fixed time step method.

Looks like a roundoff error problem. You need a dt that satisfies two criteria: 1. A whole multiple of dt must equal your sampling interval. That's pretty obvious, and 0.05 does satisfy this criterion. 2. The binary representation of dt must have a finite number of bits, AND that representation must...
by ted
Fri Oct 12, 2018 12:00 pm
Forum: Other questions
Topic: Event delivery (CVode.event) not impacting simulation time
Replies: 2
Views: 92

Re: Event delivery (CVode.event) not impacting simulation time

Your intuition that you probably need to implement finite rise and fall times is probably correct. Don't be too concerned about the exact details of the transients, in particular their duration--anything that is "very short" compared to the smaller of [duration of an action potential | duration of y...
by ted
Fri Oct 12, 2018 11:24 am
Forum: The GUI
Topic: Can I import a neuron model into CellBuilder?
Replies: 2
Views: 111

Re: Can I import a neuron model into CellBuilder?

Regarding your first question--use the Import3d tool. See the Import3d tutorials on the Documentation page of NEURON's web site https://neuron.yale.edu/neuron/docs . Regarding your second question--the CellBuilder can import detailed morphometric data from an existing model cell. Execute the program...
by ted
Wed Oct 10, 2018 11:17 pm
Forum: UNIX/Linux
Topic: Either nrngui or conda-forge neuron work, but not both?
Replies: 6
Views: 296

Re: Either nrngui or conda-forge neuron work, but not both?

I know what to do to make Python use NEURON as a module, I just have to install the module via $ conda install -c conda-forge neuron But, the problem is that when I do that, nrngui does not work any more. My suggestion would have been to install NEURON from source code*--specifically, source code d...
by ted
Wed Oct 10, 2018 8:57 am
Forum: Getting started
Topic: The math behind extracellular mechanisms
Replies: 21
Views: 12415

Re: The math behind extracellular mechanisms

. . . in the post it was written Starting from scratch, treating the potential at each node as "relative to ground," and using these definitions (...) v, vext[0], and vext[1] are the potentials indicated in the diagram that is part of NEURON's documentation of the extracellular mechanism (...) You'...
by ted
Tue Oct 09, 2018 10:56 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 3
Views: 126

Re: Where to find squid.hoc associated with hh.mod

Okay, I believe I found it here: Nope. The COMMENT block at the start of hh.mod was apparently written by Stuart Jaslove in 1992, a time at which NEURON was known only to a small circle of people. Stuart was at Duke then, where he interacted with Michael Hines and John Moore. That was well before t...
by ted
Tue Oct 09, 2018 12:28 pm
Forum: Getting started
Topic: The math behind extracellular mechanisms
Replies: 21
Views: 12415

Re: The math behind extracellular mechanisms

Perhaps this is the source of confusion: The schematic diagram in the documentation of extracellular uses v to refer to membrane potential, i.e. the difference between intracellular potential and the potential adjacent to the outer surface of the neurite. However, in yesterday's post I used v to ref...
by ted
Mon Oct 08, 2018 3:11 pm
Forum: Getting started
Topic: The math behind extracellular mechanisms
Replies: 21
Views: 12415

Re: The math behind extracellular mechanisms

Yes indeed, there are mistakes in those equations that I wrote. I treated membrane potential as if it were potential relative to ground. Also, notation was bad. It's a good idea to revisit this stuff at least once every decade or so. Too bad I didn't do that long before now. My apologies to the conf...
by ted
Mon Oct 08, 2018 11:17 am
Forum: UNIX/Linux
Topic: Either nrngui or conda-forge neuron work, but not both?
Replies: 6
Views: 296

Re: Either nrngui or conda-forge neuron work, but not both?

Well, look at NEURON's installation tree on your machine, and if you find a src/nrnpython/setup.py file, you know what to do. If you don't find such a file, but you want Python to use NEURON as a module, you'll have to do something else.
by ted
Fri Oct 05, 2018 11:58 am
Forum: UNIX/Linux
Topic: Either nrngui or conda-forge neuron work, but not both?
Replies: 6
Views: 296

Re: Either nrngui or conda-forge neuron work, but not both?

However if I try

Code: Select all

python foo.py
then I get a ModuleNotFoundError: No module named 'neuron'
I'm assuming you installed NEURON from source code, but skipped the final step

Code: Select all

# as root
cd src/nrnpython
python setup.py install
by ted
Thu Oct 04, 2018 12:45 pm
Forum: Specific models
Topic: Weird "trap" function in Bazhenov 2002 model
Replies: 4
Views: 199

Re: Weird "trap" function in Bazhenov 2002 model

I have checked the source code you referenced (written in C++), and it incorporates this exact trap function. It's so bizarre that it makes the function discontinuous. Just got an email from HAL 9000, which I quote here: "I wouldn't dump core about this, which is unlikely to cause a qualitative cha...