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genesis and kkit are reverted back to master.
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Dilawar Singh committed Apr 8, 2020
1 parent 6535c46 commit 0ce71ac
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Showing 13 changed files with 372 additions and 270 deletions.
150 changes: 70 additions & 80 deletions kinetics/Reac.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -17,150 +17,140 @@

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

//////////////////////////////////////////////////////////////
// MsgDest Definitions
//////////////////////////////////////////////////////////////

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

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

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

sub_ = kf_;
prd_ = kb_;
sub_ = kf_;
prd_ = kb_;
}

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

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

//////////////////////////////////////////////////////////////
// Field Definitions
//////////////////////////////////////////////////////////////

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

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

void Reac::vSetNumKb( const Eref& e, double v )
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);
*/
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 volScale = convertConcToNumRateUsingMesh(e, prdOut, false);
concKb_ = kb_ * volScale;
}

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

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

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

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

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

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