Sundials implementation called CVODE. More...

#include <Cvode.h>

Inheritance diagram for Scine::Kinetx::Cvode:

Collaboration diagram for Scine::Kinetx::Cvode:

Public Member Functions
	Cvode (Network &net)
	Constructor. More...

	~Cvode ()
	Destructor.

Eigen::MatrixXd	runIntegrationByTime (Eigen::VectorXd y, double t, double dt, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, const double tMax, const unsigned int batchInterval, const double convergenceConcentrationChange)
	Run the numerical integration until a maximum time or convergence is reached. More...

Eigen::MatrixXd	runIntegration (Eigen::VectorXd y, double t, double dt, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, const unsigned int batchInterval, const unsigned int nBatches, const double convergenceConcentrationChange)
	Run the numerical integration until a maximum number of steps or convergence is reached. More...

void	propagate (Eigen::VectorXd &concentrations, Eigen::VectorXd &yFlux, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, double &t, double &dt) const
	Propagate the numerical integration by one time step. More...

Detailed Description

Sundials implementation called CVODE.

Constructor & Destructor Documentation

Scine::Kinetx::Cvode::Cvode ( Network & net )

Constructor.

Parameters

net	The network of reactions.

void Scine::Kinetx::Cvode::propagate	(	Eigen::VectorXd &	concentrations,
		Eigen::VectorXd &	yFlux,
		Eigen::VectorXd &	rFlux,
		Eigen::VectorXd &	rForwardFlux,
		Eigen::VectorXd &	rBackwardFlux,
		double &	t,
		double &	dt
	)		const

virtual

Propagate the numerical integration by one time step.

Parameters

concentrations	The current concentrations. Updated inplace.
yFlux	The current vertex (aggregate) flux. Updated inplace.
rFlux	The current total edge (reaction) flux. Updated inplace.
rForwardFlux	The current forward edge flux. Updated inplace.
rBackwardFlux	The current backward edge flux. Updated inplace.
t	The current time. Updated inplace.
dt	The time increment. This may be updated inplace depending on the integration algorithm.

Eigen::MatrixXd Scine::Kinetx::Cvode::runIntegration	(	Eigen::VectorXd	y,
		double	tStart,
		double	dt,
		Eigen::VectorXd &	rFlux,
		Eigen::VectorXd &	rForwardFlux,
		Eigen::VectorXd &	rBackwardFlux,
		const unsigned int	batchInterval,
		const unsigned int	nBatches,
		const double	convergenceConcentrationChange
	)

virtual

Run the numerical integration until a maximum number of steps or convergence is reached.

Parameters

y	The input concentration.
tStart	The start time.
dt	The time increment.
rFlux	The reaction edge flux (total).
rForwardFlux	The forward reaction edge flux.
rBackwardFlux	The backward reaction edge flux.
batchInterval	The number of steps per batch.
nBatches	The number of integration batches.
convergenceConcentrationChange	The concentration convergence threshold.

Returns: The final concentrations, max. concentrations, and vertex fluxes as a matrix with columns in this order.

Eigen::MatrixXd Scine::Kinetx::Cvode::runIntegrationByTime	(	Eigen::VectorXd	y,
		double	tStart,
		double	dt,
		Eigen::VectorXd &	rFlux,
		Eigen::VectorXd &	rForwardFlux,
		Eigen::VectorXd &	rBackwardFlux,
		const double	tMax,
		const unsigned int	batchInterval,
		const double	convergenceConcentrationChange
	)

virtual

Run the numerical integration until a maximum time or convergence is reached.

Parameters

y	The input concentration.
tStart	The start time.
dt	The time increment.
rFlux	The reaction edge flux (total).
rForwardFlux	The forward reaction edge flux.
rBackwardFlux	The backward reaction edge flux.
tMax	The final time to integrate to.
batchInterval	The number of steps per batch.
convergenceConcentrationChange	The concentration convergence threshold.

Returns: The final concentrations, max. concentrations, and vertex fluxes as a matrix with columns in this order.

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