Reac.cpp

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2010 Upinder S. Bhalla. and NCBS
** It is made available under the terms of the
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/

#include "header.h"
#include "ElementValueFinfo.h"
#include "lookupVolumeFromMesh.h"
#include "ReacBase.h"
#include "Reac.h"

#define EPSILON 1e-15

const Cinfo* Reac::initCinfo()
{
        // 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;
}

static const Cinfo* reacCinfo = Reac::initCinfo();

static const SrcFinfo2< double, double >* subOut =
    dynamic_cast< const SrcFinfo2< double, double >* >(
                    reacCinfo->findFinfo( "subOut" ) );

static const SrcFinfo2< double, double >* prdOut =
    dynamic_cast< const SrcFinfo2< double, double >* >(
                    reacCinfo->findFinfo( "prdOut" ) );

// Reac internal functions


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

/*
Reac::Reac( double kf, double kb )
    : kf_( kf ), kb_( kb ), concKf_( 0.1 ), concKb_( 0.2 ),
        sub_( 0.0 ), prd_( 0.0 )
{
    ;
}
*/

// MsgDest Definitions

void Reac::vSub( double v )
{
    sub_ *= v;
}

void Reac::vPrd( double v )
{
    prd_ *= v;
}

void Reac::vProcess( const Eref& e, ProcPtr p )
{
    prdOut->send( e, sub_, prd_ );
    subOut->send( e, prd_, sub_ );

    sub_ = kf_;
    prd_ = kb_;
}

void Reac::vReinit( const Eref& e, ProcPtr p )
{
    sub_ = kf_ = concKf_ /
        convertConcToNumRateUsingMesh( e, subOut, 0 );
    prd_ = kb_ = concKb_ /
        convertConcToNumRateUsingMesh( e, prdOut, 0 );
}

void Reac::vRemesh( const Eref& e )
{
    kf_ = concKf_ / convertConcToNumRateUsingMesh( e, subOut, 0 );
    kb_ = concKb_ / convertConcToNumRateUsingMesh( e, prdOut, 0 );
}

// Field Definitions

void Reac::vSetNumKf( const Eref& e, double v )
{
    sub_ = kf_ = v;
    double volScale = convertConcToNumRateUsingMesh( e, subOut, false );
    concKf_ = kf_ * volScale;
}

double Reac::vGetNumKf( const Eref& e) const
{
    double kf = concKf_ / convertConcToNumRateUsingMesh( e, subOut, false );
    return kf;
}

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

double Reac::vGetNumKb( const Eref& e ) const
{
    double kb = concKb_ / convertConcToNumRateUsingMesh( e, prdOut, 0 );
    return kb;
}

void Reac::vSetConcKf( const Eref& e, double v )
{
    concKf_ = v;
    sub_ = kf_ = v / convertConcToNumRateUsingMesh( e, subOut, 0 );
}

double Reac::vGetConcKf( const Eref& e ) const
{
    return concKf_;
}

void Reac::vSetConcKb( const Eref& e, double v )
{
    concKb_ = v;
    prd_ = kb_ = v / convertConcToNumRateUsingMesh( e, prdOut, 0 );
}

double Reac::vGetConcKb( const Eref& e ) const
{
    return concKb_;
}