#include <FuncRateTerm.h>

Inheritance diagram for FuncReac:

Collaboration diagram for FuncReac:

Public Member Functions
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const

	FuncReac (double k, vector< unsigned int > v)

unsigned int	getReactants (vector< unsigned int > &molIndex) const

double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array. More...

void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)

void	setReactants (const vector< unsigned int > &molIndex)

Public Member Functions inherited from FuncRate
	FuncRate (double k, unsigned int targetPoolIndex)

const string &	getExpr () const

const vector< unsigned int > &	getFuncArgIndex ()

void	setExpr (const string &s)

void	setFuncArgIndex (const vector< unsigned int > &mol)

void	setReactants (const vector< unsigned int > &molIndex)

Public Member Functions inherited from ExternReac
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const

double	getR1 () const
	Used by Zombie to return rate terms. More...

double	getR2 () const
	Used by Zombie to return rate terms. More...

unsigned int	getReactants (vector< unsigned int > &molIndex) const

double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array. More...

void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)

void	setR1 (double k1)
	Used by Zombie to assign rate terms. More...

void	setR2 (double k2)
	Used by Zombie to assign rate terms. More...

void	setRates (double k1, double k2)

Public Member Functions inherited from RateTerm
	RateTerm ()

virtual	~RateTerm ()

Private Attributes
unsigned int	numSubstrates_

vector< unsigned int >	v_

Additional Inherited Members
Static Public Attributes inherited from RateTerm
static const double	EPSILON = 1.0e-6

Protected Attributes inherited from FuncRate
FuncTerm	func_

double	funcVolPower_

double	k_

Detailed Description

This FuncReac manages a one-way NOrder reaction whose rate is determined by a Function, but which also has regular substrates and products.

dproduct/dt = func( x0, x1, x2..., t ) * [sub0] * [sub1] * ....

The values x0, x1, x2 are expected to be concentrations so that they do not depend on volume. The substrates sub0, sub1, ... are # of molecules. The term k_ is scaled so that it is unity at vol = 1/NA m^3. k_ = (NA * vol)^(numSub-1) The copyWithVolScaling operation scales it up and down from there.

Definition at line 99 of file FuncRateTerm.h.

Constructor & Destructor Documentation

FuncReac::FuncReac	(	double	k,
		vector< unsigned int >	v
	)

inline

Definition at line 102 of file FuncRateTerm.h.

Referenced by copyWithVolScaling().

             : FuncRate( k, 0 ),
             v_( v )
         {;}

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Member Function Documentation

RateTerm* FuncReac::copyWithVolScaling	(	double	vol,
		double	sub,
		double	prd
	)		const

inlinevirtual

Duplicates rate term and then applies volume scaling. Arguments are volume of reference voxel, product of vol/refVol for all substrates: applied to R1 product of vol/refVol for all products: applied to R2

Note that unless the reaction is cross-compartment, the vol/refVol will be one.

Reimplemented from FuncRate.

Definition at line 137 of file FuncRateTerm.h.

References FuncRate::func_, FuncReac(), FuncRate::funcVolPower_, FuncRate::k_, NA, and v_.

         {
             assert( v_.size() > 0 );
             double ratio = sub * pow( NA * vol,
                             funcVolPower_ + (int)( v_.size() ) - 1 );
             FuncReac* ret = new FuncReac( k_ / ratio, v_ );
             ret->func_ = func_;
             ret->funcVolPower_ = funcVolPower_;
             return ret;
             // return new FuncReac( k_ / ratio, v_ );
         }

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unsigned int FuncReac::getReactants ( vector< unsigned int > & molIndex ) const

inlinevirtual

This function finds the reactant indices in the vector S. It returns the number of substrates found, which are the first entries in molIndex. The products are the remaining ones. Note that it does NOT find products for unidirectional reactions, which is a bit of a problem.

Reimplemented from FuncRate.

Definition at line 118 of file FuncRateTerm.h.

References numSubstrates_, and v_.

                                                                            {
             molIndex = v_;
             return numSubstrates_;
         }

double FuncReac::operator() ( const double * S ) const

inlinevirtual

Computes the rate. The argument is the molecule array.

Reimplemented from FuncRate.

Definition at line 107 of file FuncRateTerm.h.

References FuncRate::func_, and v_.

                                                     {
             // double ret = k_ * func_( S, 0.0 ); // get rate from func calculation.
             double ret = func_( S, 0.0 ); // get rate from func calculation.
             vector< unsigned int >::const_iterator i;
             for ( i = v_.begin(); i != v_.end(); i++) {
                 assert( !std::isnan( S[ *i ] ) );
                 ret *= S[ *i ];
             }
             return ret;
         }

void FuncReac::rescaleVolume	(	short	comptIndex,
		const vector< short > &	compartmentLookup,
		double	ratio
	)

inlinevirtual

This is used to rescale the RateTerm kinetics when the compartment volume changes. This is needed because the kinetics are in extensive units, that is, mol numbers, rather than in intensive units like concentration. So when the volume changes the rate terms change. Each Rate term checks if any of its reactant molecules are affected, and if so, rescales. Ratio is newVol / oldVol

Implements RateTerm.

Definition at line 127 of file FuncRateTerm.h.

References FuncRate::k_, and v_.

         {
             for ( unsigned int i = 1; i < v_.size(); ++i ) {
                 if ( comptIndex == compartmentLookup[ v_[i] ] )
                     k_ /= ratio;
             }
         }

void FuncReac::setReactants ( const vector< unsigned int > & molIndex )

inline

Definition at line 123 of file FuncRateTerm.h.

References v_.

                                                                     {
             v_ = molIndex;
         }

Member Data Documentation

unsigned int FuncReac::numSubstrates_

private

Definition at line 152 of file FuncRateTerm.h.

Referenced by getReactants().

vector< unsigned int > FuncReac::v_

private

Definition at line 151 of file FuncRateTerm.h.

Referenced by copyWithVolScaling(), getReactants(), operator()(), rescaleVolume(), and setReactants().

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

moose-core/ksolve/FuncRateTerm.h

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation