ZombieReac Class Reference

#include <ZombieReac.h>

Inheritance diagram for ZombieReac:

Collaboration diagram for ZombieReac:

Public Member Functions
void	setSolver (Id solver, Id orig)
	Assign solver info. More...
double	vGetConcKb (const Eref &e) const
double	vGetConcKf (const Eref &e) const
double	vGetNumKb (const Eref &e) const
double	vGetNumKf (const Eref &e) const
void	vSetConcKb (const Eref &e, double v)
void	vSetConcKf (const Eref &e, double v)
void	vSetNumKb (const Eref &e, double v)
void	vSetNumKf (const Eref &e, double v)
	ZombieReac ()
	~ZombieReac ()
Public Member Functions inherited from ReacBase
double	getConcKb (const Eref &e) const
	get Kb in concentration units More...
double	getConcKf (const Eref &e) const
	get Kf in concentration units More...
double	getNumKb (const Eref &e) const
double	getNumKf (const Eref &e) const
unsigned int	getNumPrd (const Eref &e) const
	Get number of products. More...
unsigned int	getNumSub (const Eref &e) const
	Get number of substrates. More...
void	prd (double v)
void	process (const Eref &e, ProcPtr p)
	ReacBase ()
void	reinit (const Eref &e, ProcPtr p)
void	remesh (const Eref &e)
void	setConcKb (const Eref &e, double v)
	set Kb in concentration units More...
void	setConcKf (const Eref &e, double v)
	set Kf in concentration units More...
void	setNumKb (const Eref &e, double v)
void	setNumKf (const Eref &e, double v)
void	sub (double v)
virtual void	vPrd (double v)
virtual void	vProcess (const Eref &e, ProcPtr p)
virtual void	vReinit (const Eref &e, ProcPtr p)
virtual void	vRemesh (const Eref &e)
virtual void	vSub (double v)
virtual	~ReacBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()
Static Public Member Functions inherited from ReacBase
static const Cinfo *	initCinfo ()
static void	zombify (Element *original, const Cinfo *zClass, Id solver)

Private Attributes
Stoich *	stoich_

Additional Inherited Members
Protected Attributes inherited from ReacBase
double	concKb_
double	concKf_

Detailed Description

Definition at line 13 of file ZombieReac.h.

Constructor & Destructor Documentation

ZombieReac::ZombieReac

(

)

Definition at line 65 of file ZombieReac.cpp.

        : stoich_( 0 )
{;}

ZombieReac::~ZombieReac

(

)

Definition at line 69 of file ZombieReac.cpp.

{;}

Member Function Documentation

const Cinfo * ZombieReac::initCinfo ( )

static

Definition at line 28 of file ZombieReac.cpp.

References ReacBase::initCinfo(), and zombieReacCinfo.

{
        // Field Definitions: All inherited.
        // MsgDest Definitions: All inherited.
        // SharedMsg Definitions: All inherited

    static Dinfo< ZombieReac > dinfo( true );
    static Cinfo zombieReacCinfo (
        "ZombieReac",
        ReacBase::initCinfo(),
        0,
        0,
        &dinfo
    );

    return &zombieReacCinfo;
}

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void ZombieReac::setSolver ( Id  solver, Id  orig  )

virtual

Assign solver info.

Reimplemented from ReacBase.

Definition at line 151 of file ZombieReac.cpp.

References Element::cinfo(), Eref::data(), Id::element(), Id::eref(), Element::getNeighbors(), Stoich::installReaction(), Cinfo::isA(), ReacBase::prd(), stoich_, and ReacBase::sub().

{
    assert( stoich != Id() );

    vector< Id > sub;
    vector< Id > prd;
    orig.element()->getNeighbors( sub, subOut );
    orig.element()->getNeighbors( prd, prdOut );

    assert( stoich.element()->cinfo()->isA( "Stoich" ) );
    stoich_ = reinterpret_cast< Stoich* >( stoich.eref().data( ) );
    stoich_->installReaction( orig, sub, prd );
}

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double ZombieReac::vGetConcKb ( const Eref &  e ) const

virtual

Implements ReacBase.

Definition at line 138 of file ZombieReac.cpp.

References ReacBase::concKb_.

{
    // double volScale = convertConcToNumRateUsingMesh( e, prdOut, 0 );
    // double kb = stoich_->getReacNumKb( e );
    // return kb / volScale;
    return concKb_;
}

double ZombieReac::vGetConcKf ( const Eref &  e ) const

virtual

Implements ReacBase.

Definition at line 127 of file ZombieReac.cpp.

References ReacBase::concKf_.

{
    return concKf_;
}

double ZombieReac::vGetNumKb ( const Eref &  e ) const

virtual

Implements ReacBase.

Definition at line 115 of file ZombieReac.cpp.

References ReacBase::concKb_, and convertConcToNumRateUsingMesh().

{
    double volScale = convertConcToNumRateUsingMesh( e, prdOut, 0 );
    return concKb_ / volScale;
}

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double ZombieReac::vGetNumKf ( const Eref &  e ) const

virtual

Implements ReacBase.

Definition at line 97 of file ZombieReac.cpp.

References ReacBase::concKf_, and convertConcToNumRateUsingMesh().

{
    // Return value for voxel 0. Conceivably I might want to use the
    // DataId part to specify which voxel to use, but that isn't in the
    // current definition for Reacs as being a single entity for the entire
    // compartment.
    double volScale = convertConcToNumRateUsingMesh( e, subOut, 0 );
    return concKf_ / volScale;
}

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void ZombieReac::vSetConcKb ( const Eref &  e, double  v  )

virtual

Implements ReacBase.

Definition at line 132 of file ZombieReac.cpp.

References ReacBase::concKb_, Stoich::setReacKb(), and stoich_.

{
    concKb_ = v;
    stoich_->setReacKb( e, v );
}

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void ZombieReac::vSetConcKf ( const Eref &  e, double  v  )

virtual

Implements ReacBase.

Definition at line 121 of file ZombieReac.cpp.

References ReacBase::concKf_, Stoich::setReacKf(), and stoich_.

{
    concKf_ = v;
    stoich_->setReacKf( e, v );
}

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void ZombieReac::vSetNumKb ( const Eref &  e, double  v  )

virtual

Implements ReacBase.

Definition at line 108 of file ZombieReac.cpp.

References ReacBase::concKb_, convertConcToNumRateUsingMesh(), Stoich::setReacKb(), and stoich_.

{
    double volScale = convertConcToNumRateUsingMesh( e, prdOut, 0 );
    concKb_ = v * volScale;
    stoich_->setReacKb( e, concKb_ );
}

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void ZombieReac::vSetNumKf ( const Eref &  e, double  v  )

virtual

Implements ReacBase.

Definition at line 90 of file ZombieReac.cpp.

References ReacBase::concKf_, convertConcToNumRateUsingMesh(), Stoich::setReacKf(), and stoich_.

{
    double volScale = convertConcToNumRateUsingMesh( e, subOut, 0 );
    concKf_ = v * volScale;
    stoich_->setReacKf( e, concKf_ );
}

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Member Data Documentation

Stoich* ZombieReac::stoich_

private

Definition at line 49 of file ZombieReac.h.

Referenced by setSolver(), vSetConcKb(), vSetConcKf(), vSetNumKb(), and vSetNumKf().

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

• moose-core/ksolve/ZombieReac.h
• moose-core/ksolve/ZombieReac.cpp