Search found 81 matches

by patoorio
Tue Dec 21, 2010 3:20 pm
Forum: UNIX/Linux
Topic: Leave neuron running and close the session
Replies: 8
Views: 5128

Re: Leave neuron running and close the session

Thanks,
Then I guess neuron will have to be started without the GUI, right? but nrniv doesn't read additional mechanisms present in the directory as nrngui does, so what would be the correct way of starting the process?
by patoorio
Mon Dec 20, 2010 2:19 pm
Forum: UNIX/Linux
Topic: Leave neuron running and close the session
Replies: 8
Views: 5128

Leave neuron running and close the session

Hi, I've set up a Linux machine to be used exclusively for running simulations. The idea is to run neuron both locally and remotely, depending on the kind of simulation. In the remote case (and maybe in the local case too), I would like to start a simulation and be able to close the session (to shut...
by patoorio
Thu Nov 18, 2010 4:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: STATEs which are arrays
Replies: 18
Views: 6474

Re: STATEs which are arrays

Well, it compiled but didn't work properly. There were more errors in the .c file that permitted compilation but made a completely different mechanism. To illustrate it better, I experimented with a simpler model; 4 states in a line. In the 'non-array' version, the DERIVATIVE block is DERIVATIVE sta...
by patoorio
Thu Nov 11, 2010 7:03 am
Forum: Adding new mechanisms and functions to NEURON
Topic: STATEs which are arrays
Replies: 18
Views: 6474

Re: STATEs which are arrays

Doh!
Now it works. Thanks a lot!!
by patoorio
Wed Nov 10, 2010 3:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: STATEs which are arrays
Replies: 18
Views: 6474

Re: STATEs which are arrays

Almost, almost there!! The DERIVATIVE block is: DERIVATIVE states { mh'[0] = (-3*am-ah)*mh[0] + bm*mh[1] + bh*mh[4] mh'[1] = (-2*am-bm-ah)*mh[1] + 3*am*mh[0] + 2*bm*mh[2] + bh*mh[5] mh'[2] = (-am-2*bm-ah)*mh[2] + 2*am*mh[1] + 3*bm*mh[3] + bh*mh[6] mh'[3] = (-3*bm-ah)*mh[3] + am*mh[2] + bh*mh[7] mh'[...
by patoorio
Wed Nov 10, 2010 12:15 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: STATEs which are arrays
Replies: 18
Views: 6474

Re: STATEs which are arrays

Thanks a lot, Mike.
I'll give it a try. I still can use a Linux machine, though ;)
by patoorio
Wed Nov 10, 2010 8:13 am
Forum: Adding new mechanisms and functions to NEURON
Topic: STATEs which are arrays
Replies: 18
Views: 6474

Re: STATEs which are arrays

Thanks! There was indeed an error in the mod file. I fixed it, and now both mknrndll and nocmodl create a non-empty .c file. I see where and how to fix the c file it but I'm having another problem: unlike nrnivmodl, mknrndll does overwrites the .c file. It doesn't seem to care about file dates, it s...
by patoorio
Tue Nov 09, 2010 10:53 am
Forum: Adding new mechanisms and functions to NEURON
Topic: STATEs which are arrays
Replies: 18
Views: 6474

Re: STATEs which are arrays

Hi,

I'm trying to the same as sec6. When compiling, after mknrndll stops there is a "mymodfile.c" file left but it is empty. Where am I supposed to edit and fix the c code?
PS: I'm working in Windows. Please don't tell me that fixing the c code is only possible under Linux.

Regards.
by patoorio
Wed Jan 27, 2010 2:55 pm
Forum: Other questions
Topic: starting from Neuron 7.0, impedance affects simulation!
Replies: 5
Views: 1606

Re: starting from Neuron 7.0, impedance affects simulation!

Yes!! .compute(freq,1) did it.
I don't know how to try the code you posted, do I have to compile the whole program? Or there is a way to compile just those two files?

Thanks a lot!
by patoorio
Wed Jan 27, 2010 12:04 pm
Forum: Other questions
Topic: starting from Neuron 7.0, impedance affects simulation!
Replies: 5
Views: 1606

Re: starting from Neuron 7.0, impedance affects simulation!

Yes, it happens both with 7.0 and 7.1
by patoorio
Tue Jan 26, 2010 10:12 am
Forum: Other questions
Topic: starting from Neuron 7.0, impedance affects simulation!
Replies: 5
Views: 1606

starting from Neuron 7.0, impedance affects simulation!

Hi, I want to monitor the impedance of the model neuron while simulation is running, let's say every 50 ms. So I made a script that advances 50 ms, pauses the simulations and recalculates an impedance object that is inserted. However, starting from Neuron 7.0 I found out that I can't do this any lon...
by patoorio
Thu Aug 20, 2009 4:47 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: problems with cvode, at_time and something else
Replies: 13
Views: 3645

Re: problems with cvode, at_time and something else

Great! I don't know why I assumed that the previous flag=1 event was deleted or something by the new one. So now I understand that I was creating and creating events at each voltage change. The fixed (and probably final) code looks like this: TITLE Mock stochastic voltage-dependent sodium channel : ...
by patoorio
Wed Aug 19, 2009 1:12 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: problems with cvode, at_time and something else
Replies: 13
Views: 3645

Re: problems with cvode, at_time and something else

A flag=2 event sends a flag=1 event. And a flag=1 event sends a flag=1 event. Right, but all events are sent with a proper next_ev time delay, isn't it? This is what seems not to be working when WATCH is present. Is there a way to monitor event generation, delays, and arrivals while the simulation ...
by patoorio
Wed Aug 19, 2009 9:20 am
Forum: Adding new mechanisms and functions to NEURON
Topic: problems with cvode, at_time and something else
Replies: 13
Views: 3645

Re: problems with cvode, at_time and something else

I believe the problem is that every time the voltage changes from vlast by more than 5mV you start a whole new series of flag=1 streams that never ends. And why is that? I can't see it in the code. Did I miss something in the way WATCH works? This is occurring with the fixed step method as well but...