Flux Class Reference
#include <RateTerm.h>
Public Member Functions | |
| Flux (double k, unsigned int y) | |
| double | operator() (const double *S) const |
| Computes the rate. The argument is the molecule array. | |
| unsigned int | getReactants (vector< unsigned int > &molIndex) const |
| void | rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio) |
| RateTerm * | copyWithVolScaling (double vol, double sub, double prd) const |
Detailed Description
This rather odd reaction is used when we have an amount y of a molecule and we want it to proceed to zero at a fixed rate k. k would usually be 1/dt. Following dt seconds, we need to update y as it has nominally all been used up.
Constructor & Destructor Documentation
| Flux::Flux | ( | double | k, | |
| unsigned int | y | |||
| ) | [inline] |
Referenced by copyWithVolScaling().
Member Function Documentation
| RateTerm* Flux::copyWithVolScaling | ( | double | vol, | |
| double | sub, | |||
| double | prd | |||
| ) | const [inline, virtual] |
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 ZeroOrder.
References Flux(), and ZeroOrder::k_.
| unsigned int Flux::getReactants | ( | vector< unsigned int > & | molIndex | ) | const [inline, virtual] |
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 ZeroOrder.
| double Flux::operator() | ( | const double * | S | ) | const [inline, virtual] |
Computes the rate. The argument is the molecule array.
Reimplemented from ZeroOrder.
References ZeroOrder::k_.
| void Flux::rescaleVolume | ( | short | comptIndex, | |
| const vector< short > & | compartmentLookup, | |||
| double | ratio | |||
| ) | [inline, virtual] |
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
Reimplemented from ZeroOrder.
The documentation for this class was generated from the following file:
- ksolve/RateTerm.h
