Search found 68 matches

by stephanmg
Thu Jun 05, 2014 6:52 am
Forum: Adding new mechanisms and functions to NEURON
Topic: use a hoc statement to "load" a compiled mechanism?
Replies: 6
Views: 3119

Re: use a hoc statement to "load" a compiled mechanism?

To clarify this: it works! Basically, you can just assume the behaviour of the standalone NEURON version (N1), iff the compiled membrane mechanism (.mod - NMODL file) is compiled by N1 and N1 is included in another C/C++ project as a shared library (dynamically linked). Then basically if you init yo...
by stephanmg
Thu Jun 05, 2014 5:33 am
Forum: Reaction-diffusion in NEURON
Topic: Basic modelling question
Replies: 7
Views: 14257

Re: Basic modelling question

Okay thanks for your charming comments, firstly. I end up with this setup: from neuron import rxd, h from nrn import * dend = Section() dend.nseg = 10 dend.Ra = 1.00 dend.diam = 10 dend.L = 100 dend.insert('CaT') stim = h.IClamp(10.0, sec=dend) stim.delay = 50 stim.dur = 50 stim.amp = 0.1 h.CVode()....
by stephanmg
Wed Jun 04, 2014 11:45 am
Forum: Reaction-diffusion in NEURON
Topic: Basic modelling question
Replies: 7
Views: 14257

Basic modelling question

Dear all, I've implemented a CaT and a CaN (dependent on variable intracellular calcium concentration: cai) voltage gated calcium channel within NMODL for NEURON usage with the HOC interpreter.I want to construct a basic example which makes use of Calcium Diffusion within a single compartment model....
by stephanmg
Wed Jun 04, 2014 11:32 am
Forum: OS X
Topic: Mavericks (OSX 10.9): cannot start Neuron
Replies: 11
Views: 9773

Re: Mavericks (OSX 10.9): cannot start Neuron

Dear Ted&Hines,

i found the solution to my problem.
I just needed to start my application from within the applications folder, somehow this fixes it when i run it via a terminal/shell.

I think this could be somehow related to the LD_LIBRARY_PATH or DYLD_LIBRARY_PATH on MacOSX?

Best,
Stephan
by stephanmg
Mon Jun 02, 2014 3:00 am
Forum: OS X
Topic: Mavericks (OSX 10.9): cannot start Neuron
Replies: 11
Views: 9773

Re: Mavericks (OSX 10.9): cannot start Neuron

Dear Ted,

Code: Select all

dyld: Library not loaded: /Applications/NEURON-7.3/nrn/x86_64/lib/libnrnoc.0.dylib
  Referenced from: /Volumes/NEURON-7.3/NEURON-7.3/nrn/x86_64/bin/nrniv
  Reason: image not found
Trace/BPT trap: 5
Best,
Stephan
by stephanmg
Fri May 30, 2014 2:20 pm
Forum: OS X
Topic: Mavericks (OSX 10.9): cannot start Neuron
Replies: 11
Views: 9773

Re: Mavericks (OSX 10.9): cannot start Neuron

Hey,

I just get a plain "xterm" or "MacTerm" - no OC> Prompt or NEURON specific stuff at all.

Best,
Stephan
by stephanmg
Fri May 30, 2014 9:50 am
Forum: OS X
Topic: Mavericks (OSX 10.9): cannot start Neuron
Replies: 11
Views: 9773

Re: Mavericks (OSX 10.9): cannot start Neuron

Hey Ted,

i used OS X 10.7 and later (64 bit) - and i've installed XQuartz latest.

Best,
Stephan
by stephanmg
Fri May 30, 2014 9:02 am
Forum: OS X
Topic: Mavericks (OSX 10.9): cannot start Neuron
Replies: 11
Views: 9773

Re: Mavericks (OSX 10.9): cannot start Neuron

Dear all, after downloading and installing NEURON from the dmg for Mavericks I'm unable to execute NEURON, i. e. it just appears a terminal, no GUI etc. Previosuly, Mountain Lion , worked flawless... I'm curious how to resolve this issue. That's not the unauthorized App problem, which I figured out ...
by stephanmg
Mon May 19, 2014 10:58 am
Forum: Other questions
Topic: Information PIC
Replies: 1
Views: 900

Information PIC

Dear Users, i recognized, that in the NEURON 7.3 Sourcecode Snapshot, the --with-pic option isn't interpreted correctly, that means: not all shared objects (e. g. nvkludge.o) end up with PIC enabled! This leads to complications, i. e. relocation R_X86_64_32 against "nvkludge.o" since -fPIC is missin...
by stephanmg
Thu Mar 27, 2014 11:59 am
Forum: Adding new mechanisms and functions to NEURON
Topic: use a hoc statement to "load" a compiled mechanism?
Replies: 6
Views: 3119

Re: use a hoc statement to "load" a compiled mechanism?

Ah okay,

i thought it could be done with ivoc_main's args array, but i could not figure out. sorry for that.

it works.

best,
Stephan
by stephanmg
Thu Mar 27, 2014 11:21 am
Forum: Adding new mechanisms and functions to NEURON
Topic: use a hoc statement to "load" a compiled mechanism?
Replies: 6
Views: 3119

Re: use a hoc statement to "load" a compiled mechanism?

Ah thanks, ted.

So, yes, basically it should be working for Linux/UNIX too, so that's the only possibility? Would be glad to here any suggestions or any solution for making it work on Linux/Unix.

Best,
Stephan
by stephanmg
Thu Mar 27, 2014 6:21 am
Forum: Adding new mechanisms and functions to NEURON
Topic: use a hoc statement to "load" a compiled mechanism?
Replies: 6
Views: 3119

use a hoc statement to "load" a compiled mechanism?

After I compiled with nrnivmodl my Channel Model, let's say MyChannel.mod i want to load it with a hoc statement.
I don't want to execute nrngui, but instead when i call ivoc_main() in my C code. Is this possible? If how please state.

Thanks in advance.

Best,
Stephan
by stephanmg
Thu Mar 06, 2014 3:08 pm
Forum: Other questions
Topic: Intracellular resistance and setting a variable
Replies: 3
Views: 3696

Re: Intracellular resistance and setting a variable

Dear Ted, thanks for your quick and excellent answer. (I'm glad to be a NEURON user) 1) Okay, indeed, I wanted to adjust the axial resistance between adjacent internal nodes - I'm sorry for my misleading phrasing. So e. g. I access/modify the Ra for the section to adjust the axial resistance. (If th...
by stephanmg
Thu Mar 06, 2014 11:30 am
Forum: Other questions
Topic: Intracellular resistance and setting a variable
Replies: 3
Views: 3696

Intracellular resistance and setting a variable

Dear NEURON users, I've come up with two questions again: 1) I want to access each compartments instracellular resistance variable which is utilized for membrane potential calculation and adjust it, i. e. i want to set for different compartments different intracellular resistances. 2) I have a K+ de...
by stephanmg
Sat Nov 23, 2013 3:31 am
Forum: Other questions
Topic: C/C++ API
Replies: 43
Views: 15772

Re: C/C++ API

I will try this, hines. Thank you so much. Okay this seems reasonable, and works, but isn't there any way to automatically "reinit" the hoc interpreter? I mean I should be able to quit() the hoc interpreter, but quit() seems to call exit(0) which is not what i want, since my program then quits too! ...