Base class for all Runge-Kutta methods/implementations. More...

#include <RungeKutta.h>

Inheritance diagram for Scine::Kinetx::RungeKutta:

Collaboration diagram for Scine::Kinetx::RungeKutta:

Public Member Functions
	RungeKutta (Network &net)
	Constructor. 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...

Public Member Functions inherited from Scine::Kinetx::IntegratorBase
	IntegratorBase (Network &net)
	Constructor. More...

virtual Eigen::MatrixXd	runIntegration (Eigen::VectorXd y, double tStart, double dt, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, const unsigned int batchInterval=1000, const unsigned int nBatches=100000, const double convergenceConcentrationChange=1e-10)
	Run the numerical integration until a maximum number of steps or convergence is reached. More...

virtual Eigen::MatrixXd	runIntegrationByTime (Eigen::VectorXd y, double tStart, double dt, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, const double tMax, const unsigned int batchInterval=1000, const double convergenceConcentrationChange=1e-10)
	Run the numerical integration until a maximum time or convergence is reached. More...

Protected Member Functions
virtual void	propagateY (Eigen::VectorXd &concentrations, double &t, double &dt) const =0
	Propagate the concentration. More...

Protected Member Functions inherited from Scine::Kinetx::IntegratorBase
void	trackVertexAndEdgeFluxes (const Eigen::VectorXd &y, const Eigen::VectorXd &yInitial, Eigen::VectorXd &yFlux, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, const double &dt) const
	Keep track on the vertex and edge fluxes. More...

Eigen::VectorXd	g (const Eigen::VectorXd &concentrations) const
	Calculate the concentration gradient. More...

Eigen::VectorXd	gFlux (const Eigen::VectorXd &concentrationsT0, const Eigen::VectorXd &concentrationsT1, Eigen::VectorXd &flux, Eigen::VectorXd &forwardFlux, Eigen::VectorXd &backwardFlux) const
	Calculate the concentration flux gradient. More...

Eigen::MatrixXd	fFlux (const Eigen::VectorXd &concentrationsT0, const Eigen::VectorXd &concentrationsT1) const
	Calculate the total edge flux gradient. More...

std::tuple< Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd >	fFluxDirected (const Eigen::VectorXd &concentrationsT0, const Eigen::VectorXd &concentrationsT1) const
	Calculate the edge flux while keeping track on the direction. More...

Eigen::MatrixXd	f (const Eigen::VectorXd &concentrations) const

std::pair< Eigen::MatrixXd, Eigen::MatrixXd >	fDirected (const Eigen::VectorXd &concentrations) const
	The same as f(..) but keeping track on the directions. More...

Eigen::SparseMatrix< double >	jacobi (const Eigen::VectorXd &concentrations) const

void	printHeader (const Eigen::VectorXd &y, const double dt, const double t)

bool	printTimeAndCheckConvergenceStep (const Eigen::VectorXd &y, const Eigen::VectorXd &yOld, Eigen::VectorXd &yMax, const unsigned int batchInterval, const unsigned int iBatch, const double dt, const double t, const double convergenceConcentrationChange)

Additional Inherited Members
Static Protected Member Functions inherited from Scine::Kinetx::IntegratorBase
static double	fast_pow (const double &x, const int &n)

Protected Attributes inherited from Scine::Kinetx::IntegratorBase
Network &	_net

Detailed Description

Base class for all Runge-Kutta methods/implementations.

Constructor & Destructor Documentation

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

Constructor.

Parameters

net	The network of reactions.

Member Function Documentation

void Scine::Kinetx::RungeKutta::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.

Implements Scine::Kinetx::IntegratorBase.

virtual void Scine::Kinetx::RungeKutta::propagateY	(	Eigen::VectorXd &	concentrations,
		double &	t,
		double &	dt
	)		const

protectedpure virtual

Propagate the concentration.

Parameters

concentrations	The concentration.
t	The current time.
dt	The time increment.

Implemented in Scine::Kinetx::CashKarp5, Scine::Kinetx::ImplicitEuler, and Scine::Kinetx::ExplicitEuler.

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

src/Kinetx/Kinetx/Integrator/RungeKutta.h
src/Kinetx/Kinetx/Integrator/RungeKutta.cpp

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation