Search found 52 matches

by csh
Sun Jan 11, 2009 11:01 am
Forum: Other questions
Topic: forsec doesn't seem to work in templates
Replies: 3
Views: 2110

Re: forsec doesn't seem to work in templates

Hi, from the online documentation of forall ( http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/secspec.html#forall ): Within an object, forall refers to all the sections declared in the object. This is generally the right thing to do when a template creates sections but is inconvenie...
by csh
Mon Nov 24, 2008 9:54 am
Forum: NEURON + Python
Topic: Setting equilibrium potential in latest hg changeset
Replies: 1
Views: 1783

Setting equilibrium potential in latest hg changeset

Hi, I found that there was a change in how one has to set the equilibrium potential from Python that introduced some bugs in my simulations. In versions 6.2 and 7 up to svn rev. 2227, I could set the equilibrium potential as follows: from neuron import h s = h.Section() s.insert("hh") for seg in s: ...
by csh
Sat Nov 15, 2008 11:05 pm
Forum: UNIX/Linux
Topic: Alienated i686 Neuron 7.2
Replies: 1
Views: 1828

Re: Alienated i686 Neuron 7.2

Here is a debian package of the latest hg revision:
http://www.stimfit.org/nrn-7.0-223_Ubun ... d.i386.deb
It's not alienated and I haven't extensively tested it, so please report bugs.
Christoph
by csh
Thu Oct 23, 2008 1:26 pm
Forum: UNIX/Linux
Topic: Fail to import hoc file using mos2nrn on Ubuntu
Replies: 8
Views: 4164

Re: Fail to import hoc file using mos2nrn on Ubuntu

I don't have any experience with 64 bit systems. However, my guess would be that the 64-bit version of the ncurses library is missing on your system. Maybe

Code: Select all

sudo apt-get install lib64ncurses5 lib64ncurses5-dev
or

Code: Select all

sudo apt-get install libncurses5 libncurses5-dev
will help?
by csh
Thu Oct 23, 2008 4:44 am
Forum: UNIX/Linux
Topic: Fail to import hoc file using mos2nrn on Ubuntu
Replies: 8
Views: 4164

Re: Fail to import hoc file using mos2nrn on Ubuntu

Could you give some more details, e.g. which nrnzip file exactly did you use, and what was the error message? On my system, mos2nrn works when installed from an "alienated" rpm. From the command line, I can do: $ /usr/local/nrn/i686/bin/mos2nrn file.nrnzip which will pop up a new shell, compile the ...
by csh
Wed Oct 22, 2008 6:06 am
Forum: UNIX/Linux
Topic: IV Build Fails at OS/math.cpp on Fedora 9
Replies: 8
Views: 4091

Re: IV Build Fails at OS/math.cpp on Fedora 9

I had to include stdlib.h in src/nrncvode/netcvode.cpp in addition to the files mentioned above on my system (gcc 4.3.2). Here is the patch against hg changeset 210: diff -r 482ea9727cc4 src/ivoc/ivocrand.cpp --- a/src/ivoc/ivocrand.cpp Mon Oct 20 14:36:51 2008 -0400 +++ b/src/ivoc/ivocrand.cpp Wed ...
by csh
Thu Sep 04, 2008 1:10 pm
Forum: UNIX/Linux
Topic: Debian packages for Ubuntu
Replies: 0
Views: 2138

Debian packages for Ubuntu

Hi, I have created a debian package for Ubuntu (Hardy, 8.04.1) by converting the rpm with alien. I've tested it on a naive system (i.e. NEURON wasn't previously installed) which worked without any obvious problems. I would be happy to share the Debian package if anyone has some 4.2 MB of web space t...
by csh
Mon Aug 25, 2008 7:22 am
Forum: The GUI
Topic: Plotting current (i) delivered by IClamp
Replies: 2
Views: 3699

Re: Plotting current (i) delivered by IClamp

From hoc, you could do: objref ic, g g = new Graph() ic = new IClamp1(0.5) g.addvar("ic.i") addplot(g, 0) Alternatively, you can use the GUI: Choose "Graph->Current axis" from the menu, right-click on the graph, select "Plot what", left-click "Show->All" in the dialog, select your IClamp1 object in ...
by csh
Sun Aug 24, 2008 12:49 pm
Forum: NEURON + Python
Topic: Mechanisms at terminal nodes in hoc vs. Python
Replies: 1
Views: 1499

Re: Mechanisms at terminal nodes in hoc vs. Python

I just saw the changes to the "for seg in sec" and "for seg in sec.allseg()" syntax in http://www.neuron.yale.edu/cgi-bin/trac ... geset/2195. That fixes the problem, thank you very much!
Christoph
by csh
Sat Aug 23, 2008 4:07 am
Forum: NEURON + Python
Topic: Better conductance input idiom?
Replies: 1
Views: 2241

Re: Better conductance input idiom?

The following code worked fine for me: #! /usr/bin/python from neuron import h import numpy h("""load_file("stdrun.hoc")""") h.tstop = 10; h.dt = 0.01; h.steps_per_ms = 1.0/h.dt soma = h.Section() estim = h.SEClamp( soma(0.5) ) g_exc = numpy.arange( 10, 10+h.tstop, h.dt ) rs_exc = h.Vector() rs_exc....
by csh
Mon Aug 18, 2008 6:55 am
Forum: NEURON + Python
Topic: Mechanisms at terminal nodes in hoc vs. Python
Replies: 1
Views: 1499

Mechanisms at terminal nodes in hoc vs. Python

There is a slight inconsistency regarding how mechanisms in terminal nodes are handled from hoc and Python. Consider the following hoc code: create s s { nseg = 1 insert pas for (x) print x, g_pas(x) } This will print: 0 0.001 0.5 0.001 1 0.001 Obviously, calling g_pas(0) or g_pas(1) will return its...
by csh
Wed Jan 30, 2008 5:28 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: TABLE command
Replies: 1
Views: 1603

Re: TABLE command

I have not found any reference to it in the NMODL documentation, and the forum search only results in examples of it, with question unrelated to the command itself. What does it do? It's basically a look-up table that may help to speed up simulations: http://www.neuron.yale.edu/neuron/static/docs/h...
by csh
Thu Dec 20, 2007 2:15 pm
Forum: Other questions
Topic: Improving voltage resolution
Replies: 6
Views: 3419

And yes my data file has same time values in many rows ! I'm a bit puzzled: Did you use the code that I've posted above, but you still have the same time values in subsequent rows? That would be strange. Can one set the accuracy of the data in NEURON like one can do in C++ ? If you refer to the pur...
by csh
Thu Dec 20, 2007 11:38 am
Forum: Other questions
Topic: Improving voltage resolution
Replies: 6
Views: 3419

Re: code used in my simulations

matvol.fprint(filvol) I have to admit that I had great problems making the File class produce formatted output using format specifiers such as "%.4f" or similar on my system. It always resulted in some truncation errors. The same may have happened to you, which might explain why there were sudden "...
by csh
Thu Dec 20, 2007 5:18 am
Forum: Other questions
Topic: Improving voltage resolution
Replies: 6
Views: 3419

Re: Improving voltage resolution

How can I improve the voltage resolution of my simulations. Using a step size of 25 usec I often get same voltage values for a period of 250usec at a stretch. I want resolution on the scale of 25usec. Could you provide a minimal, stand-alone hoc sample that will reproduce the behaviour that you des...