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This repository has been archived by the owner on Mar 20, 2023. It is now read-only.
Some scripts in NEURON when instantiating the cells might define the initial value of ion variables like:
ko0_k_ion = 3.82 //mM
ki0_k_ion = 140 //mM
These variables (from my understanding) seem that when CoreNEURON gets executed in file mode (using its coredat files) are not passed to CoreNEURON to set them when it registers the ions in
cc: @pramodk@nrnhines This issue is a bit related to the issue we were debugging together in the past with NetPyNE simulations however the issue we were seeing then is fixed from this PR #775
The text was updated successfully, but these errors were encountered:
It seems like this issue doesn't influence the spikes of the simulation tested with small circuits of the M1 and S1 NetPyNE models. Still I have created a draft PR to solve this issue here: #780
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Some scripts in NEURON when instantiating the cells might define the initial value of ion variables like:
These variables (from my understanding) seem that when CoreNEURON gets executed in file mode (using its
coredat
files) are not passed to CoreNEURON to set them when it registers the ions inCoreNeuron/coreneuron/mechanism/eion.cpp
Line 63 in c1093ba
The default values come from:
https://github.com/BlueBrain/CoreNeuron/blob/master/coreneuron/membrane_definitions.h
The ion registration and calculation is done correctly in direct mode, when CoreNEURON is launched from NEURON.
To Reproduce
I was only able to reproduce this with a NetPyNE closed source simulation. I can provide more details if needed.
Expected behavior
I suppose that those variables should be passed to the
coredat
files, so that they can be read by CoreNEURON?Logs
NEURON values:
CoreNEURON values:
System (please complete the following information)
master
branch, CoreNEURONmagkanar/fix_pdata
branchcc: @pramodk @nrnhines This issue is a bit related to the issue we were debugging together in the past with NetPyNE simulations however the issue we were seeing then is fixed from this PR #775
The text was updated successfully, but these errors were encountered: