Inheritance diagram for Scine::Kinetx::Cvode::Impl:

Collaboration diagram for Scine::Kinetx::Cvode::Impl:

Public Member Functions
	Impl (Network &net)

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...

void	propagateY (Eigen::VectorXd &concentrations, double &tStart, double &dt) const

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...

Static Public Member Functions
static int	rhs_func (realtype, N_Vector c, N_Vector g, void *user_data)

Public Attributes
bool	first_run = true

SUNLinearSolver	LS

realtype	abstol = 1e-21

realtype	reltol = 1e-9

sundials::Context	context

N_Vector	y

void *	cvode_mem = NULL

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

Member Function Documentation

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

inlinevirtual

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.

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

src/Kinetx/Kinetx/Integrator/Cvode.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Additional Inherited Members

Member Function Documentation