Sirene.c File Reference

Main functions of the SiReNe Software. More...

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <time.h>
#include <sys/time.h>
#include "SireneComponents.h"

Include dependency graph for Sirene.c:

Functions
void	Iter (Simul *Simulation, double *TmpVar, double *TmpDer)
	Computation of one time-step from (t) to (t + dt) More...
void	Advance (Simul *Simulation)
	Simulation process over time-steps. More...
void	InitSimu (Simul *Simulation)
	Initialization of the simulation structure. More...
void	PrepareSimu (Simul *Simulation, ushort VerboseMask, ushort SaveMask, int ResultsInterval)
	Preparation of simulation data according to the neural network description. More...

Variables
unsigned long	MEMORY =0
	Total amount of requested memory. More...
unsigned long	ALLOCATED =0
	Total amount of actually allocated memory. More...
unsigned long	FREED =0
	Total amount of de-allocated memory. More...

Detailed Description

Main functions of the iterative process to simulate biological neuronal networks with adjustable properties (normal state, Parkinson's disease,...).

Function Documentation

Advance()

void Advance

(

Simul *

Simulation

)

---

Iterative process over the time-steps:

• Calls to the Iter() function to solve the ODE system of the network at each time-step

Possibility to save data like VARIABLES, POTENTIALS, INPUT_CURRENTS, SYNAPTIC_CURRENTS, LFP, SPIKES and NBSPIKES.
All files are saved in binary mode.

Parameters

Simulation

Structure where all simulation information is stored

References Simul::BufferSpikes, Simul::Chrono_Advance, Simul::CrtNum, Neuron::GlobalNumNeuron, INPUT_CALL, Neuron::InputCurrent, Simul::InputCurrentsFileName, Iter(), Simul::LFPFileName, MYFREE(), MYMALLOC(), Simul::NbSpikesFileName, Simul::NbSpInBuf, Simul::NeuralModels, NeuralModel::Neurons, NO_RECORD, Simul::NumberNeuralModels, NeuralModel::NumberOfNeurons, Neuron::NumberOfSpikes, Simul::NumberOfVariables, Neuron::PotentialIndex, Simul::PotentialsFileName, PrintTimes(), Simul::PrvNum, Simul::ResultsInterval, RETURN_CALL, SAVE_INPUT_CURRENTS, SAVE_LFP, SAVE_NBSPIKES, SAVE_POTENTIALS, SAVE_SPIKES, SAVE_SYNAPTIC_CURRENTS, SAVE_VARIABLES, Simul::SaveMask, Simul::sLFP, Simul::SpikesFile, Simul::SpikesFileName, Simul::Start, Neuron::SynapticCurrent, Simul::SynapticCurrentsFileName, Simul::t, Simul::Time_Advance, Simul::TimeStep, Simul::TotalNumberOfNeurons, Simul::TotalTimeSim, Simul::Variables, and Simul::VariablesFileName.

Referenced by main().

InitSimu()

void InitSimu

(

Simul *

Simulation

)

---

Parameters

Simulation

Structure where all simulation information is stored

References Simul::BufferSpikes, Simul::CrtNum, Simul::DVar, Euler(), Simul::InterpolationType, NBMEMSTEP, Simul::NbSpInBuf, Simul::NbThreads, Simul::NeuralModels, NO_INTERP, Simul::NumberNeuralModels, Simul::NumberOfVariables, Simul::NumberSynapseModels, Simul::NumericalMethod, Simul::PrvNum, Simul::RandGenerConnect, RandomConnections(), Simul::ResultsInterval, Simul::SaveMask, Simul::sLFP, Simul::SpikesFile, Simul::Start, Simul::SynapseModels, Simul::t, Simul::TimeStep, Simul::TotalNumberOfNeurons, Simul::TotalTimeSim, Simul::Variables, and Simul::VerboseMask.

Referenced by main().

Iter()

void Iter	(	Simul *	Simulation,
		double *	TmpVar,
		double *	TmpDer
	)

---

Network state is computed at (t + dt) using a numerical method (Euler or Runge-Kutta 2).
Detection of spikes using the SpikeDetection() function.

Parameters

Simulation	Structure where all simulation information is stored
TmpVar	Variables array for intermediate time-steps computed in the numerical method
TmpDer	Derivatives array for intermediate time-steps computed in the numerical method

References Simul::Chrono_Iter, Simul::CrtNum, INPUT_CALL, Simul::NumericalMethod, Simul::PrvNum, RETURN_CALL, SpikeDetection(), Simul::t, Simul::Time_Iter, Simul::TimeStep, and UpdateModels().

Referenced by Advance().

PrepareSimu()

void PrepareSimu	(	Simul *	Simulation,
		ushort	VerboseMask,
		ushort	SaveMask,
		int	ResultsInterval
	)

---

Initialization of:

• Simulation structure:
  • SaveMask for data saving during the simulation
  • Time index PrvNum (previous time-step)
  • Crt (current time-step)
  • Time t0 = simulation starting point
  • Total number of neurons
  • Number of variables
  • Allocation of the variables array
  • Allocation of the derivatives of the variables array
  • Sum of the LFP
• Neuron structure:
  • Input/Synaptic current
  • Global number neuron
  • Number of parameters
  • Parameters
  • Synaptic current factor
  • Spike threshold
  • Potential index
  • Mid-time step potential
  • Mid-time step derivative of the potential
  • Number of spikes
  • Last spike time
• Message:
  • Display of initialization information
    • Initialization display is activated via the VerboseMask parameter
• Chrono:
  • Time initalization for each function

Parameters

Simulation	Structure where all simulation information is stored
VerboseMask	Mask of information to display
SaveMask	Mask of variables to save to file
ResultsInterval	Number of iterations between results display / save

References BUFFER_SIZE, Simul::BufferSpikes, Simul::Chrono_Init, Simul::ChronoStart, Simul::CrtNum, Simul::DVar, Neuron::dVMidStep, NeuralModel::FirstNeuronNumber, Neuron::GlobalNumNeuron, Neuron::InitialValues, INPUT_CALL, Neuron::InputCurrent, Neuron::LastSpikeTime, MAXTHREADS, MYMALLOC(), NBMEMSTEP, Simul::NbSpInBuf, Simul::NbThreads, NeuralModelPrint(), Simul::NeuralModels, NeuronPrint(), NeuralModel::Neurons, Simul::NumberNeuralModels, SynapseModel::NumberOfConnections, NeuralModel::NumberOfNeurons, Neuron::NumberOfParameters, NeuralModel::NumberOfParameters, Neuron::NumberOfSpikes, NeuralModel::NumberOfVariables, Simul::NumberOfVariables, Neuron::Parameters, NeuralModel::Parameters, Neuron::PotentialIndex, Simul::PrvNum, Simul::ResultsInterval, RETURN_CALL, Simul::SaveMask, Simul::sLFP, Neuron::SpikeTreshold, NeuralModel::SpikeTreshold, Simul::Start, SynapseModelPrint(), Simul::SynapseModels, Neuron::SynapticCurrent, Neuron::SynCurrentFactor, Simul::t, Simul::Time_Advance, Simul::Time_Detection, Simul::Time_Init, Simul::Time_Iter, Simul::Time_NumericalMethod, Simul::Time_RandGenConn, Simul::Time_SpikeProcessing, Simul::Time_UpdateModels, Simul::Time_UpdateNeuron, Simul::TimeStep, Simul::TotalNumberOfNeurons, Simul::TotalTimeSim, Simul::Variables, VERBOSE_CONFIG, VERBOSE_DETAILS, Simul::VerboseMask, and Neuron::VMidStep.

Referenced by main().

Variable Documentation

ALLOCATED

unsigned long ALLOCATED =0

Referenced by DISPLAYMEM(), and MYMALLOC().

FREED

unsigned long FREED =0

Referenced by DISPLAYMEM(), and MYFREE().

MEMORY

unsigned long MEMORY =0

Referenced by DISPLAYMEM(), and MYMALLOC().