VoxelPools Class Reference

#include <VoxelPools.h>

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List of all members.

Public Member Functions
	VoxelPools ()
virtual	~VoxelPools ()
void	reinit (double dt)
void	setStoich (Stoich *stoich, const OdeSystem *ode)
void	advance (const ProcInfo *p)
	Do the numerical integration. Advance the simulation.
void	setInitDt (double dt)
	Set initial timestep to use by the solver.
void	setVolumeAndDependencies (double vol)
void	updateAllRateTerms (const vector< RateTerm * > &rates, unsigned int numCoreRates)
	Updates all the rate constants from the reference rates vector.
void	updateRateTerms (const vector< RateTerm * > &rates, unsigned int numCoreRates, unsigned int index)
void	updateRates (const double *s, double *yprime) const
void	updateReacVelocities (const double *s, vector< double > &v) const
void	print () const
	Used for debugging.
Static Public Member Functions
static int	gslFunc (double t, const double *y, double *dydt, void *params)
	This is the function which evaluates the rates.

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Detailed Description

This is the class for handling reac-diff voxels used for deterministic computations.

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Constructor & Destructor Documentation

VoxelPools::VoxelPools

(

)

VoxelPools::~VoxelPools

(

)

[virtual]

References VoxelPoolsBase::rates_.

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Member Function Documentation

void VoxelPools::advance

(

const ProcInfo *

p

)

Do the numerical integration. Advance the simulation.

References ProcInfo::currTime, ProcInfo::dt, and VoxelPoolsBase::varS().

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int VoxelPools::gslFunc	(	double	t,
		const double *	y,
		double *	dydt,
		void *	params
	)			[static]

This is the function which evaluates the rates.

References q, VoxelPoolsBase::stoichPtr_, Stoich::updateFuncs(), and updateRates().

Referenced by Ksolve::setStoich().

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void VoxelPools::print

(

)

const

Used for debugging.

For debugging: Print contents of voxel pool.

Changes cross rate terms to zero if there is no junction void filterCrossRateTerms( const vector< pair< Id, Id > >& vec );

Reimplemented from VoxelPoolsBase.

References Stoich::getNumCoreRates(), VoxelPoolsBase::rates_, and VoxelPoolsBase::stoichPtr_.

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void VoxelPools::reinit

(

double

dt

)

References VoxelPoolsBase::reinit().

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void VoxelPools::setInitDt

(

double

dt

)

Set initial timestep to use by the solver.

void VoxelPools::setStoich	(	Stoich *	stoich,
		const OdeSystem *	ode
	)

setStoich: Assigns the ODE system and Stoich. Stoich may be modified to create a new RateTerm vector in case the volume of this VoxelPools is new.

References OdeSystem::epsAbs, OdeSystem::epsRel, OdeSystem::initStepSize, VoxelPoolsBase::reinit(), and VoxelPoolsBase::stoichPtr_.

Referenced by SteadyState::setStoich().

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void VoxelPools::setVolumeAndDependencies

(

double

vol

)

[virtual]

Handles volume change and subsequent cascading updates.

Handle volume updates. Inherited Virtual func.

Reimplemented from VoxelPoolsBase.

References Stoich::getNumCoreRates(), Stoich::getRateTerms(), Stoich::setupCrossSolverReacVols(), VoxelPoolsBase::stoichPtr_, and updateAllRateTerms().

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void VoxelPools::updateAllRateTerms	(	const vector< RateTerm * > &	rates,
		unsigned int	numCoreRates
	)			[virtual]

Updates all the rate constants from the reference rates vector.

Implements VoxelPoolsBase.

Referenced by SteadyState::setStoich(), and setVolumeAndDependencies().

void VoxelPools::updateRates	(	const double *	s,
		double *	yprime
	)			const

Core computation function. Updates the reaction velocities vector yprime given the current mol 'n' vector s.

References KinSparseMatrix::computeRowRate(), Stoich::getNumAllPools(), Stoich::getNumBufPools(), Stoich::getNumProxyPools(), Stoich::getNumVarPools(), Stoich::getStoichiometryMatrix(), N, SparseMatrix< T >::nColumns(), SparseMatrix< T >::nRows(), VoxelPoolsBase::rates_, and VoxelPoolsBase::stoichPtr_.

Referenced by SteadyState::classifyState(), and gslFunc().

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void VoxelPools::updateRateTerms	(	const vector< RateTerm * > &	rates,
		unsigned int	numCoreRates,
		unsigned int	index
	)			[virtual]

updateRateTerms updates the rate consts of a belonging to the specified index on the rates vector. It does recaling and assigning using values from the internal rates vector.

Implements VoxelPoolsBase.

void VoxelPools::updateReacVelocities	(	const double *	s,
		vector< double > &	v
	)			const

updateReacVelocities computes the velocity *v* of each reaction from the vector *s* of pool s. This is a utility function for programs like SteadyState that need to analyze velocity.

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

• ksolve/VoxelPools.h
• ksolve/VoxelPools.cpp