#include <IzhIF.h>

Inheritance diagram for moose::IzhIF:

Collaboration diagram for moose::IzhIF:

Public Member Functions
double	getA (const Eref &e) const

double	getA0 (const Eref &e) const

double	getB (const Eref &e) const

double	getB0 (const Eref &e) const

double	getC0 (const Eref &e) const

double	getD (const Eref &e) const

double	getU (const Eref &e) const

double	getUInit (const Eref &e) const

double	getVPeak (const Eref &e) const

	IzhIF ()

void	setA (const Eref &e, double val)

void	setA0 (const Eref &e, double val)

void	setB (const Eref &e, double val)

void	setB0 (const Eref &e, double val)

void	setC0 (const Eref &e, double val)

void	setD (const Eref &e, double val)

void	setU (const Eref &e, double val)

void	setUInit (const Eref &e, double val)

void	setVPeak (const Eref &e, double val)

void	vProcess (const Eref &e, ProcPtr p)

void	vReinit (const Eref &e, ProcPtr p)

virtual	~IzhIF ()

Public Member Functions inherited from moose::IntFireBase
void	activation (double val)

double	getLastEventTime (const Eref &e) const

double	getRefractoryPeriod (const Eref &e) const

double	getThresh (const Eref &e) const

double	getVReset (const Eref &e) const

bool	hasFired (const Eref &e) const

	IntFireBase ()

void	setRefractoryPeriod (const Eref &e, double val)

void	setThresh (const Eref &e, double val)

void	setVReset (const Eref &e, double val)

virtual	~IntFireBase ()

Public Member Functions inherited from moose::Compartment
void	cable ()

	Compartment ()

virtual double	vGetCm (const Eref &e) const

virtual double	vGetEm (const Eref &e) const

virtual double	vGetIm (const Eref &e) const

virtual double	vGetInitVm (const Eref &e) const

virtual double	vGetInject (const Eref &e) const

virtual double	vGetRa (const Eref &e) const

virtual double	vGetRm (const Eref &e) const

virtual double	vGetVm (const Eref &e) const

void	vHandleAxial (double Vm)

void	vHandleChannel (const Eref &e, double Gk, double Ek)

void	vHandleRaxial (double Ra, double Vm)

void	vInitProc (const Eref &e, ProcPtr p)

void	vInitReinit (const Eref &e, ProcPtr p)

void	vInjectMsg (const Eref &e, double current)

void	vRandInject (const Eref &e, double prob, double current)

virtual void	vSetCm (const Eref &e, double Cm)

virtual void	vSetEm (const Eref &e, double Em)

virtual void	vSetInitVm (const Eref &e, double initVm)

virtual void	vSetInject (const Eref &e, double Inject)

virtual void	vSetRa (const Eref &e, double Ra)

virtual void	vSetRm (const Eref &e, double Rm)

virtual void	vSetVm (const Eref &e, double Vm)

virtual	~Compartment ()

Public Member Functions inherited from moose::CompartmentBase
void	cable ()

	CompartmentBase ()

void	displace (double dx, double dy, double dz)
	Displaces compartment by specified distance vector. More...

double	getCm (const Eref &e) const

double	getDiameter () const

double	getEm (const Eref &e) const

double	getIm (const Eref &e) const

double	getInitVm (const Eref &e) const

double	getInject (const Eref &e) const

double	getLength () const

double	getRa (const Eref &e) const

double	getRm (const Eref &e) const

double	getVm (const Eref &e) const

double	getX () const

double	getX0 () const

double	getY () const

double	getY0 () const

double	getZ () const

double	getZ0 () const

void	handleAxial (double Vm)

void	handleChannel (const Eref &e, double Gk, double Ek)

void	handleRaxial (double Ra, double Vm)

void	initProc (const Eref &e, ProcPtr p)

void	initReinit (const Eref &e, ProcPtr p)

void	injectMsg (const Eref &e, double current)

void	process (const Eref &e, ProcPtr p)

void	randInject (const Eref &e, double prob, double current)

bool	rangeWarning (const string &field, double value)

void	reinit (const Eref &e, ProcPtr p)

void	setCm (const Eref &e, double Cm)

void	setDiameter (double diameter)

void	setEm (const Eref &e, double Em)

void	setGeomAndElec (const Eref &e, double length, double dia)
	Scales electrical values along with setting length, dia. More...

void	setInitVm (const Eref &e, double initVm)

void	setInject (const Eref &e, double Inject)

void	setLength (double length)

void	setRa (const Eref &e, double Ra)

void	setRm (const Eref &e, double Rm)

void	setVm (const Eref &e, double Vm)

void	setX (double value)

void	setX0 (double value)

void	setY (double value)

void	setY0 (double value)

void	setZ (double value)

void	setZ0 (double value)

void	updateLength ()

virtual void	vSetSolver (const Eref &e, Id hsolve)

virtual	~CompartmentBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from moose::IntFireBase
static const Cinfo *	initCinfo ()

static SrcFinfo1< double > *	spikeOut ()
	Message src for outgoing spikes. More...

Static Public Member Functions inherited from moose::Compartment
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from moose::CompartmentBase
static const Cinfo *	initCinfo ()

static SrcFinfo1< double > *	VmOut ()

static void	zombify (Element orig, const Cinfo zClass, Id hsolve)

Private Attributes
double	a0_

double	a_

double	b0_

double	b_

double	c0_

double	d_

double	u_

double	uInit_

double	vPeak_

Additional Inherited Members
Protected Attributes inherited from moose::IntFireBase
double	activation_

bool	fired_

double	lastEvent_

double	refractT_

double	threshold_

double	vReset_

Protected Attributes inherited from moose::Compartment
double	A_

double	B_

double	Cm_

double	Em_

double	Im_

double	initVm_

double	inject_

double	lastIm_

double	Ra_

double	Rm_

double	sumInject_

double	Vm_

Detailed Description

The IntFire class sets up an integrate-and-fire compartment.

Definition at line 19 of file IzhIF.h.

Constructor & Destructor Documentation

IzhIF::IzhIF ( )

Definition at line 134 of file IzhIF.cpp.

References a0_, a_, b0_, b_, c0_, d_, u_, uInit_, and vPeak_.

 {
 // by default, a0 = 0.04e6/V/s, b0 = 5e3/s, c0 = 140 V/s are set to SI units,
 // so use SI consistently,
 // or change a0, b0, c0 via python if you wish to use other units.
 a0_ = 0.04e6;   // V^-1 s^-1
 b0_ = 5e3;      // s^-1
 c0_ = 140;      // V/s
 a_ = 0.0;
 b_ = 0.0;
 d_ = 0.0;
 uInit_ = 0.0;
 u_ = 0.0;
 vPeak_ = 0.0;
 }

IzhIF::~IzhIF ( )

virtual

Definition at line 150 of file IzhIF.cpp.

151 {;}

Member Function Documentation

double IzhIF::getA ( const Eref & e ) const

Definition at line 238 of file IzhIF.cpp.

References a_.

Referenced by initCinfo().

 {
     return a_;
 }

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double IzhIF::getA0 ( const Eref & e ) const

Definition at line 208 of file IzhIF.cpp.

References a0_.

Referenced by initCinfo().

 {
     return a0_;
 }

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double IzhIF::getB ( const Eref & e ) const

Definition at line 248 of file IzhIF.cpp.

References b_.

Referenced by initCinfo().

 {
     return b_;
 }

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double IzhIF::getB0 ( const Eref & e ) const

Definition at line 218 of file IzhIF.cpp.

References b0_.

Referenced by initCinfo().

 {
     return b0_;
 }

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double IzhIF::getC0 ( const Eref & e ) const

Definition at line 228 of file IzhIF.cpp.

References c0_.

Referenced by initCinfo().

 {
     return c0_;
 }

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double IzhIF::getD ( const Eref & e ) const

Definition at line 258 of file IzhIF.cpp.

References d_.

Referenced by initCinfo().

 {
     return d_;
 }

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double IzhIF::getU ( const Eref & e ) const

Definition at line 278 of file IzhIF.cpp.

References u_.

Referenced by initCinfo().

 {
     return u_;
 }

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double IzhIF::getUInit ( const Eref & e ) const

Definition at line 288 of file IzhIF.cpp.

References uInit_.

Referenced by initCinfo().

 {
     return uInit_;
 }

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double IzhIF::getVPeak ( const Eref & e ) const

Definition at line 268 of file IzhIF.cpp.

References vPeak_.

Referenced by initCinfo().

 {
     return vPeak_;
 }

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const Cinfo * IzhIF::initCinfo ( )

static

Initializes the class info.

Definition at line 19 of file IzhIF.cpp.

References getA(), getA0(), getB(), getB0(), getC0(), getD(), getU(), getUInit(), getVPeak(), moose::IntFireBase::initCinfo(), IzhIFCinfo, setA(), setA0(), setB(), setB0(), setC0(), setD(), setU(), setUInit(), and setVPeak().

 {
     static string doc[] =
     {
         "Name", "IzhIF",
         "Author", "Aditya Gilra",
         "Description", "Izhikevich neuron (integrate and fire)."
         "d Vm /dt = a0 * Vm^2 + b0 * Vm + c0 - u + I/Cm "
         "d u / dt = a * ( b * Vm - u ) "
         "at each spike, u -> u + d "
         "by default, a0 = 0.04e6/V/s, b0 = 5e3/s, c0 = 140 V/s are set to SI units, "
         "so use SI consistently, or change a0, b0, c0 also if you wish to use other units. "
         "Rm, Em from Compartment are not used here, vReset is same as c in the usual formalism. "
         "At rest, u0 = b V0, and V0 = ( -(-b0-b) +/- sqrt((b0-b)^2 - 4*a0*c0)) / (2*a0) "
         "equivalently, to obtain resting Em, set b = (a0*Em^2 + b0*Em + c0)/Em"
     };
 
     static ElementValueFinfo< IzhIF, double > a0(
         "a0",
         "factor for Vm^2 term in evolution equation for Vm: "
         "d Vm /dt = a0 * Vm^2 + b0 * Vm + c0 - u + I/Cm ",
         &IzhIF::setA0,
         &IzhIF::getA0
     );
 
     static ElementValueFinfo< IzhIF, double > b0(
         "b0",
         "factor for Vm term in evolution equation for Vm: "
         "d Vm /dt = a0 * Vm^2 + b0 * Vm + c0 - u + I/Cm ",
         &IzhIF::setB0,
         &IzhIF::getB0
     );
 
     static ElementValueFinfo< IzhIF, double > c0(
         "c0",
         "constant term in evolution equation for Vm: "
         "d Vm /dt = a0 * Vm^2 + b0 * Vm + c0 - u + I/Cm ",
         &IzhIF::setC0,
         &IzhIF::getC0
     );
 
     static ElementValueFinfo< IzhIF, double > a(
         "a",
         "a as in d u / dt = a * ( b * Vm - u ) ",
         &IzhIF::setA,
         &IzhIF::getA
     );
 
     static ElementValueFinfo< IzhIF, double > b(
         "b",
         "b as in d u / dt = a * ( b * Vm - u ) ",
         &IzhIF::setB,
         &IzhIF::getB
     );
 
     static ElementValueFinfo< IzhIF, double > d(
         "d",
         "u jumps by d at every spike",
         &IzhIF::setD,
         &IzhIF::getD
     );
 
     static ElementValueFinfo< IzhIF, double > u(
         "u",
         "u is an adaptation variable",
         &IzhIF::setU,
         &IzhIF::getU
     );
 
     static ElementValueFinfo< IzhIF, double > vPeak(
         "vPeak",
         "Vm is reset when Vm > vPeak",
         &IzhIF::setVPeak,
         &IzhIF::getVPeak
     );
 
     static ElementValueFinfo< IzhIF, double > uInit(
         "uInit",
         "Initial value of u. It is reset at reinit()",
         &IzhIF::setUInit,
         &IzhIF::getUInit
     );
 
     static Finfo* IzhIFFinfos[] = {
         &a0,            // Value
         &b0,            // Value
         &c0,            // Value
         &a,             // Value
         &b,             // Value
         &d,             // Value
         &u,             // Value
         &uInit,         // Value
         &vPeak,         // Value
     };
 
     static Dinfo< IzhIF > dinfo;
     static Cinfo IzhIFCinfo(
                 "IzhIF",
                 IntFireBase::initCinfo(),
                 IzhIFFinfos,
                 sizeof( IzhIFFinfos ) / sizeof (Finfo*),
                 &dinfo,
                 doc,
                 sizeof(doc)/sizeof(string)
     );
 
     return &IzhIFCinfo;
 }

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void IzhIF::setA	(	const Eref &	e,
		double	val
	)

Definition at line 233 of file IzhIF.cpp.

References a_.

Referenced by initCinfo().

 {
     a_ = val;
 }

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void IzhIF::setA0	(	const Eref &	e,
		double	val
	)

Definition at line 203 of file IzhIF.cpp.

References a0_.

Referenced by initCinfo().

 {
     a0_ = val;
 }

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void IzhIF::setB	(	const Eref &	e,
		double	val
	)

Definition at line 243 of file IzhIF.cpp.

References b_.

Referenced by initCinfo().

 {
     b_ = val;
 }

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void IzhIF::setB0	(	const Eref &	e,
		double	val
	)

Definition at line 213 of file IzhIF.cpp.

References b0_.

Referenced by initCinfo().

 {
     b0_ = val;
 }

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void IzhIF::setC0	(	const Eref &	e,
		double	val
	)

Definition at line 223 of file IzhIF.cpp.

References c0_.

Referenced by initCinfo().

 {
     c0_ = val;
 }

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void IzhIF::setD	(	const Eref &	e,
		double	val
	)

Definition at line 253 of file IzhIF.cpp.

References d_.

Referenced by initCinfo().

 {
     d_ = val;
 }

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void IzhIF::setU	(	const Eref &	e,
		double	val
	)

Definition at line 273 of file IzhIF.cpp.

References u_.

Referenced by initCinfo().

 {
     u_ = val;
 }

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void IzhIF::setUInit	(	const Eref &	e,
		double	val
	)

Definition at line 283 of file IzhIF.cpp.

References uInit_.

Referenced by initCinfo().

 {
     uInit_ = val;
 }

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void IzhIF::setVPeak	(	const Eref &	e,
		double	val
	)

Definition at line 263 of file IzhIF.cpp.

References vPeak_.

Referenced by initCinfo().

 {
     vPeak_ = val;
 }

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void IzhIF::vProcess	(	const Eref &	e,
		ProcPtr	p
	)

virtual

The process function does the object updating and sends out messages to channels, nernsts, and so on.

Implements moose::IntFireBase.

Definition at line 157 of file IzhIF.cpp.

References a0_, a_, moose::IntFireBase::activation_, b0_, b_, c0_, moose::Compartment::Cm_, ProcInfo::currTime, d_, ProcInfo::dt, moose::IntFireBase::fired_, moose::Compartment::Im_, moose::Compartment::inject_, moose::IntFireBase::lastEvent_, moose::Compartment::lastIm_, moose::IntFireBase::refractT_, moose::IntFireBase::spikeOut(), moose::Compartment::sumInject_, u_, moose::Compartment::Vm_, moose::CompartmentBase::VmOut(), vPeak_, and moose::IntFireBase::vReset_.

 {
     // fully taking over Compartment's vProcess due to quadratic term in Vm
     // we no longer care about A and B
     fired_ = false;
     if ( p->currTime < lastEvent_ + refractT_ ) {
         Vm_ = vReset_;
         sumInject_ = 0.0;
         VmOut()->send( e, Vm_ );
     } else {
         // activation can be a continous variable (graded synapse).
         // So integrate it at every time step, thus *dt.
         // For a delta-fn synapse, SynHandler-s divide by dt and send activation.
         // See: http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-26.html#synchan
         //          for this continuous definition of activation.
         Vm_ += activation_ * p->dt;
         activation_ = 0.0;
         if ( Vm_ > vPeak_ ) {
             Vm_ = vReset_;
             u_ += d_;
             lastEvent_ = p->currTime;
             fired_ = true;
             spikeOut()->send( e, p->currTime );
             VmOut()->send( e, Vm_ );
         } else {
             Vm_ += ( (inject_+sumInject_) / Cm_
                     + a0_*pow(Vm_,2.0) + b0_*Vm_ + c0_ - u_ ) * p->dt;
             u_ += a_ * (b_*Vm_ - u_) * p->dt;
             lastIm_ = Im_;
             Im_ = 0.0;
             sumInject_ = 0.0;
             // Send out Vm to channels, SpikeGens, etc.
             VmOut()->send( e, Vm_ );
         }
     }
 }

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void IzhIF::vReinit	(	const Eref &	e,
		ProcPtr	p
	)

virtual

The reinit function reinitializes all fields.

Implements moose::IntFireBase.

Definition at line 194 of file IzhIF.cpp.

References moose::IntFireBase::activation_, moose::IntFireBase::fired_, moose::IntFireBase::lastEvent_, moose::IntFireBase::refractT_, u_, uInit_, and moose::Compartment::vReinit().

 {
     activation_ = 0.0;
     u_ = uInit_;
     fired_ = false;
     lastEvent_ = -refractT_; // Allow it to fire right away.
     Compartment::vReinit( e, p );
 }