Inheritance diagram for Scine::Kinetx::IntegratorBase:

Collaboration diagram for Scine::Kinetx::IntegratorBase:

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

virtual void	propagate (Eigen::VectorXd &concentrations, Eigen::VectorXd &yFlux, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, double &t, double &dt) const =0
	Propagate the numerical integration by one time step. 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
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
static double	fast_pow (const double &x, const int &n)

Protected Attributes
Network &	_net

Constructor & Destructor Documentation

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

Constructor.

Parameters

net	The network of reactions.

Member Function Documentation

Eigen::MatrixXd Scine::Kinetx::IntegratorBase::f ( const Eigen::VectorXd & concentrations ) const

protected

Calculate the reaction rates f for each reaction using a mass-weight ansatz. This returns a matrix in case several elementary steps are used for at least one reaction. Otherwise, this matrix will have only one column. Hence, it will generally be densely populated.

Parameters

concentrations The current concentrations.

Returns: The reaction rates as a vector/matrix.

std::pair< Eigen::MatrixXd, Eigen::MatrixXd > Scine::Kinetx::IntegratorBase::fDirected ( const Eigen::VectorXd & concentrations ) const

protected

The same as f(..) but keeping track on the directions.

Parameters

concentrations The concentration.

Returns: The forward and backward reaction rates.

Eigen::MatrixXd Scine::Kinetx::IntegratorBase::fFlux	(	const Eigen::VectorXd &	concentrationsT0,
		const Eigen::VectorXd &	concentrationsT1
	)		const

protected

Calculate the total edge flux gradient.

Parameters

concentrationsT0	The original concentration.
concentrationsT1	The updated concentration.

Returns: The total edge flux.

std::tuple< Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd > Scine::Kinetx::IntegratorBase::fFluxDirected	(	const Eigen::VectorXd &	concentrationsT0,
		const Eigen::VectorXd &	concentrationsT1
	)		const

protected

Calculate the edge flux while keeping track on the direction.

Parameters

concentrationsT0	The original concentration.
concentrationsT1	The updated concentration.

Returns: The total, forward, and backward flux (in this order) as a tuple.

Eigen::VectorXd Scine::Kinetx::IntegratorBase::g ( const Eigen::VectorXd & concentrations ) const

protected

Calculate the concentration gradient.

Parameters

concentrations The current concentration.

Returns: The concentration gradient.

Eigen::VectorXd Scine::Kinetx::IntegratorBase::gFlux	(	const Eigen::VectorXd &	concentrationsT0,
		const Eigen::VectorXd &	concentrationsT1,
		Eigen::VectorXd &	flux,
		Eigen::VectorXd &	forwardFlux,
		Eigen::VectorXd &	backwardFlux
	)		const

protected

Calculate the concentration flux gradient.

Parameters

concentrationsT0	The original concentraion.
concentrationsT1	The updated concentation.
flux	The total reaction edge flux.
forwardFlux	The reaction edge forward flux.
backwardFlux	The reaction edge backward flux.

Returns: The vertex flux gradient.

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

pure 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::Integrator.

Implemented in Scine::Kinetx::Cvode::Impl, and Scine::Kinetx::RungeKutta.

Eigen::MatrixXd Scine::Kinetx::IntegratorBase::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`
	)

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.

Implements Scine::Kinetx::Integrator.

Eigen::MatrixXd Scine::Kinetx::IntegratorBase::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`
	)

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.

Implements Scine::Kinetx::Integrator.

void Scine::Kinetx::IntegratorBase::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

protected

Keep track on the vertex and edge fluxes.

Parameters

y	The concentration after concentration propagation.
yInitial	The original concentration.
yFlux	The vertex flux. Updated inplace.
rFlux	The total edge flux.
rForwardFlux	The forward edge flux.
rBackwardFlux	The backward edge flux.
dt	The time increment.

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

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

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation