Workflow Code Paths

The intention of the following section is to give an overview of important functions and code paths executed to perform certain actions.

NEURON simulations

A summary of the workflow of a typical NEURON simulation can be given with the following graph:

The parts of the simulation can be described as:

Register Mechanisms

Mechanisms in NEURON are defined in .mod files. Apart from some built in mechanisms if the user wants to use any additional mechanisms those need to be compiled using the nrnivmodl executable.

The nrnivmodl executable translates the MOD files from the NMODL language to C++. Those C++ files apart from the computation kernels also include a function named <mechanism_name>_reg_(void) that is essential for registering the mechanism functions in NEURON so that later the user can insert the mechanism in the needed compartments.

Circuit creation

During this part of the simulation the segments, sections and their connections are created. All these are created based on the circuit which is defined by the users in Python or HOC scripts with the respective API.

See: Topology and Topology.

During this part all the Node s are created as well as the Section s.

See C++ documentation: Node, Section and SectionPool.

The call graph of this part can be found below:

Insert Mechanisms

After registering the mechanisms the user can insert them in the needed compartments. To do so they need to call the insert function on the proper section.

Memory allocation of field data

During the mechanism insertion the needed data structures to hold their data are also allocated. This is done by appending to the SoA data structures of the data a new element for the newly inserted mechanism.

Initialization

After all the simulation Section have been created, along with the data structures assigned to them and their mechanisms, all the underlying data structures are ordered and initialized. At this stage, the INITIAL blocks of the inserted MOD files are also executed.