network

This document describes the "network" C++ class. This class describes the network object, that is used as an entry point for all other objects.

Abstract can contain contained in
no compartment nothing (root)

Methods

checkSolvers

Function Signature

void checkSolvers(void) 

Description

This method verifies that all components can integrate using the requested solver order. What this method does is to call the checkSolvers in every compartment, which in turn calls the checkSolvers method in every component contained in every compartment.

Code

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resolveTree

Function Signature

bool resolveTree(void) 

Description

This method "resolves" a multi-compartment neuron model. What this means is that it works out which compartment is "upstream" (closer to the soma) or "downstream" (further from soma) for every compartment in a multi-compartment model. It does so using the tree_idx property in every compartment, setting it if need be.

It returns true if there is a multi-compartment neuron model somewhere in the network, and false otherwise.

Code

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Function Signature

        mexPrintf("[C++] resolveTree() called\n");

Description

This method "resolves" a multi-compartment neuron model. What this means is that it works out which compartment is "upstream" (closer to the soma) or "downstream" (further from soma) for every compartment in a multi-compartment model. It does so using the tree_idx property in every compartment, setting it if need be.

It returns true if there is a multi-compartment neuron model somewhere in the network, and false otherwise.

bool network::resolveTree(void) { compartment * connected_comp = NULL; bool is_multi_comp = false; if (verbosity > 0) {

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addCompartment

Function Signature

void addCompartment(compartment *comp_) 

Description

This method adds a compartment to the network. It does the following things: 1. adds a pointer to the compartment being added to a vector called comp 2. Broadcasts certain global parameters like temperature, dt, etc to all compartments. 3. Updates n_comp to that network knows how many compartments there are.

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integrateMS

Function Signature

void integrateMS(double * I_ext_now) 

Description

This method is used to integrate the network using a multi-step Runge Kutta solver. This method assumes that no compartment is being voltage clamped.

Code

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integrateMSClamp

Function Signature

void integrateMSClamp(double * V_clamp) 

Description

This method is used to integrate the network using a multi-step Runge-Kutta solver. This method assumes that one compartment is being voltage-clamped.

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integrate

Function Signature

void integrate(double * I_ext_now) 

Description

This method is used to integrate the network using the default single step solver. Typically, this means using the exponential- Euler method to integrate conductances and integrate the voltages and Calcium levels in compartments, though mechanisms can implement their own integration schemes. Multi-compartment models are integrated using the Crank-Nicholson scheme.

This method assumes that no compartment anywhere is being voltage clamped.

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integrateClamp

Function Signature

void integrateClamp(double *V_clamp) 

Description

This method is used to integrate the network using the default single step solver. Typically, this means using the exponential- Euler method to integrate conductances and integrate the voltages and Calcium levels in compartments, though mechanisms can implement their own integration schemes. Multi-compartment models are integrated using the Crank-Nicholson scheme.

This method assumes that some compartment is being voltage clamped, and also assumes that no current is being injected into any compartment.

Code

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