Search found 28 matches

by JustasB
Fri Apr 06, 2018 7:41 pm
Forum: NEURON + Python
Topic: Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()
Replies: 4
Views: 2647

Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()

I am having trouble using Vector.play() and NetCon/NetStim together with CVODE and SaveState.restore(). I run the simulation until my model reaches steady state, then I save with SaveState.save(), and then I inject an arbitrary current into the cell after SaveState.restore(). A NetCon/NetStim combin...
by JustasB
Mon Mar 05, 2018 5:00 pm
Forum: Other questions
Topic: Two issues with cvode.event when using cvode.active(1)
Replies: 7
Views: 2875

Re: Two issues with cvode.event when using cvode.active(1)

so it has NOT YET been documented in the Programmer's Reference! even though it appears in several blocks of example code in the Programmer's Reference!! Haha. Understood. Thank you for the explanation. I will make sure I use cvode_active() whenever I use cvode. Just an update, the problematic mode...
by JustasB
Mon Mar 05, 2018 3:40 pm
Forum: Other questions
Topic: Two issues with cvode.event when using cvode.active(1)
Replies: 7
Views: 2875

Re: Two issues with cvode.event when using cvode.active(1)

Hmmm I had tried cvode_active() in the original code, but without the test section it still produced the same error. However, test section + cvode_active(1) both issues disappear. Thank you for the suggestion. I will try it in my full script. In the hot tip about using cvode_active() , you mention t...
by JustasB
Mon Mar 05, 2018 12:39 pm
Forum: Other questions
Topic: Two issues with cvode.event when using cvode.active(1)
Replies: 7
Views: 2875

Re: Two issues with cvode.event when using cvode.active(1)

Ok, when I add a section, Issue #2 dissapears, but Issue #1 (h.t >> h.tstop) remains (code below). However, the reason why I'm posting what appears to be a contrived example is because I'm experiencing an intermittent, hard-to-reproduce issue in a script that works with more complex model's I'm work...
by JustasB
Sun Mar 04, 2018 6:30 pm
Forum: Other questions
Topic: Two issues with cvode.event when using cvode.active(1)
Replies: 7
Views: 2875

Two issues with cvode.event when using cvode.active(1)

I'm running into issues where h.t runs past h.tstop and cvode.events are triggered too early while using cvode. I've managed to reproduce the issues with this snippet: Using NEURON 7.5 master (6b4c19f) on Windows (same issue on NRN 7.4 on Ubuntu 16.04), paste the following in python console: from ne...
by JustasB
Mon Jan 22, 2018 4:47 pm
Forum: Modeling networks
Topic: Obtaining NetCon actual pre-section along fraction x value?
Replies: 5
Views: 2687

Obtaining NetCon actual pre-section along fraction x value?

Given a NetCon instance whose source is section membrane potential, is it possible to extract the actual x value location on the pre-section? For example, the following minimal python code only returns either 0, 0.5, or 1.0 fractions. from neuron import h, gui soma = h.Section() soma.nseg = 10 h.Net...
by JustasB
Sun Jan 14, 2018 5:38 pm
Forum: Other questions
Topic: Off-by-a-bit timing problem with NetStim.noise = 0
Replies: 2
Views: 1582

Off-by-a-bit timing problem with NetStim.noise = 0

Should NetStim events not be expected to be exact when noise=0? I observe the following dt dependent variations in the event timing with noise = 0. After running the following: from neuron import h,gui t = [] def collect(): t.append(h.t) ns = h.NetStim(0.5) ns.start = 0 ns.interval = 1 ns.number = 1...
by JustasB
Sat Dec 30, 2017 4:42 pm
Forum: NEURON + Python
Topic: Creating NetCon with null source in NEURON+Python
Replies: 10
Views: 15174

Re: Creating NetCon with null source in NEURON+Python

To summarize, the following, fully Python, code will stimulate a synapse at 50, 60, and 100 ms: from neuron import h, gui soma=h.Section() soma.insert('pas') syn=h.ExpSyn(soma(0.5)) nc=h.NetCon(None,syn) nc.weight[0]=1.0 def synStim(): nc.event(50) nc.event(60) nc.event(100) fih = h.FInitializeHandl...
by JustasB
Sat Nov 04, 2017 7:04 pm
Forum: UNIX/Linux
Topic: long suffix in .mod files results in *** buffer overflow detected *** error
Replies: 1
Views: 9604

long suffix in .mod files results in *** buffer overflow detected *** error

Hello, It appears that if the SUFFIX in the NEURON section of a .mod file is more than 48 characters long, then compiling the mod file with "nrnivmodl" command results in a hard-to-debug error. For example, the following suffix: NEURON { SUFFIX napf_spinstell__a0__b0__c0__d0__fastNa_shiftmin2_:5 ......
by JustasB
Wed Dec 09, 2015 3:51 pm
Forum: OS X
Topic: OSX Yosemite 10.10.1 make install error
Replies: 4
Views: 8420

Re: OSX Yosemite 10.10.1 make install error

Commenting out the "gcc -g ..." lines avoided the problem, but then sent me down another rabbit hole of issues.

I was able to get past the error by following the suggestion here:
http://stackoverflow.com/questions/2797 ... re-headers
by JustasB
Wed Dec 09, 2015 2:38 pm
Forum: Suggestions and Feedback
Topic: StackOverflow-like site for NEURON?
Replies: 1
Views: 14890

StackOverflow-like site for NEURON?

Would anyone support a StackOverflow -like Q&A site for NEURON and computational neuroscience in general? The benefits of such a site would be as follows: Best questions and answers are voted up by the community, flowing to the top of the page People with best questions and best answers gain reputat...