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Thanks, with 8.2.2 I always get past the init() without segfault. However, when I stop the simulation with CTR+C I always get a segfault. That wouldn't necessarily be a problem if my simulations always finished. It seems the simulation is very sensitive to the NTdiffusion value, which is expected I ...

I have a list of pointers, in my case I get them from myvec = [x._ref_concentration for x in mySpecies.nodes] When I write "print(myvec[0])" I get "<pointer to hoc scalar 0>", but I'd like to know more about it and I don't know how. Is there a way to know what are the addresses t...

I'm getting some Segmentation fault errors after using the node.include_flux in a bit longer script that simulates a number of presynaptic spines and postsynaptic sections and random connections between them. This may be a technical issue somewhere else in my code but I haven't found the cause despi...

Thanks, that seems to work.

Is it possible to make a MultiCompartmentReaction that involves species in non-connected sections? I get an error "RxDException: Multicompartment reactions the membrane and sources and destinations must share common sections." which suggests this is not possible. Here's a MWE where I would...

Thanks to both of you - yes probably better to convert the CaDynamics_E2 mechanism to RxD to avoid conflicting cai update. I'm using NEURON 7.8.2.

Thanks, changing the compartment size and making the clamp stimulus longer indeed solved part of the problem (previously the Ca flux through the RxD rate input was very large compared to the Ca flux through the N-type channels). So now I see that both Ca fluxes contribute to cai. However, I'm puzzle...

I'm trying to have both MOD mechanisms and RxD reactions affect my calcium concentrations. Based on previous examples this seems to be possible but I haven't got it to work properly. Here's a MWE: from pylab import * from neuron import h,rxd h(""" load_file("stdlib.hoc") loa...

I think I resolved the issue. The problem seems to be that I first defined a "master" RxD region 'cyt' and then for each of the sections (already included in 'cyt') a separate miniregion cyts , and maybe that's what caused the error message "Rates and Reactions with species defined on...

I'm trying to introduce RxD species and reactions into a set of compartments in a multicompartmental neuron model and give inputs to some of the species. I have a list of sections for which I'm creating the Rxd Region (after defining a cell model L5PC, in this case a regular Hay model) as seclist = ...

I'm trying to make a .mod ion-channel mechanism file where the maximal conductance of the channel would depend on the concentration of a certain species. Currently all my molecular species are part of a list, meaning that they are called 'specs[0]' ... 'specs[19]' and I define my reactions as e.g. r...

I've got another issue related to this topic. I used to run my simulator from the command line (even inside a python script) to make sure there are no issues with reinitialization of the RxD model. Now I'm trying to rewrite the code to be run as a normal python function to avoid i/o overload on the ...

How to implement a decay reaction (a reaction with no products)?

In an earlier NEURON version it was possible to write
but now (v. 7.7) I get an error "AttributeError: 'Reaction' object has no attribute '_react_regions'"

Thanks for the reply. However, the problem persists even if I remove "nrn_region='i'", or change it to None or 'o'.

I get a weird "Abort trap: 6" error that seems to depend on the length of the names of my species. MWE: from neuron import h, rxd from pylab import * h.load_file('stdrun.hoc') dend = h.Section(name='dend') cyt = rxd.Region([dend], name='cyt', nrn_region='i') specNameLen=21 specs = [] vecs ...