Documentation about NEURON source code, algorithms pipeline, file structure etc
Posted: Fri Jul 08, 2022 9:21 am
Good Day!
Sometimes I want to debug the cells model behavior and to log some variables to understand algorithms how the voltage was calculated.However NEURON source code is big https://github.com/neuronsimulator/nrn/tree/master/src and it is not always clear where to search.
I have found general algorithms descriptions, so I can only guess that pipeline starts somewhere with nrn/nrncvode. then for each time it creates Jacobian matrix for the tree. then for each section it iteratively aligns voltage for non-linear mechanisms with its section voltage. but this is just a guess..
It would be nice if some extra documentation would be published that would help to browse through NEURON code
Sometimes I want to debug the cells model behavior and to log some variables to understand algorithms how the voltage was calculated.However NEURON source code is big https://github.com/neuronsimulator/nrn/tree/master/src and it is not always clear where to search.
I have found general algorithms descriptions, so I can only guess that pipeline starts somewhere with nrn/nrncvode. then for each time it creates Jacobian matrix for the tree. then for each section it iteratively aligns voltage for non-linear mechanisms with its section voltage. but this is just a guess..
It would be nice if some extra documentation would be published that would help to browse through NEURON code