Numerical integration according to the cash-karp-5 algorithm. This algorithm automatically generates the time step. (Ref. https://arxiv.org/pdf/1309.2710.pdf, https://doi.org/10.1016/j.jcp.2013.09.025) More...

#include <CashKarp5.h>

Inheritance diagram for Scine::Kinetx::CashKarp5:

Collaboration diagram for Scine::Kinetx::CashKarp5:

Public Member Functions
	CashKarp5 (Network &net)
	Constructor. More...

void	propagateY (Eigen::VectorXd &y, double &t, double &dt) const overridefinal
	Propagate the concentration. More...

Public Member Functions inherited from Scine::Kinetx::RungeKutta
	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...

Additional Inherited Members
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)

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

Numerical integration according to the cash-karp-5 algorithm. This algorithm automatically generates the time step. (Ref. https://arxiv.org/pdf/1309.2710.pdf, https://doi.org/10.1016/j.jcp.2013.09.025)

Constructor & Destructor Documentation

Scine::Kinetx::CashKarp5::CashKarp5 ( Network & net )

Constructor.

Parameters

net	The network of reactions.

Member Function Documentation

void Scine::Kinetx::CashKarp5::propagateY	(	Eigen::VectorXd &	concentrations,
		double &	t,
		double &	dt
	)		const

finaloverridevirtual

Propagate the concentration.

Parameters

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

Implements Scine::Kinetx::RungeKutta.

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

src/Kinetx/Kinetx/Integrator/CashKarp5.h
src/Kinetx/Kinetx/Integrator/CashKarp5.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation