Search found 21 matches

by tardebut
Mon Mar 02, 2015 6:24 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Global vs. Pointers
Replies: 4
Views: 2487

Re: Global vs. Pointers

Thanks Ted.

Omar
by tardebut
Thu Feb 26, 2015 2:17 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Global vs. Pointers
Replies: 4
Views: 2487

Re: Global vs. Pointers

Thanks Ted. I agree with you regarding the use of GLOBAL. And in order to declare the value of an state as GLOBAL, the assigment of xout = state1 either at the end of the DERIVATIVE block or in the BEFORE BREAKPOINT block does the trick. In this case 'state1' is the state I want to be seen by any ot...
by tardebut
Fri Feb 20, 2015 11:57 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Global vs. Pointers
Replies: 4
Views: 2487

Global vs. Pointers

Hi Ted, I have two mechanisms, each of them in a .mod file. And I want one to read an state from the other. In a somewhat related post https://www.neuron.yale.edu/phpBB/viewtopic.php?f=16&t=3192 there were two different suggestions on how to achive this. One was declaring the state a GLOBAL variable...
by tardebut
Wed Jan 07, 2015 6:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Dynamically modifying gmax outside .mod
Replies: 5
Views: 3650

Re: Dynamically modifying gmax outside .mod

Hi there NeuroRhythms, You asked, Would I create one .mod file for neuromodulator-activated current and hard code the time-dependent effect of the neuromodulator on the g(t). To solve this kind of problems one can create a .mod for the dynamics of the neuromodulator and then modify the channel's mod...
by tardebut
Sun Nov 02, 2014 11:29 am
Forum: Adding new mechanisms and functions to NEURON
Topic: OK with fixed step but not with cvode solvers
Replies: 9
Views: 4122

Re: OK with fixed step but not with cvode solvers

After some critical assistance, it become clear that the solution to this problem is to move DA = peak to the beginning of the DERIVATIVE block and GaolfGTPout = GaolfGTP to the end of the DERIVATIVE block. This is because these are not currents and the extension of BREAKPOINT to work with variables...
by tardebut
Fri Oct 31, 2014 7:09 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: OK with fixed step but not with cvode solvers
Replies: 9
Views: 4122

Re: OK with fixed step but not with cvode solvers

Sorry, the BEFORE BREAKPOINT in the .mod below is as follows,

Code: Select all

BEFORE BREAKPOINT {
	 tt = t - startrans
	 peak = bsamp + transient*mxamp*K*(exp(-k1*tt)-exp(-k2*tt))	
		   }
The rest, code and behavior, is the same.

Omar
by tardebut
Fri Oct 31, 2014 4:42 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: OK with fixed step but not with cvode solvers
Replies: 9
Views: 4122

Re: OK with fixed step but not with cvode solvers

Hi there again! Using the last example, I tried the approach with NET_RECEIVE and auto-events (net_send). First, the previous distributed mechanism was converted into a point process which is the one compatible with NET_RECEIVE. The post http://www.neuron.yale.edu/phpBB/viewtopic.php?f=16&t=2292&p=8...
by tardebut
Thu Oct 30, 2014 1:06 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: OK with fixed step but not with cvode solvers
Replies: 9
Views: 4122

Re: OK with fixed step but not with cvode solvers

Thanks Ted. I followed your suggestions. But still, the original problem of this post keeps being without solution at least with the approach based on cvode.event() that is the one I have tried so far. Here you have an small size example suitable for posting that reproduce the problem. This is the ....
by tardebut
Tue Oct 28, 2014 1:12 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: OK with fixed step but not with cvode solvers
Replies: 9
Views: 4122

Re: OK with fixed step but not with cvode solvers

Hi Ted here you have some partial results. I simplified the problem to try the pure .hoc solution. This solution worked. But in this simplified problem the old approach, if (t>tstart) { someparameter = value1 } also worked. This is the .hoc, load_file("nrngui.hoc") objref cvode cvode = new CVode() c...
by tardebut
Mon Oct 27, 2014 6:54 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: OK with fixed step but not with cvode solvers
Replies: 9
Views: 4122

Re: OK with fixed step but not with cvode solvers

Thanks Ted. You are right. I have that piece of code in the neuromodulator .mod.
I will try your suggestions, starting by the second.

Thanks again.

Omar
by tardebut
Mon Oct 27, 2014 7:52 am
Forum: Adding new mechanisms and functions to NEURON
Topic: OK with fixed step but not with cvode solvers
Replies: 9
Views: 4122

OK with fixed step but not with cvode solvers

Hi there, I'm running a neuron model fetched from ModelDB (149100) to which I have added three new mechanism (I mean .mod files) to simulate the effects of neuromodulators. When I run the model using a fixed step solver (cvode.active(0)) the results are the expected: the spike train amplitude and fr...
by tardebut
Fri Sep 26, 2014 7:50 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Esoteric but wrong compilation
Replies: 9
Views: 3428

Re: Esoteric but wrong compilation

Thanks Mike. I change those 0s and now it compiles OK.
I need to change the solver, because the fixed step methods doesn't seem to work OK with this problem.

Thanks again,

Omar
by tardebut
Fri Sep 26, 2014 12:16 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Esoteric but wrong compilation
Replies: 9
Views: 3428

Re: Esoteric but wrong compilation

I have changed all parameter and states names to k# and sp# respectively. Now the parameter names are like k105 and the species like sp63. This new .mod went through nmodlunit smoothly. But when trying to compile, a new error popped up. mine$ nrnivmodl peaktrainglobal diptrainglobal GolfAC5GiSynParS...
by tardebut
Fri Sep 26, 2014 6:26 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Esoteric but wrong compilation
Replies: 9
Views: 3428

Re: Esoteric but wrong compilation

I forgot to mention that if in this position I change PDE1 for PDE1aa or any other trailing character then this compiling error disappears and instead mine$ nrnivmodl peaktrainglobal diptrainglobal GolfAC5GiSyn /mine peaktrainglobal diptrainglobal GolfAC5GiSyn peaktrainglobal diptrainglobal GolfAC5G...