ZombieCompartment Class Reference

#include <ZombieCompartment.h>

Inheritance diagram for ZombieCompartment:

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Public Member Functions
void	dummy (const Eref &e, ProcPtr p)
double	mtrand (void)
double	vGetCm (const Eref &e) const
double	vGetEm (const Eref &e) const
double	vGetIm (const Eref &e) const
double	vGetInitVm (const Eref &e) const
double	vGetInject (const Eref &e) const
double	vGetRa (const Eref &e) const
double	vGetRm (const Eref &e) const
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)
void	vSetCm (const Eref &e, double Cm)
void	vSetEm (const Eref &e, double Em)
void	vSetInitVm (const Eref &e, double initVm)
void	vSetInject (const Eref &e, double Inject)
void	vSetRa (const Eref &e, double Ra)
void	vSetRm (const Eref &e, double Rm)
void	vSetSolver (const Eref &e, Id hsolve)
	Assigns the solver to the zombie. More...
void	vSetVm (const Eref &e, double Vm)
	ZombieCompartment ()
virtual	~ZombieCompartment ()
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	~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)

Private Member Functions
void	copyFields (moose::Compartment *c)

Private Attributes
HSolve *	hsolve_
moose::RNG< double >	rng

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

Detailed Description

Zombie object that lets HSolve do its calculations, while letting the user interact with this object as if it were the original object.

Definition at line 35 of file ZombieCompartment.h.

Constructor & Destructor Documentation

ZombieCompartment::ZombieCompartment

(

)

Definition at line 58 of file ZombieCompartment.cpp.

{
    hsolve_   = NULL;
}

ZombieCompartment::~ZombieCompartment ( )

virtual

Definition at line 63 of file ZombieCompartment.cpp.

{
    ;
}

Member Function Documentation

void ZombieCompartment::copyFields ( moose::Compartment *  c )

private

void ZombieCompartment::dummy	(	const Eref &	e,
		ProcPtr	p
	)

const Cinfo * ZombieCompartment::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 24 of file ZombieCompartment.cpp.

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

Referenced by HSolve::zombify().

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

    static string doc[] =
    {
        "Name", "ZombieCompartment",
        "Author", "Upi Bhalla",
        "Description", "Compartment object, for branching neuron models.",
    };

    static Dinfo< ZombieCompartment > dinfo;
    static Cinfo zombieCompartmentCinfo(
        "ZombieCompartment",
        CompartmentBase::initCinfo(),
        0,
        0,
        // compartmentFinfos,
        // sizeof( compartmentFinfos ) / sizeof( Finfo* ),
        &dinfo,
        doc,
        sizeof( doc )/ sizeof( string )
    );

    return &zombieCompartmentCinfo;
}

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double ZombieCompartment::mtrand

(

void

)

Definition at line 217 of file ZombieCompartment.cpp.

References moose::rng, and moose::RNG< T >::uniform().

{
    return rng.uniform( );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 97 of file ZombieCompartment.cpp.

References Eref::id().

{
    return hsolve_->getCm( e.id() );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 86 of file ZombieCompartment.cpp.

References Eref::id().

{
    return hsolve_->getEm( e.id() );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 129 of file ZombieCompartment.cpp.

References Eref::id().

{
    return hsolve_->getIm( e.id() );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 149 of file ZombieCompartment.cpp.

References Eref::id().

{
    return hsolve_->getInitVm( e.id() );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 139 of file ZombieCompartment.cpp.

References Eref::id().

{
    return hsolve_->getInject( e.id() );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 119 of file ZombieCompartment.cpp.

References Eref::id().

{
    return hsolve_->getRa( e.id() );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 108 of file ZombieCompartment.cpp.

References Eref::id().

{
    return hsolve_->getRm( e.id() );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 75 of file ZombieCompartment.cpp.

References Eref::id().

{
    assert(hsolve_);
    return hsolve_->getVm( e.id() );
}

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void ZombieCompartment::vHandleAxial ( double  Vm )

virtual

handleAxial handles incoming axial message data.

Implements moose::CompartmentBase.

Definition at line 188 of file ZombieCompartment.cpp.

{
    ;
}

void ZombieCompartment::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 178 of file ZombieCompartment.cpp.

References Eref::id().

{
    hsolve_->addGkEk( e.id(), Gk, Ek );
}

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

virtual

handleRaxial handles incoming raxial message data.

Implements moose::CompartmentBase.

Definition at line 183 of file ZombieCompartment.cpp.

{
    ;
}

void ZombieCompartment::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.

Definition at line 168 of file ZombieCompartment.cpp.

{
    ;
}

void ZombieCompartment::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.

Definition at line 173 of file ZombieCompartment.cpp.

{
    ;
}

void ZombieCompartment::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 193 of file ZombieCompartment.cpp.

References Eref::id().

{
    hsolve_->addInject( e.id(), current );
}

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void ZombieCompartment::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.

Definition at line 158 of file ZombieCompartment.cpp.

{
    ;
}

void ZombieCompartment::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 198 of file ZombieCompartment.cpp.

{
    //~ if ( mtrand() < prob * dt_ ) {
    //~ hsolve_->addInject( e.id(), current );
    //~ }
}

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

virtual

The reinit function reinitializes all fields.

Implements moose::CompartmentBase.

Definition at line 163 of file ZombieCompartment.cpp.

References moose::__rng_seed__, moose::rng, and moose::RNG< T >::setSeed().

{
    rng.setSeed( moose::__rng_seed__ );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 91 of file ZombieCompartment.cpp.

References Eref::id().

{
    if ( rangeWarning( "Cm", Cm ) ) return;
    hsolve_->setCm( e.id(), Cm );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 81 of file ZombieCompartment.cpp.

References Eref::id().

{
    hsolve_->setEm( e.id(), Em );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 144 of file ZombieCompartment.cpp.

References Eref::id().

{
    hsolve_->setInitVm( e.id(), initVm );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 134 of file ZombieCompartment.cpp.

References Eref::id().

{
    hsolve_->setInject( e.id(), Inject );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 113 of file ZombieCompartment.cpp.

References Eref::id().

{
    if ( rangeWarning( "Ra", Ra ) ) return;
    hsolve_->setRa( e.id(), Ra );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 102 of file ZombieCompartment.cpp.

References Eref::id().

{
    if ( rangeWarning( "Rm", Rm ) ) return;
    hsolve_->setRm( e.id(), Rm );
}

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

virtual

Assigns the solver to the zombie.

Reimplemented from moose::CompartmentBase.

Definition at line 206 of file ZombieCompartment.cpp.

References Element::cinfo(), Eref::data(), Id::element(), Id::eref(), Cinfo::isA(), and Id::path().

{
    if ( !hsolve.element()->cinfo()->isA( "HSolve" ) ) {
        cout << "Error: ZombieCompartment::vSetSolver: Object: " <<
                hsolve.path() << " is not an HSolve. Aborted\n";
        hsolve_ = 0;
        return;
    }
    hsolve_ = reinterpret_cast< HSolve* >( hsolve.eref().data() );
}

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

virtual

Implements moose::CompartmentBase.

Definition at line 69 of file ZombieCompartment.cpp.

References Eref::id().

{
    assert(hsolve_);
    hsolve_->setVm( e.id(), Vm );
}

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Member Data Documentation

const double ZombieCompartment::EPSILON = 1.0e-15

staticprivate

Definition at line 143 of file ZombieCompartment.h.

HSolve* ZombieCompartment::hsolve_

private

Definition at line 141 of file ZombieCompartment.h.

moose::RNG<double> ZombieCompartment::rng

private

Definition at line 147 of file ZombieCompartment.h.

---

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

• moose-core/hsolve/ZombieCompartment.h
• moose-core/hsolve/ZombieCompartment.cpp