Search found 97 matches

by eacheon
Sun Jan 20, 2008 1:04 pm
Forum: Getting started
Topic: calculating the "area under the curve"
Replies: 5
Views: 6846

How can I compute the integral if the simulation is using variable dt? EITHER use a method designed to handle a continuous variable sampled at irregular intervals (there must be at least one such method in the vast literature on numerical computation) OR sample the data stream at regular intervals,...
by eacheon
Sun Jan 20, 2008 1:57 am
Forum: Getting started
Topic: calculating the "area under the curve"
Replies: 5
Views: 6846

Re: integrating simulation results

... 1. Record the waveform to a Vector. Better, record both the y and t data to a pair of vectors. objref vvec, tvec vvec = new Vector() tvec = new Vector() // replace secname and x with the name of the section and the "range" // at which you want to record v secname vvec.record(&v(x), tvec) 2. Iso...
by eacheon
Sun Dec 16, 2007 11:42 pm
Forum: Other questions
Topic: Document for Impedance-class
Replies: 3
Views: 2782

Re: Document for Impedance-class

I see one small typographical error near the end of the introductory paragraphs on the Impedance class: in this line in the line (jwc + gnabar*m^3*h) gnabar*3*m^2*h*(v-ena) gnavar*m^3*(v-ena) this v ^ should be a b, like so: (jwc + gnabar*m^3*h) gnabar*3*m^2*h*(v-ena) gnabar*m^3*(v-ena) ^ Knowing t...
by eacheon
Sun Dec 16, 2007 3:45 pm
Forum: Other questions
Topic: Document for Impedance-class
Replies: 3
Views: 2782

Document for Impedance-class

It is highly interesting. But for a beginner I am having a hard time understanding some of the formula, say this one http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/classes/impedanc.html#Impedance ... yields the linearized impedance matrix [(jwc - di/dv)v = i0 ] * exp(jwt) ... Is th...
by eacheon
Sat Dec 15, 2007 7:53 pm
Forum: Other questions
Topic: How to access and plot derivatives of variables?
Replies: 9
Views: 7264

Re: How to access and plot derivatives of variables?

You are of course referring to total ionic current, not total membrane current. Exactly. Ted, I might miss something here. Shouldn't I be plotting i_cap versus v as the dV/dt ~ V phase plot? And I am thinking i_cap (for a segment in a section) almost always does not equal to total ionic current (fo...
by eacheon
Sat Dec 08, 2007 11:16 pm
Forum: Other questions
Topic: How to access and plot derivatives of variables?
Replies: 9
Views: 7264

Re: How to access and plot derivatives of variables?

You are of course referring to total ionic current, not total membrane current. Exactly. Numerical integration always produces approximate results. The best one can get is results that are internally consistent and within an acceptable error tolerance. NEURON's default integrator is implicit Euler,...
by eacheon
Thu Dec 06, 2007 2:32 am
Forum: Other questions
Topic: How to access and plot derivatives of variables?
Replies: 9
Views: 7264

How to access and plot derivatives of variables?

I am using the phase plane plot tool in NEURON GUI. I find if I want to plot dV/dt ~ V, I can plot total current of that segment versus V. However, is there a variable which I can access from hoc that is exactly this dV/dt value? If that is possible, it would be much easier for me to plot also, say,...
by eacheon
Tue Nov 27, 2007 1:32 pm
Forum: Getting started
Topic: vector recorded from CVODE simulation
Replies: 2
Views: 2554

Events normally cause discontinuities in some parameter or state variable. I assume you do not have an event that does that for voltage. Is that voltage difference on the order of your absolute tolerance? If you send me your model I will determine the cause of the discontinuity. No I do not have su...
by eacheon
Mon Nov 26, 2007 3:46 pm
Forum: Getting started
Topic: vector recorded from CVODE simulation
Replies: 2
Views: 2554

vector recorded from CVODE simulation

Hi, I am trying out using CVODE in simulation. Without changing my hoc code, the time is recorded in one vector using Vector.record (I am not using local variable time step here). My problem and confusing is that in the time vector (referred to as "tvec" in the following) I got a few time steps that...
by eacheon
Sun Oct 21, 2007 3:04 pm
Forum: Anatomically detailed models
Topic: Problem using multisplit and cache efficiency?
Replies: 5
Views: 4759

I'm afraid there is no documentation yet. And the usage at the level of the primitives certainly requires advanced hoc programming. However the svn repository version of the standard hoc library now has higher level code that supports multisplit with load balance. We are in the last stages of writi...
by eacheon
Sat Oct 20, 2007 11:17 pm
Forum: Anatomically detailed models
Topic: Problem using multisplit and cache efficiency?
Replies: 5
Views: 4759

1) multisplit. Especially if you have more than two processors. splitcell is also limited in that (in the whole cell) sections can only be connected at positions 0 or 1 of the parent. This is a problem for a lot of cells in which dendrites are connected to soma(.5) 2) At present, no simpler manual ...
by eacheon
Wed Oct 03, 2007 9:40 pm
Forum: Suggestions and Feedback
Topic: Missing documents for pointprocess.get_loc() and .has_loc()
Replies: 6
Views: 17943

Missing documents for pointprocess.get_loc() and .has_loc()

these two methods would be very useful to everybody, but they do not appear in the on line reference.
by eacheon
Mon Sep 17, 2007 11:26 am
Forum: NEURON + Python
Topic: a caveat
Replies: 3
Views: 4217

Restarting the hoc interpreter in a pristine state is not supported. See https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=1029 However, since I don't know anything about ipython, I can assume you can easily unexport neuron and start over that way. That doesn't seem to be the case: it is pretty ha...
by eacheon
Sat Sep 15, 2007 9:59 pm
Forum: NEURON + Python
Topic: a caveat
Replies: 3
Views: 4217

a caveat

From a python shell, if I do >> import neuron >> h = neuron.HocObject() >> h("a = 10") >> h("print a") 10 >> h.quit() # this quits the python shell. While I would rather destroy h instead of quit my python shell. Is it possible at all? I was actually trying to clear everything I did with this sessio...
by eacheon
Sat Sep 15, 2007 9:26 pm
Forum: Getting started
Topic: How to reinit the hoc interpreter?
Replies: 1
Views: 2364

How to reinit the hoc interpreter?

How can I clear everything I did in hoc interpreter without a quit() and re-lauch nrniv/nrngui?