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A few things I figured out, in case they're helpful for future readers. myvec.record(…) - Vector class record 1) I’m doing a parameter sweep to get strength duration data. I’m sweeping the pulse width and using a binary search algorithm to find threshold at each pulse width. For some of my vectors, ...

Fair enough. I'm just not currently using Vector.play() to apply my stimulus.

But if a modeller would want e_extracellular initialized to non-zero values, they will explicitly initialize it as appropriate for their simulation. However, in my case, I assumed it would be initialized to zero, which thankfully manifested itself in a visibly incorrect results. I then knew I had to...

Because when I do a parameter sweep (let's say I'm changing the stimulation amplitude), and I repeatedly call my stimulation procedure, the e_extracellular values will still be unchanged from the end of the previous parameter value, rather than being reinitialized to zero.

Nikki

Hi,

I think it would make sense for finitialize() to zero all extracellular potentials if that mechanism is being used.

Nikki

So, I'm still getting an integration error (below) at the time of my stimulus onset, even though I'm using dt/1000 for 5*dt before and after the time point when the stimulus turns on. Any other suggestions? All I'm trying to do is apply a pulse of extracellular current (i.e. "pulse" of Ve)...

Quick follow-up questions: 1) How is your last example a ramp...? Doesn't it still turn on and off abruptly? 2) Did I just get lucky then that I did not get an error when I used an intracellular current pulse? 3) Should I still use cvode.event of some form when using a ramp? 4) How do I know how gen...

Very helpful clarifications. I've sorted out most of my issues (and I'll try to make a post this weekend about my solutions for future readers). I think I have the myvec.play(...) figured out as well. I'm stumped on one bug though, which is causing my code to crash with the following error... t: 1.9...

Thank you Ted. So let me start with addressing the issue of the possible need for CVODE. I have a model for which I'm extracting the conduction speed and strength-duration curve for validation against published experimental data. This model is a modification of the MRG model. Based upon this thread....

I'm using CVODE for the first time, and I have a few implementation questions. Sorry for the long post; I'm just missing some basics despite digging through the documentation/forum/book. 1) I'm running my simulation multiple times (parameter sweep). Should I call cvode.record(...) just once (outside...

Thank you Ted! I was just working on understanding pack, post, and retval/upkscalar/upkvec/etc. I now have this working. However, I'm still struggling with retrieving the input arguments. I can obtain the user ID, as suggested in your post, but then to which function to I feed the user ID to unpack ...

Setting cvode.condition_order(2) also causes my NEURON to crash. Did you ever resolve this issue?

I am using a simple bulletin board setup to parallelize my simulations in hoc. However, I'm struggling with 2 things: A) I would like to return 2 result values (threshold and conduction speed). B) I would also like to return/read the input arguments of the pc.submit() corresponding to each set of re...