moose::Compartment Class Reference

#include <Compartment.h>

Inheritance diagram for moose::Compartment:

Collaboration diagram for moose::Compartment:

Public Member Functions
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	vProcess (const Eref &e, ProcPtr p)
void	vRandInject (const Eref &e, double prob, double current)
void	vReinit (const Eref &e, ProcPtr p)
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::CompartmentBase
static const Cinfo *	initCinfo ()
static SrcFinfo1< double > *	VmOut ()
static void	zombify (Element *orig, const Cinfo *zClass, Id hsolve)

Protected Attributes
double	A_
double	B_
double	Cm_
double	Em_
double	Im_
double	initVm_
double	inject_
double	lastIm_
double	Ra_
double	Rm_
double	sumInject_
double	Vm_

Private Attributes
double	dt_
double	invRm_

Static Private Attributes
static const double	EPSILON = 1.0e-15

Detailed Description

Definition at line 22 of file Compartment.h.

Constructor & Destructor Documentation

Compartment::Compartment

(

)

Definition at line 74 of file Compartment.cpp.

References A_, B_, Cm_, Em_, Im_, initVm_, inject_, invRm_, lastIm_, Ra_, Rm_, sumInject_, and Vm_.

{
    Vm_ = -0.06;
    Em_ = -0.06;
    Cm_ = 1.0;
    Rm_ = 1.0;
    invRm_ = 1.0;
    Ra_ = 1.0;
    Im_ = 0.0;
    lastIm_ = 0.0;
    inject_ = 0.0;
    sumInject_ = 0.0;
    initVm_ = -0.06;
    A_ = 0.0;
    B_ = 0.0;
}

Compartment::~Compartment ( )

virtual

Definition at line 91 of file Compartment.cpp.

{
    ;
}

Member Function Documentation

void moose::Compartment::cable

(

)

Dummy function to act as recipient of 'cable' message, which is just for grouping compartments.

const Cinfo * Compartment::initCinfo ( )

static

Initializes the class info.

The initCinfo() function sets up the Compartment class. This function uses the common trick of having an internal static value which is created the first time the function is called. There are several static arrays set up here. The ones which use SharedFinfos are for shared messages where multiple kinds of information go along the same connection.

Definition at line 26 of file Compartment.cpp.

References compartmentCinfo, and moose::CompartmentBase::initCinfo().

Referenced by SymCompartment::initCinfo(), and moose::IntFireBase::initCinfo().

{
    // static Finfo* compartmentFinfos[] = { };

    static string doc[] =
    {
        "Name", "Compartment",
        "Author", "Upi Bhalla",
        "Description", "Compartment object, for branching neuron models.",
    };
    static Dinfo< Compartment > dinfo;
    static Cinfo compartmentCinfo(
        "Compartment",
        CompartmentBase::initCinfo(),
        0,
        0,
        // compartmentFinfos,
        // sizeof( compartmentFinfos ) / sizeof( Finfo* ),
        &dinfo,
        doc,
        sizeof(doc)/sizeof(string)
    );

    return &compartmentCinfo;
}

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double Compartment::vGetCm ( const Eref &  e ) const

virtual

Implements moose::CompartmentBase.

Definition at line 123 of file Compartment.cpp.

References Cm_.

{
    return Cm_;
}

double Compartment::vGetEm ( const Eref &  e ) const

virtual

Implements moose::CompartmentBase.

Definition at line 112 of file Compartment.cpp.

References Em_.

{
    return Em_;
}

double Compartment::vGetIm ( const Eref &  e ) const

virtual

Implements moose::CompartmentBase.

Definition at line 151 of file Compartment.cpp.

References lastIm_.

{
    return lastIm_;
}

double Compartment::vGetInitVm ( const Eref &  e ) const

virtual

Implements moose::CompartmentBase.

Definition at line 171 of file Compartment.cpp.

References initVm_.

{
    return initVm_;
}

double Compartment::vGetInject ( const Eref &  e ) const

virtual

Implements moose::CompartmentBase.

Definition at line 161 of file Compartment.cpp.

References inject_.

{
    return inject_;
}

double Compartment::vGetRa ( const Eref &  e ) const

virtual

Implements moose::CompartmentBase.

Definition at line 146 of file Compartment.cpp.

References Ra_.

{
    return Ra_;
}

double Compartment::vGetRm ( const Eref &  e ) const

virtual

Implements moose::CompartmentBase.

Definition at line 135 of file Compartment.cpp.

References Rm_.

{
    return Rm_;
}

double Compartment::vGetVm ( const Eref &  e ) const

virtual

Implements moose::CompartmentBase.

Definition at line 102 of file Compartment.cpp.

References Vm_.

{
    return Vm_;
}

void Compartment::vHandleAxial ( double  Vm )

virtual

handleAxial handles incoming axial message data.

Implements moose::CompartmentBase.

Definition at line 245 of file Compartment.cpp.

References A_, B_, Im_, Ra_, and Vm_.

{
    A_ += Vm / Ra_;
    B_ += 1.0 / Ra_;
    Im_ += ( Vm - Vm_ ) / Ra_;
}

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

virtual

handleChannel handles information coming from the channel to the compartment

Implements moose::CompartmentBase.

Definition at line 232 of file Compartment.cpp.

References A_, and B_.

{
    A_ += Gk * Ek;
    B_ += Gk;
}

void Compartment::vHandleRaxial ( double  Ra, double  Vm  )

virtual

handleRaxial handles incoming raxial message data.

Implements moose::CompartmentBase.

Definition at line 238 of file Compartment.cpp.

References A_, B_, Im_, and Vm_.

{
    A_ += Vm / Ra;
    B_ += 1.0 / Ra;
    Im_ += ( Vm - Vm_ ) / Ra;
}

void Compartment::vInitProc ( const Eref &  e, ProcPtr  p  )

virtual

The initProc function is for a second phase of 'process' operations. It sends the axial and raxial messages to other compartments. It has to be executed out of phase with the main process so that all compartments are equivalent and there is no calling order dependence in the results.

Implements moose::CompartmentBase.

Reimplemented in SymCompartment.

Definition at line 219 of file Compartment.cpp.

References axialOut, Ra_, raxialOut, and Vm_.

{
    // Send out the axial messages
    axialOut->send( e, Vm_ );
    // Send out the raxial messages
    raxialOut->send( e, Ra_, Vm_ );
}

void Compartment::vInitReinit ( const Eref &  e, ProcPtr  p  )

virtual

Empty function to do another reinit step out of phase with the main one. Nothing needs doing there.

Implements moose::CompartmentBase.

Reimplemented in SymCompartment.

Definition at line 227 of file Compartment.cpp.

{
    ; // Nothing happens here
}

void Compartment::vInjectMsg ( const Eref &  e, double  current  )

virtual

Injects a constantly updated current into the compartment. Unlike the 'inject' field, this injected current is applicable only for a single timestep. So this is meant to be used as the destination of a message rather than as a one-time assignment.

Implements moose::CompartmentBase.

Definition at line 252 of file Compartment.cpp.

References Im_, and sumInject_.

{
    sumInject_ += current;
    Im_ += current;
}

void Compartment::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::CompartmentBase.

Reimplemented in moose::IzhIF, moose::IntFireBase, moose::AdExIF, moose::AdThreshIF, moose::QIF, moose::ExIF, and moose::LIF.

Definition at line 181 of file Compartment.cpp.

References A_, B_, Cm_, ProcInfo::dt, Em_, EPSILON, Im_, inject_, invRm_, lastIm_, sumInject_, Vm_, and moose::CompartmentBase::VmOut().

Referenced by moose::LIF::vProcess(), moose::ExIF::vProcess(), moose::AdExIF::vProcess(), and moose::AdThreshIF::vProcess().

{
    //cout << "Compartment " << e.id().path() << ":: process: A = " << A_ << ", B = " << B_ << endl;
    A_ += inject_ + sumInject_ + Em_ * invRm_;
    if ( B_ > EPSILON )
    {
        double x = exp( -B_ * p->dt / Cm_ );
        Vm_ = Vm_ * x + ( A_ / B_ )  * ( 1.0 - x );
    }
    else
    {
        Vm_ += ( A_ - Vm_ * B_ ) * p->dt / Cm_;
    }
    A_ = 0.0;
    B_ = invRm_;
    lastIm_ = Im_;
    Im_ = 0.0;
    sumInject_ = 0.0;
    // Send out Vm to channels, SpikeGens, etc.
    VmOut()->send( e, Vm_ );

    // The axial/raxial messages go out in the 'init' phase.
}

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

virtual

Injects a constantly updated current into the compartment, with a probability prob. Note that it isn't the current amplitude that is random, it is the presence or absence of the current that is probabilistic.

Implements moose::CompartmentBase.

Definition at line 258 of file Compartment.cpp.

References dt_, Im_, moose::mtrand(), and sumInject_.

{
    if ( moose::mtrand() < prob * dt_ )
    {
        sumInject_ += current;
        Im_ += current;
    }
}

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

virtual

The reinit function reinitializes all fields.

Implements moose::CompartmentBase.

Reimplemented in moose::IzhIF, moose::IntFireBase, moose::AdExIF, moose::AdThreshIF, moose::QIF, SymCompartment, moose::ExIF, and moose::LIF.

Definition at line 205 of file Compartment.cpp.

References A_, B_, ProcInfo::dt, dt_, Im_, initVm_, invRm_, lastIm_, sumInject_, Vm_, and moose::CompartmentBase::VmOut().

Referenced by moose::LIF::vReinit(), moose::ExIF::vReinit(), SymCompartment::vReinit(), moose::QIF::vReinit(), moose::AdExIF::vReinit(), moose::AdThreshIF::vReinit(), and moose::IzhIF::vReinit().

{
    Vm_ = initVm_;
    A_ = 0.0;
    B_ = invRm_;
    Im_ = 0.0;
    lastIm_ = 0.0;
    sumInject_ = 0.0;
    dt_ = p->dt;

    // Send out the resting Vm to channels, SpikeGens, etc.
    VmOut()->send( e, Vm_ );
}

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void Compartment::vSetCm ( const Eref &  e, double  Cm  )

virtual

Implements moose::CompartmentBase.

Definition at line 117 of file Compartment.cpp.

References Cm_, and moose::CompartmentBase::rangeWarning().

{
    if ( rangeWarning( "Cm", Cm ) ) return;
    Cm_ = Cm;
}

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void Compartment::vSetEm ( const Eref &  e, double  Em  )

virtual

Implements moose::CompartmentBase.

Definition at line 107 of file Compartment.cpp.

References Em_.

{
    Em_ = Em;
}

void Compartment::vSetInitVm ( const Eref &  e, double  initVm  )

virtual

Implements moose::CompartmentBase.

Definition at line 166 of file Compartment.cpp.

References initVm_.

{
    initVm_ = initVm;
}

void Compartment::vSetInject ( const Eref &  e, double  Inject  )

virtual

Implements moose::CompartmentBase.

Definition at line 156 of file Compartment.cpp.

References inject_.

{
    inject_ = inject;
}

void Compartment::vSetRa ( const Eref &  e, double  Ra  )

virtual

Implements moose::CompartmentBase.

Definition at line 140 of file Compartment.cpp.

References Ra_, and moose::CompartmentBase::rangeWarning().

{
    if ( rangeWarning( "Ra", Ra ) ) return;
    Ra_ = Ra;
}

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void Compartment::vSetRm ( const Eref &  e, double  Rm  )

virtual

Implements moose::CompartmentBase.

Definition at line 128 of file Compartment.cpp.

References invRm_, moose::CompartmentBase::rangeWarning(), and Rm_.

{
    if ( rangeWarning( "Rm", Rm ) ) return;
    Rm_ = Rm;
    invRm_ = 1.0/Rm;
}

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void Compartment::vSetVm ( const Eref &  e, double  Vm  )

virtual

Implements moose::CompartmentBase.

Definition at line 97 of file Compartment.cpp.

References Vm_.

{
    Vm_ = Vm;
}

Member Data Documentation

double moose::Compartment::A_

protected

Definition at line 128 of file Compartment.h.

Referenced by Compartment(), SymCompartment::raxialCylinder(), SymCompartment::raxialSphere(), SymCompartment::raxialSym(), vHandleAxial(), vHandleChannel(), vHandleRaxial(), moose::LIF::vProcess(), moose::ExIF::vProcess(), moose::AdExIF::vProcess(), moose::AdThreshIF::vProcess(), vProcess(), and vReinit().

double moose::Compartment::B_

protected

Definition at line 129 of file Compartment.h.

Referenced by Compartment(), SymCompartment::raxialCylinder(), SymCompartment::raxialSphere(), SymCompartment::raxialSym(), vHandleAxial(), vHandleChannel(), vHandleRaxial(), moose::LIF::vProcess(), moose::ExIF::vProcess(), moose::AdExIF::vProcess(), moose::AdThreshIF::vProcess(), vProcess(), and vReinit().

double moose::Compartment::Cm_

protected

Definition at line 122 of file Compartment.h.

Referenced by Compartment(), vGetCm(), moose::ExIF::vProcess(), moose::QIF::vProcess(), moose::AdExIF::vProcess(), moose::IzhIF::vProcess(), vProcess(), and vSetCm().

double moose::Compartment::dt_

private

Definition at line 134 of file Compartment.h.

Referenced by vRandInject(), and vReinit().

double moose::Compartment::Em_

protected

Definition at line 121 of file Compartment.h.

Referenced by Compartment(), vGetEm(), moose::QIF::vProcess(), moose::AdExIF::vProcess(), moose::AdThreshIF::vProcess(), vProcess(), and vSetEm().

const double Compartment::EPSILON = 1.0e-15

staticprivate

Definition at line 135 of file Compartment.h.

Referenced by vProcess().

double moose::Compartment::Im_

protected

Definition at line 125 of file Compartment.h.

Referenced by Compartment(), SymCompartment::raxialCylinder(), SymCompartment::raxialSphere(), SymCompartment::raxialSym(), vHandleAxial(), vHandleRaxial(), vInjectMsg(), moose::QIF::vProcess(), moose::IzhIF::vProcess(), vProcess(), vRandInject(), and vReinit().

double moose::Compartment::initVm_

protected

Definition at line 120 of file Compartment.h.

Referenced by Compartment(), vGetInitVm(), vReinit(), and vSetInitVm().

double moose::Compartment::inject_

protected

Definition at line 127 of file Compartment.h.

Referenced by Compartment(), vGetInject(), moose::QIF::vProcess(), moose::IzhIF::vProcess(), vProcess(), and vSetInject().

double moose::Compartment::invRm_

private

Definition at line 133 of file Compartment.h.

Referenced by Compartment(), vProcess(), vReinit(), and vSetRm().

double moose::Compartment::lastIm_

protected

Definition at line 126 of file Compartment.h.

Referenced by Compartment(), vGetIm(), moose::QIF::vProcess(), moose::IzhIF::vProcess(), vProcess(), and vReinit().

double moose::Compartment::Ra_

protected

Definition at line 124 of file Compartment.h.

Referenced by Compartment(), SymCompartment::raxialSphere(), SymCompartment::sumRaxial(), vGetRa(), vHandleAxial(), SymCompartment::vInitProc(), vInitProc(), SymCompartment::vReinit(), and vSetRa().

double moose::Compartment::Rm_

protected

Definition at line 123 of file Compartment.h.

Referenced by Compartment(), vGetRm(), moose::LIF::vProcess(), moose::ExIF::vProcess(), moose::QIF::vProcess(), moose::AdExIF::vProcess(), moose::AdThreshIF::vProcess(), and vSetRm().

double moose::Compartment::sumInject_

protected

Definition at line 130 of file Compartment.h.

Referenced by Compartment(), vInjectMsg(), moose::LIF::vProcess(), moose::ExIF::vProcess(), moose::QIF::vProcess(), moose::AdThreshIF::vProcess(), moose::AdExIF::vProcess(), moose::IzhIF::vProcess(), vProcess(), vRandInject(), and vReinit().

double moose::Compartment::Vm_

protected

Definition at line 119 of file Compartment.h.

Referenced by Compartment(), SymCompartment::raxialCylinder(), SymCompartment::raxialSphere(), SymCompartment::raxialSym(), vGetVm(), vHandleAxial(), vHandleRaxial(), SymCompartment::vInitProc(), vInitProc(), moose::LIF::vProcess(), moose::ExIF::vProcess(), moose::QIF::vProcess(), moose::AdThreshIF::vProcess(), moose::AdExIF::vProcess(), moose::IzhIF::vProcess(), vProcess(), vReinit(), and vSetVm().

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The documentation for this class was generated from the following files:

• moose-core/biophysics/Compartment.h
• moose-core/biophysics/Compartment.cpp