ReacBase Class Reference

#include <ReacBase.h>

Inheritance diagram for ReacBase:

Collaboration diagram for ReacBase:

Public Member Functions
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 double	vGetConcKb (const Eref &e) const =0
virtual double	vGetConcKf (const Eref &e) const =0
virtual double	vGetNumKb (const Eref &e) const =0
virtual double	vGetNumKf (const Eref &e) const =0
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	vSetConcKb (const Eref &e, double v)=0
virtual void	vSetConcKf (const Eref &e, double v)=0
virtual void	vSetNumKb (const Eref &e, double v)=0
virtual void	vSetNumKf (const Eref &e, double v)=0
virtual void	vSub (double v)
virtual	~ReacBase ()

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

Protected Attributes
double	concKb_
double	concKf_

Detailed Description

Definition at line 13 of file ReacBase.h.

Constructor & Destructor Documentation

ReacBase::ReacBase

(

)

Definition at line 164 of file ReacBase.cpp.

    : concKf_( 0.1 ), concKb_( 0.2 )
{
    ;
}

ReacBase::~ReacBase ( )

virtual

Definition at line 170 of file ReacBase.cpp.

{;}

Member Function Documentation

double ReacBase::getConcKb

(

const Eref &

e

)

const

get Kb in concentration units

Definition at line 273 of file ReacBase.cpp.

References vGetConcKb().

Referenced by initCinfo(), and zombify().

{
    return vGetConcKb( e );
}

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double ReacBase::getConcKf

(

const Eref &

e

)

const

get Kf in concentration units

Definition at line 263 of file ReacBase.cpp.

References vGetConcKf().

Referenced by initCinfo(), and zombify().

{
    return vGetConcKf( e );
}

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double ReacBase::getNumKb

(

const Eref &

e

)

const

Definition at line 251 of file ReacBase.cpp.

References vGetNumKb().

Referenced by initCinfo().

{
    return vGetNumKb( e );
}

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double ReacBase::getNumKf

(

const Eref &

e

)

const

Definition at line 241 of file ReacBase.cpp.

References vGetNumKf().

Referenced by initCinfo().

{
    return vGetNumKf( e );
}

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unsigned int ReacBase::getNumPrd

(

const Eref &

e

)

const

Get number of products.

Definition at line 286 of file ReacBase.cpp.

References Eref::element(), Element::getMsgAndFunc(), and prdOut().

Referenced by initCinfo().

{
    const vector< MsgFuncBinding >* mfb =
        e.element()->getMsgAndFunc( prdOut()->getBindIndex() );
    assert( mfb );
    return ( mfb->size() );
}

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unsigned int ReacBase::getNumSub

(

const Eref &

e

)

const

Get number of substrates.

Definition at line 278 of file ReacBase.cpp.

References Eref::element(), Element::getMsgAndFunc(), and subOut().

Referenced by initCinfo().

{
    const vector< MsgFuncBinding >* mfb =
        e.element()->getMsgAndFunc( subOut()->getBindIndex() );
    assert( mfb );
    return ( mfb->size() );
}

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const Cinfo * ReacBase::initCinfo ( )

static

Definition at line 33 of file ReacBase.cpp.

References getConcKb(), getConcKf(), getNumKb(), getNumKf(), getNumPrd(), getNumSub(), Neutral::initCinfo(), prd(), prdOut(), process(), reacBaseCinfo, reinit(), setConcKb(), setConcKf(), setNumKb(), setNumKf(), sub(), and subOut().

Referenced by findParentComptOfReac(), ZombieReac::initCinfo(), and Reac::initCinfo().

{
        // Field Definitions
        static ElementValueFinfo< ReacBase, double > kf(
            "numKf",
            "Forward rate constant, in # units",
            &ReacBase::setNumKf,
            &ReacBase::getNumKf
        );

        static ElementValueFinfo< ReacBase, double > kb(
            "numKb",
            "Reverse rate constant, in # units",
            &ReacBase::setNumKb,
            &ReacBase::getNumKb
        );

        static ElementValueFinfo< ReacBase, double > Kf(
            "Kf",
            "Forward rate constant, in concentration units",
            &ReacBase::setConcKf,
            &ReacBase::getConcKf
        );

        static ElementValueFinfo< ReacBase, double > Kb(
            "Kb",
            "Reverse rate constant, in concentration units",
            &ReacBase::setConcKb,
            &ReacBase::getConcKb
        );

        static ReadOnlyElementValueFinfo< ReacBase, unsigned int > numSub(
            "numSubstrates",
            "Number of substrates of reaction",
            &ReacBase::getNumSub
        );

        static ReadOnlyElementValueFinfo< ReacBase, unsigned int > numPrd(
            "numProducts",
            "Number of products of reaction",
            &ReacBase::getNumPrd
        );

        // MsgDest Definitions
        static DestFinfo process( "process",
            "Handles process call",
            new ProcOpFunc< ReacBase >( &ReacBase::process ) );
        static DestFinfo reinit( "reinit",
            "Handles reinit call",
            new ProcOpFunc< ReacBase >( &ReacBase::reinit ) );

        // Shared Msg Definitions

        static DestFinfo subDest( "subDest",
                "Handles # of molecules of substrate",
                new OpFunc1< ReacBase, double >( &ReacBase::sub ) );
        static DestFinfo prdDest( "prdDest",
                "Handles # of molecules of product",
                new OpFunc1< ReacBase, double >( &ReacBase::prd ) );
        static Finfo* subShared[] = {
            subOut(), &subDest
        };
        static Finfo* prdShared[] = {
            prdOut(), &prdDest
        };
        static SharedFinfo sub( "sub",
            "Connects to substrate pool",
            subShared, sizeof( subShared ) / sizeof( const Finfo* )
        );
        static SharedFinfo prd( "prd",
            "Connects to substrate pool",
            prdShared, sizeof( prdShared ) / sizeof( const Finfo* )
        );
        static Finfo* procShared[] = {
            &process, &reinit
        };
        static SharedFinfo proc( "proc",
            "Shared message for process and reinit",
            procShared, sizeof( procShared ) / sizeof( const Finfo* )
        );


    static Finfo* reacFinfos[] = {
        &kf,    // Value
        &kb,    // Value
        &Kf,    // Value
        &Kb,    // Value
        &numSub,    // ReadOnlyValue
        &numPrd,    // ReadOnlyValue
        &sub,               // SharedFinfo
        &prd,               // SharedFinfo
        &proc,              // SharedFinfo
    };

    static string doc[] =
    {
        "Name", "ReacBase",
        "Author", "Upinder S. Bhalla, 2012, NCBS",
        "Description", "Base class for reactions. Provides the MOOSE API"
        "functions, but ruthlessly refers almost all of them to derived"
        "classes, which have to provide the man page output."
    };

    static ZeroSizeDinfo< int> dinfo;
    static Cinfo reacBaseCinfo (
        "ReacBase",
        Neutral::initCinfo(),
        reacFinfos,
        sizeof( reacFinfos ) / sizeof ( Finfo* ),
        &dinfo,
        doc,
        sizeof( doc ) / sizeof( string ),
        true // Ban creation, this is an abstract base class.
    );

    return &reacBaseCinfo;
}

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void ReacBase::prd

(

double

v

)

Definition at line 182 of file ReacBase.cpp.

References vPrd().

Referenced by initCinfo(), and ZombieReac::setSolver().

{
    vPrd( v );
}

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

Definition at line 187 of file ReacBase.cpp.

References vProcess().

Referenced by initCinfo().

{
    vProcess( e, p );
}

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

Definition at line 192 of file ReacBase.cpp.

References vReinit().

Referenced by initCinfo().

{
    vReinit( e, p );
}

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void ReacBase::remesh

(

const Eref &

e

)

Definition at line 197 of file ReacBase.cpp.

References vRemesh().

{
    vRemesh( e );
}

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void ReacBase::setConcKb	(	const Eref &	e,
		double	v
	)

set Kb in concentration units

Definition at line 268 of file ReacBase.cpp.

References vSetConcKb().

Referenced by initCinfo(), and zombify().

{
    vSetConcKb( e, v );
}

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void ReacBase::setConcKf	(	const Eref &	e,
		double	v
	)

set Kf in concentration units

Definition at line 258 of file ReacBase.cpp.

References vSetConcKf().

Referenced by initCinfo(), and zombify().

{
    vSetConcKf( e, v );
}

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void ReacBase::setNumKb	(	const Eref &	e,
		double	v
	)

Definition at line 246 of file ReacBase.cpp.

References vSetNumKb().

Referenced by initCinfo().

{
    vSetNumKb( e, v );
}

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void ReacBase::setNumKf	(	const Eref &	e,
		double	v
	)

Definition at line 236 of file ReacBase.cpp.

References vSetNumKf().

Referenced by initCinfo().

{
    vSetNumKf( e, v );
}

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

virtual

Assign solver info.

Reimplemented in ZombieReac.

Definition at line 327 of file ReacBase.cpp.

Referenced by zombify().

{
    ;
}

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void ReacBase::sub

(

double

v

)

Definition at line 177 of file ReacBase.cpp.

References vSub().

Referenced by initCinfo(), and ZombieReac::setSolver().

{
    vSub( v );
}

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virtual double ReacBase::vGetConcKb ( const Eref &  e ) const

pure virtual

Implemented in Reac, and ZombieReac.

Referenced by getConcKb().

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virtual double ReacBase::vGetConcKf ( const Eref &  e ) const

pure virtual

Implemented in Reac, and ZombieReac.

Referenced by getConcKf().

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virtual double ReacBase::vGetNumKb ( const Eref &  e ) const

pure virtual

Implemented in Reac, and ZombieReac.

Referenced by getNumKb().

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virtual double ReacBase::vGetNumKf ( const Eref &  e ) const

pure virtual

Implemented in Reac, and ZombieReac.

Referenced by getNumKf().

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void ReacBase::vPrd ( double  v )

virtual

Reimplemented in Reac.

Definition at line 212 of file ReacBase.cpp.

Referenced by prd().

{
        ;
}

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

virtual

Reimplemented in Reac.

Definition at line 217 of file ReacBase.cpp.

Referenced by process().

{
        ;
}

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

virtual

Reimplemented in Reac.

Definition at line 222 of file ReacBase.cpp.

Referenced by reinit().

{
        ;
}

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void ReacBase::vRemesh ( const Eref &  e )

virtual

Reimplemented in Reac.

Definition at line 227 of file ReacBase.cpp.

Referenced by remesh().

{
        ;
}

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

pure virtual

Implemented in Reac, and ZombieReac.

Referenced by setConcKb().

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

pure virtual

Implemented in Reac, and ZombieReac.

Referenced by setConcKf().

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

pure virtual

Implemented in Reac, and ZombieReac.

Referenced by setNumKb().

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

pure virtual

Implemented in Reac, and ZombieReac.

Referenced by setNumKf().

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void ReacBase::vSub ( double  v )

virtual

Reimplemented in Reac.

Definition at line 207 of file ReacBase.cpp.

Referenced by sub().

{
        ;
}

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void ReacBase::zombify ( Element *  original, const Cinfo *  zClass, Id  solver  )

static

Zombification functions.

Definition at line 299 of file ReacBase.cpp.

References Element::cinfo(), Eref::data(), getConcKb(), getConcKf(), Element::id(), Element::localDataStart(), Element::numLocalData(), setConcKb(), setConcKf(), setSolver(), and Element::zombieSwap().

Referenced by Stoich::unZombifyModel(), and Stoich::zombifyModel().

{
    if ( orig->cinfo() == zClass )
        return;
    unsigned int start = orig->localDataStart();
    unsigned int num = orig->numLocalData();
    if ( num == 0 )
            return;
    vector< double > concKf( num, 0.0 );
    vector< double > concKb( num, 0.0 );
    for ( unsigned int i = 0; i < num; ++i ) {
        Eref er( orig, i + start );
        const ReacBase* rb =
            reinterpret_cast< const ReacBase* >( er.data() );
        concKf[ i ] = rb->getConcKf( er );
        concKb[ i ] = rb->getConcKb( er );
    }
    orig->zombieSwap( zClass );
    for ( unsigned int i = 0; i < num; ++i ) {
        Eref er( orig, i + start );
        ReacBase* rb = reinterpret_cast< ReacBase* >( er.data() );
        rb->setSolver( solver, orig->id() );
        rb->setConcKf( er, concKf[i] );
        rb->setConcKb( er, concKb[i] );
    }
}

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Member Data Documentation

double ReacBase::concKb_

protected

Definition at line 87 of file ReacBase.h.

Referenced by ZombieReac::vGetConcKb(), Reac::vGetConcKb(), ZombieReac::vGetNumKb(), Reac::vGetNumKb(), Reac::vReinit(), Reac::vRemesh(), ZombieReac::vSetConcKb(), Reac::vSetConcKb(), Reac::vSetNumKb(), and ZombieReac::vSetNumKb().

double ReacBase::concKf_

protected

Definition at line 86 of file ReacBase.h.

Referenced by ZombieReac::vGetConcKf(), Reac::vGetConcKf(), ZombieReac::vGetNumKf(), Reac::vGetNumKf(), Reac::vReinit(), Reac::vRemesh(), ZombieReac::vSetConcKf(), Reac::vSetConcKf(), Reac::vSetNumKf(), and ZombieReac::vSetNumKf().

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

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