Reac Class Reference

#include <Reac.h>

Inheritance diagram for Reac:

Collaboration diagram for Reac:

Public Member Functions
	Reac ()
double	vGetConcKb (const Eref &e) const
	get Kb in concentration units More...
double	vGetConcKf (const Eref &e) const
	vGet Kf in concentration units More...
double	vGetNumKb (const Eref &e) const
double	vGetNumKf (const Eref &e) const
void	vPrd (double v)
void	vProcess (const Eref &e, ProcPtr p)
void	vReinit (const Eref &e, ProcPtr p)
void	vRemesh (const Eref &e)
void	vSetConcKb (const Eref &e, double v)
	set Kb in concentration units More...
void	vSetConcKf (const Eref &e, double v)
	set Kf in concentration units More...
void	vSetNumKb (const Eref &e, double v)
void	vSetNumKf (const Eref &e, double v)
void	vSub (double v)
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)
virtual void	setSolver (Id solver, Id orig)
	Assign solver info. More...
void	sub (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
double	kb_
double	kf_
double	prd_
double	sub_

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

Detailed Description

Definition at line 13 of file Reac.h.

Constructor & Destructor Documentation

Reac::Reac

(

)

Definition at line 56 of file Reac.cpp.

        : kf_( 0.1 ), kb_( 0.2 ), sub_( 0.0 ), prd_( 0.0 )
{
    ;
}

Member Function Documentation

const Cinfo * Reac::initCinfo ( )

static

Definition at line 18 of file Reac.cpp.

References ReacBase::initCinfo(), and reacCinfo.

Referenced by testTwoReacGetNeighbors().

{
        // Field Definitions: All inherited from ReacBase
        // MsgDest Definitions: All inherited
        // Shared Msg Definitions: All inherited.
    static Dinfo< Reac > dinfo;
    static Cinfo reacCinfo (
        "Reac",
        ReacBase::initCinfo(),
        0,
        0,
        &dinfo
    );

    return &reacCinfo;
}

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

virtual

get Kb in concentration units

Implements ReacBase.

Definition at line 163 of file Reac.cpp.

References ReacBase::concKb_.

{
    return concKb_;
}

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

virtual

vGet Kf in concentration units

Implements ReacBase.

Definition at line 152 of file Reac.cpp.

References ReacBase::concKf_.

{
    return concKf_;
}

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

virtual

Implements ReacBase.

Definition at line 140 of file Reac.cpp.

References ReacBase::concKb_, and convertConcToNumRateUsingMesh().

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

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

virtual

Implements ReacBase.

Definition at line 119 of file Reac.cpp.

References ReacBase::concKf_, and convertConcToNumRateUsingMesh().

{
    double kf = concKf_ / convertConcToNumRateUsingMesh( e, subOut, false );
    return kf;
}

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void Reac::vPrd ( double  v )

virtual

Reimplemented from ReacBase.

Definition at line 80 of file Reac.cpp.

References prd_.

{
    prd_ *= v;
}

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

virtual

Reimplemented from ReacBase.

Definition at line 85 of file Reac.cpp.

References kb_, kf_, prd_, SrcFinfo2< T1, T2 >::send(), and sub_.

{
    prdOut->send( e, sub_, prd_ );
    subOut->send( e, prd_, sub_ );

    sub_ = kf_;
    prd_ = kb_;
}

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

virtual

Reimplemented from ReacBase.

Definition at line 94 of file Reac.cpp.

References ReacBase::concKb_, ReacBase::concKf_, convertConcToNumRateUsingMesh(), kb_, kf_, prd_, and sub_.

{
    sub_ = kf_ = concKf_ /
        convertConcToNumRateUsingMesh( e, subOut, 0 );
    prd_ = kb_ = concKb_ /
        convertConcToNumRateUsingMesh( e, prdOut, 0 );
}

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void Reac::vRemesh ( const Eref &  e )

virtual

Reimplemented from ReacBase.

Definition at line 102 of file Reac.cpp.

References ReacBase::concKb_, ReacBase::concKf_, convertConcToNumRateUsingMesh(), kb_, and kf_.

{
    kf_ = concKf_ / convertConcToNumRateUsingMesh( e, subOut, 0 );
    kb_ = concKb_ / convertConcToNumRateUsingMesh( e, prdOut, 0 );
}

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

virtual

set Kb in concentration units

Implements ReacBase.

Definition at line 157 of file Reac.cpp.

References ReacBase::concKb_, convertConcToNumRateUsingMesh(), kb_, and prd_.

{
    concKb_ = v;
    prd_ = kb_ = v / convertConcToNumRateUsingMesh( e, prdOut, 0 );
}

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

virtual

set Kf in concentration units

Implements ReacBase.

Definition at line 146 of file Reac.cpp.

References ReacBase::concKf_, convertConcToNumRateUsingMesh(), kf_, and sub_.

{
    concKf_ = v;
    sub_ = kf_ = v / convertConcToNumRateUsingMesh( e, subOut, 0 );
}

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

virtual

Implements ReacBase.

Definition at line 125 of file Reac.cpp.

References ReacBase::concKb_, convertConcToNumRateUsingMesh(), kb_, and prd_.

{
    prd_ = kb_ = v;
    /*
    double volScale = convertConcToNumRateUsingMesh( e, prdOut, true );
    vector< double > vols;
    getReactantVols( e, subOut, vols );
    assert( vols.size() > 0 );
    volScale /= (vols[0] * NA);
    */

    double volScale = convertConcToNumRateUsingMesh( e, prdOut, false );
    concKb_ = kb_ * volScale;
}

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

virtual

Implements ReacBase.

Definition at line 112 of file Reac.cpp.

References ReacBase::concKf_, convertConcToNumRateUsingMesh(), kf_, and sub_.

{
    sub_ = kf_ = v;
    double volScale = convertConcToNumRateUsingMesh( e, subOut, false );
    concKf_ = kf_ * volScale;
}

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void Reac::vSub ( double  v )

virtual

Reimplemented from ReacBase.

Definition at line 75 of file Reac.cpp.

References sub_.

{
    sub_ *= v;
}

Member Data Documentation

double Reac::kb_

private

Definition at line 51 of file Reac.h.

Referenced by vProcess(), vReinit(), vRemesh(), vSetConcKb(), and vSetNumKb().

double Reac::kf_

private

Definition at line 50 of file Reac.h.

Referenced by vProcess(), vReinit(), vRemesh(), vSetConcKf(), and vSetNumKf().

double Reac::prd_

private

Definition at line 53 of file Reac.h.

Referenced by vPrd(), vProcess(), vReinit(), vSetConcKb(), and vSetNumKb().

double Reac::sub_

private

Definition at line 52 of file Reac.h.

Referenced by vProcess(), vReinit(), vSetConcKf(), vSetNumKf(), and vSub().

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

• moose-core/kinetics/Reac.h
• moose-core/kinetics/Reac.cpp