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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,...

... 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)...

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...

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...

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...

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,...

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,...

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...

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 ...

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...

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 ...

these two methods would be very useful to everybody, but they do not appear in the on line reference.

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...

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 ...

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