moose::CompartmentBase Class Reference

#include <CompartmentBase.h>

Inheritance diagram for moose::CompartmentBase:

Collaboration diagram for moose::CompartmentBase:

Public Member Functions
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 double	vGetCm (const Eref &e) const =0
virtual double	vGetEm (const Eref &e) const =0
virtual double	vGetIm (const Eref &e) const =0
virtual double	vGetInitVm (const Eref &e) const =0
virtual double	vGetInject (const Eref &e) const =0
virtual double	vGetRa (const Eref &e) const =0
virtual double	vGetRm (const Eref &e) const =0
virtual double	vGetVm (const Eref &e) const =0
virtual void	vHandleAxial (double Vm)=0
virtual void	vHandleChannel (const Eref &e, double Gk, double Ek)=0
virtual void	vHandleRaxial (double Ra, double Vm)=0
virtual void	vInitProc (const Eref &e, ProcPtr p)=0
virtual void	vInitReinit (const Eref &e, ProcPtr p)=0
virtual void	vInjectMsg (const Eref &e, double current)=0
virtual void	vProcess (const Eref &e, ProcPtr p)=0
virtual void	vRandInject (const Eref &e, double prob, double current)=0
virtual void	vReinit (const Eref &e, ProcPtr p)=0
virtual void	vSetCm (const Eref &e, double Cm)=0
virtual void	vSetEm (const Eref &e, double Em)=0
virtual void	vSetInitVm (const Eref &e, double initVm)=0
virtual void	vSetInject (const Eref &e, double Inject)=0
virtual void	vSetRa (const Eref &e, double Ra)=0
virtual void	vSetRm (const Eref &e, double Rm)=0
virtual void	vSetSolver (const Eref &e, Id hsolve)
virtual void	vSetVm (const Eref &e, double Vm)=0
virtual	~CompartmentBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()
static SrcFinfo1< double > *	VmOut ()
static void	zombify (Element *orig, const Cinfo *zClass, Id hsolve)

Private Attributes
double	diameter_
double	length_
double	x0_
double	x_
double	y0_
double	y_
double	z0_
double	z_

Detailed Description

Definition at line 30 of file CompartmentBase.h.

Constructor & Destructor Documentation

CompartmentBase::CompartmentBase

(

)

Definition at line 364 of file CompartmentBase.cpp.

References diameter_, length_, x0_, x_, y0_, y_, z0_, and z_.

{
    x_ = 0.0;
    y_ = 0.0;
    z_ = 0.0;
    x0_ = 0.0;
    y0_ = 0.0;
    z0_ = 0.0;
    diameter_ = 0.0;
    length_ = 0.0;
}

CompartmentBase::~CompartmentBase ( )

virtual

Definition at line 376 of file CompartmentBase.cpp.

{
    ;
}

Member Function Documentation

void CompartmentBase::cable

(

)

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

Definition at line 623 of file CompartmentBase.cpp.

Referenced by initCinfo().

{
    ;
}

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void CompartmentBase::displace	(	double	dx,
		double	dy,
		double	dz
	)

Displaces compartment by specified distance vector.

Definition at line 628 of file CompartmentBase.cpp.

References x0_, x_, y0_, y_, z0_, and z_.

Referenced by initCinfo().

{
    x0_ += dx;
    x_ += dx;
    y0_ += dy;
    y_ += dy;
    z0_ += dz;
    z_ += dz;
}

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double CompartmentBase::getCm

(

const Eref &

e

)

const

Definition at line 420 of file CompartmentBase.cpp.

References vGetCm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return vGetCm( e );
}

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double CompartmentBase::getDiameter

(

)

const

Definition at line 477 of file CompartmentBase.cpp.

References diameter_.

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return diameter_;
}

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double CompartmentBase::getEm

(

const Eref &

e

)

const

Definition at line 409 of file CompartmentBase.cpp.

References vGetEm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return vGetEm( e );
}

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double CompartmentBase::getIm

(

const Eref &

e

)

const

Definition at line 447 of file CompartmentBase.cpp.

References vGetIm().

Referenced by initCinfo().

{
    return vGetIm( e );
}

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double CompartmentBase::getInitVm

(

const Eref &

e

)

const

Definition at line 467 of file CompartmentBase.cpp.

References vGetInitVm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return vGetInitVm( e );
}

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double CompartmentBase::getInject

(

const Eref &

e

)

const

Definition at line 457 of file CompartmentBase.cpp.

References vGetInject().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return vGetInject( e );
}

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double CompartmentBase::getLength

(

)

const

Definition at line 497 of file CompartmentBase.cpp.

References length_.

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return length_;
}

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double CompartmentBase::getRa

(

const Eref &

e

)

const

Definition at line 442 of file CompartmentBase.cpp.

References vGetRa().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return vGetRa( e );
}

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double CompartmentBase::getRm

(

const Eref &

e

)

const

Definition at line 431 of file CompartmentBase.cpp.

References vGetRm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return vGetRm( e );
}

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double CompartmentBase::getVm

(

const Eref &

e

)

const

Definition at line 399 of file CompartmentBase.cpp.

References vGetVm().

Referenced by initCinfo().

{
    return vGetVm( e );
}

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double CompartmentBase::getX

(

)

const

Definition at line 547 of file CompartmentBase.cpp.

References x_.

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return x_;
}

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double CompartmentBase::getX0

(

)

const

Definition at line 514 of file CompartmentBase.cpp.

References x0_.

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return x0_;
}

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double CompartmentBase::getY

(

)

const

Definition at line 558 of file CompartmentBase.cpp.

References y_.

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return y_;
}

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double CompartmentBase::getY0

(

)

const

Definition at line 525 of file CompartmentBase.cpp.

References y0_.

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return y0_;
}

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double CompartmentBase::getZ

(

)

const

Definition at line 569 of file CompartmentBase.cpp.

References z_.

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return z_;
}

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double CompartmentBase::getZ0

(

)

const

Definition at line 536 of file CompartmentBase.cpp.

References z0_.

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

{
    return z0_;
}

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void CompartmentBase::handleAxial

(

double

Vm

)

handleAxial handles incoming axial message data.

Definition at line 608 of file CompartmentBase.cpp.

References vHandleAxial().

Referenced by initCinfo().

{
    vHandleAxial( Vm );
}

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

handleChannel handles information coming from the channel to the compartment

Definition at line 598 of file CompartmentBase.cpp.

References vHandleChannel().

Referenced by initCinfo().

{
    vHandleChannel( e, Gk, Ek );
}

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void CompartmentBase::handleRaxial	(	double	Ra,
		double	Vm
	)

handleRaxial handles incoming raxial message data.

Definition at line 603 of file CompartmentBase.cpp.

References vHandleRaxial().

Referenced by initCinfo().

{
    vHandleRaxial( Ra, Vm );
}

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const Cinfo * CompartmentBase::initCinfo ( )

static

Initializes the class info.

The initCinfo() function sets up the CompartmentBase 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 59 of file CompartmentBase.cpp.

References axialOut(), cable(), compartmentCinfo, displace(), getCm(), getDiameter(), getEm(), getIm(), getInitVm(), getInject(), getLength(), getRa(), getRm(), getVm(), getX(), getX0(), getY(), getY0(), getZ(), getZ0(), handleAxial(), handleChannel(), handleRaxial(), init(), Neutral::initCinfo(), initProc(), initReinit(), injectMsg(), process(), randInject(), raxialOut(), reinit(), setCm(), setDiameter(), setEm(), setGeomAndElec(), setInitVm(), setInject(), setLength(), setRa(), setRm(), setVm(), setX(), setX0(), setY(), setY0(), setZ(), setZ0(), and VmOut().

Referenced by moose::Compartment::initCinfo(), and ZombieCompartment::initCinfo().

{
    // Shared messages
    static DestFinfo process( "process",
        "Handles 'process' call",
        new ProcOpFunc< CompartmentBase >( &CompartmentBase::process ) );

    static DestFinfo reinit( "reinit",
        "Handles 'reinit' call",
        new ProcOpFunc< CompartmentBase >( &CompartmentBase::reinit ) );

    static Finfo* processShared[] =
    {
        &process, &reinit
    };

    static SharedFinfo proc( "proc",
        "This is a shared message to receive Process messages from the scheduler"
        "objects. The Process should be called _second_ in each clock tick, after the Init message."
        "The first entry in the shared msg is a MsgDest "
        "for the Process operation. It has a single argument, "
        "ProcInfo, which holds lots of information about current "
        "time, thread, dt and so on. The second entry is a MsgDest "
        "for the Reinit operation. It also uses ProcInfo. "
        "- Handles 'reinit' and 'process' calls.",
        processShared, sizeof( processShared ) / sizeof( Finfo* )
    );

    static DestFinfo initProc( "initProc",
        "Handles Process call for the 'init' phase of the CompartmentBase "
        "calculations. These occur as a separate Tick cycle from the "
        "regular proc cycle, and should be called before the proc msg.",
        new ProcOpFunc< CompartmentBase >( &CompartmentBase::initProc ) );
    static DestFinfo initReinit( "initReinit",
        "Handles Reinit call for the 'init' phase of the CompartmentBase "
        "calculations.",
        new ProcOpFunc< CompartmentBase >( &CompartmentBase::initReinit ) );
    static Finfo* initShared[] =
    {
        &initProc, &initReinit
    };

    static SharedFinfo init( "init",
            "This is a shared message to receive Init messages from "
            "the scheduler objects. Its job is to separate the "
            "compartmental calculations from the message passing. "
            "It doesn't really need to be shared, as it does not use "
            "the reinit part, but the scheduler objects expect this "
            "form of message for all scheduled output. The first "
            "entry is a MsgDest for the Process operation. It has a "
            "single argument, ProcInfo, which holds lots of "
            "information about current time, thread, dt and so on. "
            "The second entry is a dummy MsgDest for the Reinit "
            "operation. It also uses ProcInfo. "
            "- Handles 'initProc' and 'initReinit' calls.",
        initShared, sizeof( initShared ) / sizeof( Finfo* )
    );


    static DestFinfo handleChannel( "handleChannel",
        "Handles conductance and Reversal potential arguments from Channel",
        new EpFunc2< CompartmentBase, double, double >( &CompartmentBase::handleChannel ) );
    // VmOut is declared above as it needs to be in scope for later funcs.

    static Finfo* channelShared[] =
    {
        &handleChannel, CompartmentBase::VmOut()
    };
    static SharedFinfo channel( "channel",
            "This is a shared message from a compartment to channels. "
            "The first entry is a MsgDest for the info coming from "
            "the channel. It expects Gk and Ek from the channel "
            "as args. The second entry is a MsgSrc sending Vm "
            "- Handles 'handleChannel' and 'VmOut' calls.",
        channelShared, sizeof( channelShared ) / sizeof( Finfo* )
    );
    // axialOut declared above as it is needed in file scope
    static DestFinfo handleRaxial( "handleRaxial",
        "Handles Raxial info: arguments are Ra and Vm.",
        new OpFunc2< CompartmentBase, double, double >(
            &CompartmentBase::handleRaxial )
    );

    static Finfo* axialShared[] =
    {
        axialOut(), &handleRaxial
    };
    static SharedFinfo axial( "axial",
            "This is a shared message between asymmetric compartments. "
            "axial messages (this kind) connect up to raxial "
            "messages (defined below). The soma should use raxial "
            "messages to connect to the axial message of all the "
            "immediately adjacent dendritic compartments.This puts "
            "the (low) somatic resistance in series with these "
            "dendrites. Dendrites should then use raxial messages to"
            "connect on to more distal dendrites. In other words, "
            "raxial messages should face outward from the soma. "
            "The first entry is a MsgSrc sending Vm to the axialFunc"
            "of the target compartment. The second entry is a MsgDest "
            "for the info coming from the other compt. It expects "
            "Ra and Vm from the other compt as args. Note that the "
            "message is named after the source type. "
            "- Handles 'axialOut' and 'handleRaxial' calls.",
        axialShared, sizeof( axialShared ) / sizeof( Finfo* )
    );

    static DestFinfo handleAxial( "handleAxial",
        "Handles Axial information. Argument is just Vm.",
        new OpFunc1< CompartmentBase, double >( &CompartmentBase::handleAxial ) );
    // rxialOut declared above as it is needed in file scope
    static Finfo* raxialShared[] =
    {
        &handleAxial, raxialOut()
    };
    static SharedFinfo raxial( "raxial",
            "This is a raxial shared message between asymmetric compartments. The \n"
            "first entry is a MsgDest for the info coming from the other compt. It \n"
            "expects Vm from the other compt as an arg. The second is a MsgSrc sending \n"
            "Ra and Vm to the raxialFunc of the target compartment. \n"
            "- Handles 'handleAxial' and 'raxialOut' calls.",
            raxialShared, sizeof( raxialShared ) / sizeof( Finfo* )
    );
    // Value Finfos.

        static ElementValueFinfo< CompartmentBase, double > Vm( "Vm",
            "membrane potential",
            &CompartmentBase::setVm,
            &CompartmentBase::getVm
        );
        static ElementValueFinfo< CompartmentBase, double > Cm( "Cm",
            "Membrane capacitance",
             &CompartmentBase::setCm,
            &CompartmentBase::getCm
        );
        static ElementValueFinfo< CompartmentBase, double > Em( "Em",
            "Resting membrane potential",
             &CompartmentBase::setEm,
            &CompartmentBase::getEm
        );
        static ReadOnlyElementValueFinfo< CompartmentBase, double > Im( "Im",
            "Current going through membrane",
            &CompartmentBase::getIm
        );
        static ElementValueFinfo< CompartmentBase, double > inject( "inject",
            "Current injection to deliver into compartment",
            &CompartmentBase::setInject,
            &CompartmentBase::getInject
        );
        static ElementValueFinfo< CompartmentBase, double > initVm( "initVm",
            "Initial value for membrane potential",
            &CompartmentBase::setInitVm,
            &CompartmentBase::getInitVm
        );
        static ElementValueFinfo< CompartmentBase, double > Rm( "Rm",
            "Membrane resistance",
            &CompartmentBase::setRm,
            &CompartmentBase::getRm
        );
        static ElementValueFinfo< CompartmentBase, double > Ra( "Ra",
            "Axial resistance of compartment",
            &CompartmentBase::setRa,
            &CompartmentBase::getRa
        );
        static ValueFinfo< CompartmentBase, double > diameter( "diameter",
            "Diameter of compartment",
            &CompartmentBase::setDiameter,
            &CompartmentBase::getDiameter
        );
        static ValueFinfo< CompartmentBase, double > length( "length",
            "Length of compartment",
            &CompartmentBase::setLength,
            &CompartmentBase::getLength
        );
        static ValueFinfo< CompartmentBase, double > x0( "x0",
            "X coordinate of start of compartment",
            &CompartmentBase::setX0,
            &CompartmentBase::getX0
        );
        static ValueFinfo< CompartmentBase, double > y0( "y0",
            "Y coordinate of start of compartment",
            &CompartmentBase::setY0,
            &CompartmentBase::getY0
        );
        static ValueFinfo< CompartmentBase, double > z0( "z0",
            "Z coordinate of start of compartment",
            &CompartmentBase::setZ0,
            &CompartmentBase::getZ0
        );
        static ValueFinfo< CompartmentBase, double > x( "x",
            "x coordinate of end of compartment",
            &CompartmentBase::setX,
            &CompartmentBase::getX
        );
        static ValueFinfo< CompartmentBase, double > y( "y",
            "y coordinate of end of compartment",
            &CompartmentBase::setY,
            &CompartmentBase::getY
        );
        static ValueFinfo< CompartmentBase, double > z( "z",
            "z coordinate of end of compartment",
            &CompartmentBase::setZ,
            &CompartmentBase::getZ
        );

    // DestFinfo definitions
        static DestFinfo injectMsg( "injectMsg",
            "The injectMsg corresponds to the INJECT message in the "
            "GENESIS compartment. Unlike the 'inject' field, any value "
            "assigned by handleInject applies only for a single timestep."
            "So it needs to be updated every dt for a steady (or varying)"
            "injection current",
            new EpFunc1< CompartmentBase,  double >( &CompartmentBase::injectMsg )
        );

        static DestFinfo randInject( "randInject",
            "Sends a random injection current to the compartment. Must be"
            "updated each timestep."
            "Arguments to randInject are probability and current.",
            new EpFunc2< CompartmentBase, double, double > (
                &CompartmentBase::randInject ) );

        static DestFinfo cable( "cable",
            "Message for organizing compartments into groups, called"
            "cables. Doesn't do anything.",
            new OpFunc0< CompartmentBase >( &CompartmentBase::cable )
        );
        static DestFinfo displace( "displace",
            "Displaces compartment by specified vector",
            new OpFunc3< CompartmentBase, double, double, double>(
                    &CompartmentBase::displace )
        );
        static DestFinfo setGeomAndElec( "setGeomAndElec",
            "Assigns length and dia and accounts for any electrical "
            "scaling needed as a result.",
            new EpFunc2< CompartmentBase, double, double>(
                    &CompartmentBase::setGeomAndElec )
        );
    static Finfo* compartmentFinfos[] =
    {
        &Vm,                // Value
        &Cm,                // Value
        &Em,                // Value
        &Im,                // ReadOnlyValue
        &inject,            // Value
        &initVm,            // Value
        &Rm,                // Value
        &Ra,                // Value
        &diameter,          // Value
        &length,            // Value
        &x0,                // Value
        &y0,                // Value
        &z0,                // Value
        &x,                 // Value
        &y,                 // Value
        &z,                 // Value
        &injectMsg,         // DestFinfo
        &randInject,        // DestFinfo
        &injectMsg,         // DestFinfo
        &cable,             // DestFinfo
        &displace,          // DestFinfo
        &setGeomAndElec,    // DestFinfo
        &proc,              // SharedFinfo
        &init,              // SharedFinfo
        &channel,           // SharedFinfo
        &axial,             // SharedFinfo
        &raxial             // SharedFinfo
    };

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

    return &compartmentCinfo;
}

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void CompartmentBase::initProc	(	const Eref &	e,
		ProcPtr	p
	)

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.

Definition at line 588 of file CompartmentBase.cpp.

References vInitProc().

Referenced by initCinfo().

{
    vInitProc( e, p );
}

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void CompartmentBase::initReinit	(	const Eref &	e,
		ProcPtr	p
	)

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

Definition at line 593 of file CompartmentBase.cpp.

References vInitReinit().

Referenced by initCinfo().

{
    vInitReinit( e, p );
}

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void CompartmentBase::injectMsg	(	const Eref &	e,
		double	current
	)

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.

Definition at line 613 of file CompartmentBase.cpp.

References vInjectMsg().

Referenced by initCinfo().

{
    vInjectMsg( e, current );
}

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void CompartmentBase::process	(	const Eref &	e,
		ProcPtr	p
	)

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

Definition at line 578 of file CompartmentBase.cpp.

References vProcess().

Referenced by initCinfo().

{
    vProcess( e, p );
}

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

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.

Definition at line 618 of file CompartmentBase.cpp.

References vRandInject().

Referenced by initCinfo().

{
    vRandInject( e, prob, current );
}

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bool CompartmentBase::rangeWarning	(	const string &	field,
		double	value
	)

A utility function to check for assignment to fields that must be > 0

Definition at line 381 of file CompartmentBase.cpp.

References RANGE.

Referenced by setCm(), setRa(), setRm(), moose::Compartment::vSetCm(), moose::Compartment::vSetRa(), and moose::Compartment::vSetRm().

{
    if ( value < RANGE ) {
        cout << "Warning: Ignored attempt to set " << field <<
                " of compartment " <<
                // c->target().e->name() <<
                " to " << value << " as it is less than " << RANGE << endl;
        return 1;
    }
    return 0;
}

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void CompartmentBase::reinit	(	const Eref &	e,
		ProcPtr	p
	)

The reinit function reinitializes all fields.

Definition at line 583 of file CompartmentBase.cpp.

References vReinit().

Referenced by initCinfo().

{
    vReinit( e, p );
}

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void CompartmentBase::setCm	(	const Eref &	e,
		double	Cm
	)

Definition at line 414 of file CompartmentBase.cpp.

References rangeWarning(), and vSetCm().

Referenced by initCinfo(), makeCompt(), and moose::CompartmentDataHolder::writeData().

{
    if ( rangeWarning( "Cm", Cm ) ) return;
    vSetCm( e, Cm );
}

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void CompartmentBase::setDiameter

(

double

diameter

)

Definition at line 472 of file CompartmentBase.cpp.

References diameter_, and value.

Referenced by initCinfo(), makeCompt(), setGeomAndElec(), and moose::CompartmentDataHolder::writeData().

{
    diameter_ = value;
}

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void CompartmentBase::setEm	(	const Eref &	e,
		double	Em
	)

Definition at line 404 of file CompartmentBase.cpp.

References vSetEm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

{
    vSetEm( e, Em );
}

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void CompartmentBase::setGeomAndElec	(	const Eref &	e,
		double	length,
		double	dia
	)

Scales electrical values along with setting length, dia.

Definition at line 647 of file CompartmentBase.cpp.

References allChildren(), ALLDATA, diameter_, doubleEq(), Field< A >::get(), hasScaleFormula(), length_, Eref::objId(), Field< A >::set(), setDiameter(), setLength(), vGetCm(), vGetRa(), vGetRm(), vSetCm(), vSetRa(), vSetRm(), x0_, x_, y0_, y_, z0_, and z_.

Referenced by initCinfo().

{
    if ( length_ > 0 && diameter_ > 0 && len > 0 && dia > 0 &&
            doubleEq( length_ * length_,
            (x_-x0_)*(x_-x0_) + (y_-y0_)*(y_-y0_) + (z_-z0_)*(z_-z0_) ) ) {
        vSetRm( e, vGetRm( e ) * diameter_ * length_ / ( dia * len ) );
        vSetCm( e, vGetCm( e ) * dia * len / ( diameter_ * length_ ) );
        vSetRa( e, vGetRa( e ) * len * (diameter_ * diameter_) /
                ( length_ * dia * dia ) );
        // Rescale channel Gbars here
        vector< ObjId > chans;
        allChildren( e.objId(), ALLDATA, "ISA=ChanBase", chans );
        for ( unsigned int i = 0; i < chans.size(); ++i ) {
            if ( hasScaleFormula( chans[i].eref() ) )
                continue; // Later we will eval the formula with len and dia
            double gbar = Field< double >::get( chans[i], "Gbar" );
            gbar *= len * dia / ( length_ * diameter_ );
            Field< double >::set( chans[i], "Gbar", gbar );
        }
        // Rescale CaConc sizes here
        vector< ObjId > concs;
        allChildren( e.objId(), ALLDATA, "ISA=CaConcBase", concs );
        for ( unsigned int i = 0; i < concs.size(); ++i ) {
            Field< double >::set( concs[i], "length", len );
            Field< double >::set( concs[i], "diameter", dia );
        }

        setLength( len );
        setDiameter( dia );
    }
}

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void CompartmentBase::setInitVm	(	const Eref &	e,
		double	initVm
	)

Definition at line 462 of file CompartmentBase.cpp.

References vSetInitVm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

{
    vSetInitVm( e, initVm );
}

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void CompartmentBase::setInject	(	const Eref &	e,
		double	Inject
	)

Definition at line 452 of file CompartmentBase.cpp.

References vSetInject().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

{
    vSetInject( e, Inject );
}

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void CompartmentBase::setLength

(

double

length

)

Definition at line 482 of file CompartmentBase.cpp.

References doubleEq(), length_, value, x0_, x_, y0_, y_, z0_, and z_.

Referenced by initCinfo(), makeCompt(), setGeomAndElec(), and moose::CompartmentDataHolder::writeData().

{
    // If length is assigned correctly, also redo the end coords to match.
    if ( value > 0 && length_ > 0 &&
            doubleEq( length_ * length_,
            (x_-x0_)*(x_-x0_) + (y_-y0_)*(y_-y0_) + (z_-z0_)*(z_-z0_) ) ) {
        double ratio = value / length_;
        x_ = x0_ + ratio * ( x_ - x0_ );
        y_ = y0_ + ratio * ( y_ - y0_ );
        z_ = z0_ + ratio * ( z_ - z0_ );
    }

    length_ = value;
}

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void CompartmentBase::setRa	(	const Eref &	e,
		double	Ra
	)

Definition at line 436 of file CompartmentBase.cpp.

References rangeWarning(), and vSetRa().

Referenced by initCinfo(), makeCompt(), and moose::CompartmentDataHolder::writeData().

{
    if ( rangeWarning( "Ra", Ra ) ) return;
    vSetRa( e, Ra );
}

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void CompartmentBase::setRm	(	const Eref &	e,
		double	Rm
	)

Definition at line 425 of file CompartmentBase.cpp.

References rangeWarning(), and vSetRm().

Referenced by initCinfo(), makeCompt(), and moose::CompartmentDataHolder::writeData().

{
    if ( rangeWarning( "Rm", Rm ) ) return;
    vSetRm( e, Rm );
}

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void CompartmentBase::setVm	(	const Eref &	e,
		double	Vm
	)

Definition at line 394 of file CompartmentBase.cpp.

References vSetVm().

Referenced by initCinfo().

{
    vSetVm( e, Vm );
}

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void CompartmentBase::setX

(

double

value

)

Definition at line 541 of file CompartmentBase.cpp.

References updateLength(), value, and x_.

Referenced by initCinfo(), makeCompt(), and moose::CompartmentDataHolder::writeData().

{
    x_ = value;
    updateLength();
}

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void CompartmentBase::setX0

(

double

value

)

Definition at line 508 of file CompartmentBase.cpp.

References updateLength(), value, and x0_.

Referenced by initCinfo(), makeCompt(), and moose::CompartmentDataHolder::writeData().

{
    x0_ = value;
    updateLength();
}

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void CompartmentBase::setY

(

double

value

)

Definition at line 552 of file CompartmentBase.cpp.

References updateLength(), value, and y_.

Referenced by initCinfo(), makeCompt(), and moose::CompartmentDataHolder::writeData().

{
    y_ = value;
    updateLength();
}

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void CompartmentBase::setY0

(

double

value

)

Definition at line 519 of file CompartmentBase.cpp.

References updateLength(), value, and y0_.

Referenced by initCinfo(), makeCompt(), and moose::CompartmentDataHolder::writeData().

{
    y0_ = value;
    updateLength();
}

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void CompartmentBase::setZ

(

double

value

)

Definition at line 563 of file CompartmentBase.cpp.

References updateLength(), value, and z_.

Referenced by initCinfo(), makeCompt(), and moose::CompartmentDataHolder::writeData().

{
    z_ = value;
    updateLength();
}

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void CompartmentBase::setZ0

(

double

value

)

Definition at line 530 of file CompartmentBase.cpp.

References updateLength(), value, and z0_.

Referenced by initCinfo(), makeCompt(), and moose::CompartmentDataHolder::writeData().

{
    z0_ = value;
    updateLength();
}

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void CompartmentBase::updateLength

(

)

A utility function update length if any of the coords change

Definition at line 502 of file CompartmentBase.cpp.

References length_, x0_, x_, y0_, y_, z0_, and z_.

Referenced by setX(), setX0(), setY(), setY0(), setZ(), and setZ0().

{
    length_ = sqrt( (x_-x0_)*(x_-x0_) +
                    (y_-y0_)*(y_-y0_) + (z_-z0_)*(z_-z0_) );
}

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virtual double moose::CompartmentBase::vGetCm ( const Eref &  e ) const

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by getCm(), and setGeomAndElec().

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virtual double moose::CompartmentBase::vGetEm ( const Eref &  e ) const

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by getEm().

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virtual double moose::CompartmentBase::vGetIm ( const Eref &  e ) const

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by getIm().

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virtual double moose::CompartmentBase::vGetInitVm ( const Eref &  e ) const

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by getInitVm().

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virtual double moose::CompartmentBase::vGetInject ( const Eref &  e ) const

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by getInject().

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virtual double moose::CompartmentBase::vGetRa ( const Eref &  e ) const

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by getRa(), and setGeomAndElec().

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virtual double moose::CompartmentBase::vGetRm ( const Eref &  e ) const

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by getRm(), and setGeomAndElec().

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virtual double moose::CompartmentBase::vGetVm ( const Eref &  e ) const

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by getVm().

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virtual void moose::CompartmentBase::vHandleAxial ( double  Vm )

pure virtual

handleAxial handles incoming axial message data.

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by handleAxial().

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virtual void moose::CompartmentBase::vHandleChannel ( const Eref &  e, double  Gk, double  Ek  )

pure virtual

handleChannel handles information coming from the channel to the compartment

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by handleChannel().

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virtual void moose::CompartmentBase::vHandleRaxial ( double  Ra, double  Vm  )

pure virtual

handleRaxial handles incoming raxial message data.

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by handleRaxial().

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virtual void moose::CompartmentBase::vInitProc ( const Eref &  e, ProcPtr  p  )

pure 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.

Implemented in ZombieCompartment, moose::Compartment, and SymCompartment.

Referenced by initProc().

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virtual void moose::CompartmentBase::vInitReinit ( const Eref &  e, ProcPtr  p  )

pure virtual

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

Implemented in ZombieCompartment, moose::Compartment, and SymCompartment.

Referenced by initReinit().

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virtual void moose::CompartmentBase::vInjectMsg ( const Eref &  e, double  current  )

pure 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.

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by injectMsg().

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SrcFinfo1< double > * CompartmentBase::VmOut ( )

static

This Finfo is used to send out Vm to channels, spikegens, etc

It is exposed here so that HSolve can also use it to send out the Vm to the recipients.

Definition at line 26 of file CompartmentBase.cpp.

Referenced by initCinfo(), HSolveActive::sendValues(), moose::LIF::vProcess(), moose::ExIF::vProcess(), moose::QIF::vProcess(), moose::AdExIF::vProcess(), moose::AdThreshIF::vProcess(), moose::IzhIF::vProcess(), moose::Compartment::vProcess(), and moose::Compartment::vReinit().

                                            {
    static SrcFinfo1< double > VmOut( "VmOut",
        "Sends out Vm value of compartment on each timestep" );
    return &VmOut;
}

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virtual void moose::CompartmentBase::vProcess ( const Eref &  e, ProcPtr  p  )

pure virtual

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

Implemented in ZombieCompartment, moose::Compartment, moose::IzhIF, moose::IntFireBase, moose::AdExIF, moose::AdThreshIF, moose::QIF, moose::ExIF, and moose::LIF.

Referenced by process().

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virtual void moose::CompartmentBase::vRandInject ( const Eref &  e, double  prob, double  current  )

pure 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.

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by randInject().

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virtual void moose::CompartmentBase::vReinit ( const Eref &  e, ProcPtr  p  )

pure virtual

The reinit function reinitializes all fields.

Implemented in ZombieCompartment, moose::Compartment, moose::IzhIF, moose::IntFireBase, moose::AdExIF, moose::AdThreshIF, moose::QIF, SymCompartment, moose::ExIF, and moose::LIF.

Referenced by reinit().

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

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by setCm(), and setGeomAndElec().

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

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by setEm().

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

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by setInitVm().

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

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by setInject().

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

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by setGeomAndElec(), and setRa().

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

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by setGeomAndElec(), and setRm().

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void CompartmentBase::vSetSolver ( const Eref &  e, Id  hsolve  )

virtual

Reimplemented in ZombieCompartment.

Definition at line 685 of file CompartmentBase.cpp.

Referenced by zombify().

{;}

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

pure virtual

Implemented in ZombieCompartment, and moose::Compartment.

Referenced by setVm().

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void CompartmentBase::zombify ( Element *  orig, const Cinfo *  zClass, Id  hsolve  )

static

This function is used to swap Cinfos of any CompartmentBase derived class. Used for making ZombieCompartments.

Definition at line 689 of file CompartmentBase.cpp.

References Element::cinfo(), Eref::data(), Element::localDataStart(), Element::numLocalData(), vSetSolver(), and Element::zombieSwap().

{
    if ( orig->cinfo() == zClass )
        return;
    unsigned int start = orig->localDataStart();
    unsigned int num = orig->numLocalData();
    if ( num == 0 )
        return;
    vector< CompartmentDataHolder > cdh( num );

    for ( unsigned int i = 0; i < num; ++i ) {
        Eref er( orig, i + start );
        const CompartmentBase* cb =
            reinterpret_cast< const CompartmentBase* >( er.data() );
        cdh[i].readData( cb, er );
    }
    orig->zombieSwap( zClass );
    for ( unsigned int i = 0; i < num; ++i ) {
        Eref er( orig, i + start );
        CompartmentBase* cb = reinterpret_cast< CompartmentBase* >( er.data() );
        cb->vSetSolver( er, hsolve );
        cdh[i].writeData( cb, er );
    }
}

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Member Data Documentation

double moose::CompartmentBase::diameter_

private

Definition at line 262 of file CompartmentBase.h.

Referenced by CompartmentBase(), getDiameter(), setDiameter(), and setGeomAndElec().

double moose::CompartmentBase::length_

private

Definition at line 263 of file CompartmentBase.h.

Referenced by CompartmentBase(), getLength(), setGeomAndElec(), setLength(), and updateLength().

double moose::CompartmentBase::x0_

private

Definition at line 264 of file CompartmentBase.h.

Referenced by CompartmentBase(), displace(), getX0(), setGeomAndElec(), setLength(), setX0(), and updateLength().

double moose::CompartmentBase::x_

private

Definition at line 267 of file CompartmentBase.h.

Referenced by CompartmentBase(), displace(), getX(), setGeomAndElec(), setLength(), setX(), and updateLength().

double moose::CompartmentBase::y0_

private

Definition at line 265 of file CompartmentBase.h.

Referenced by CompartmentBase(), displace(), getY0(), setGeomAndElec(), setLength(), setY0(), and updateLength().

double moose::CompartmentBase::y_

private

Definition at line 268 of file CompartmentBase.h.

Referenced by CompartmentBase(), displace(), getY(), setGeomAndElec(), setLength(), setY(), and updateLength().

double moose::CompartmentBase::z0_

private

Definition at line 266 of file CompartmentBase.h.

Referenced by CompartmentBase(), displace(), getZ0(), setGeomAndElec(), setLength(), setZ0(), and updateLength().

double moose::CompartmentBase::z_

private

Definition at line 269 of file CompartmentBase.h.

Referenced by CompartmentBase(), displace(), getZ(), setGeomAndElec(), setLength(), setZ(), and updateLength().

---

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

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