#include <RateTerm.h>

Inheritance diagram for ExternReac:

Collaboration diagram for ExternReac:

Public Member Functions
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 ()

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

Detailed Description

Definition at line 205 of file RateTerm.h.

Member Function Documentation

RateTerm* ExternReac::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.

Implements RateTerm.

Definition at line 245 of file RateTerm.h.

         {
             return new ExternReac();
         }

double ExternReac::getR1 ( ) const

inlinevirtual

Used by Zombie to return rate terms.

Implements RateTerm.

Definition at line 226 of file RateTerm.h.

                              {
             return 0.0;
         }

double ExternReac::getR2 ( ) const

inlinevirtual

Used by Zombie to return rate terms.

Implements RateTerm.

Definition at line 230 of file RateTerm.h.

                              {
             return 0.0;
         }

unsigned int ExternReac::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.

Implements RateTerm.

Definition at line 234 of file RateTerm.h.

                                                                            {
             molIndex.resize( 0 );
             return 0;
         }

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

inlinevirtual

Computes the rate. The argument is the molecule array.

Implements RateTerm.

Definition at line 210 of file RateTerm.h.

                                                     {
             double ret = 0.0;
             return ret;
         }

void ExternReac::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 239 of file RateTerm.h.

         {
             return; // Need to figure out what to do here.
         }

void ExternReac::setR1 ( double k1 )

inlinevirtual

Used by Zombie to assign rate terms.

Implements RateTerm.

Definition at line 218 of file RateTerm.h.

                                 {
             ;
         }

void ExternReac::setR2 ( double k2 )

inlinevirtual

Used by Zombie to assign rate terms.

Implements RateTerm.

Definition at line 222 of file RateTerm.h.

                                 {
             ;
         }

void ExternReac::setRates	(	double	k1,
		double	k2
	)

inlinevirtual

Assign the rates.

Implements RateTerm.

Definition at line 214 of file RateTerm.h.

                                               {
             ; // Dummy function to keep compiler happy
         }

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

moose-core/ksolve/RateTerm.h

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation