GssaVoxelPools Class Reference

#include <GssaVoxelPools.h>

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List of all members.

Public Member Functions
	GssaVoxelPools ()
virtual	~GssaVoxelPools ()
void	advance (const ProcInfo *p)
void	updateDependentMathExpn (const GssaSystem *g, unsigned int rindex)
void	updateDependentRates (const vector< unsigned int > &deps, const Stoich *stoich)
unsigned int	pickReac () const
void	setNumReac (unsigned int n)
void	advance (const ProcInfo *p, const GssaSystem *g)
bool	refreshAtot (const GssaSystem *g)
void	reinit (const GssaSystem *g)
void	updateAllRateTerms (const vector< RateTerm * > &rates, unsigned int numCoreRates)
void	updateRateTerms (const vector< RateTerm * > &rates, unsigned int numCoreRates, unsigned int index)
double	getReacVelocity (unsigned int r, const double *s) const
void	updateReacVelocities (const GssaSystem *g, const double *s, vector< double > &v) const
void	setVolumeAndDependencies (double vol)
void	xferIn (XferInfo &xf, unsigned int voxelIndex, const GssaSystem *g)
void	xferInOnlyProxies (const vector< unsigned int > &poolIndex, const vector< double > &values, unsigned int numProxyPools, unsigned int voxelIndex)
void	setStoich (const Stoich *stoichPtr)

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Constructor & Destructor Documentation

GssaVoxelPools::GssaVoxelPools

(

)

GssaVoxelPools::~GssaVoxelPools

(

)

[virtual]

References VoxelPoolsBase::rates_.

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Member Function Documentation

void GssaVoxelPools::advance	(	const ProcInfo *	p,
		const GssaSystem *	g
	)

References ProcInfo::currTime, GssaSystem::dependency, KinSparseMatrix::fireReac(), Stoich::getNumRates(), mtrand(), pickReac(), refreshAtot(), GssaSystem::stoich, VoxelPoolsBase::Svec(), GssaSystem::transposeN, updateDependentMathExpn(), updateDependentRates(), Stoich::updateFuncs(), and VoxelPoolsBase::varS().

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void GssaVoxelPools::advance

(

const ProcInfo *

p

)

double GssaVoxelPools::getReacVelocity	(	unsigned int	r,
		const double *	s
	)			const

References VoxelPoolsBase::rates_.

unsigned int GssaVoxelPools::pickReac

(

)

const

References mtrand().

Referenced by advance().

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bool GssaVoxelPools::refreshAtot

(

const GssaSystem *

g

)

Cleans out all reac rates and recalculates atot. Needed whenever a mol conc changes, or if there is a roundoff error. Returns true if OK, returns false if it is in a stuck state and atot<=0

References VoxelPoolsBase::S(), SAFETY_FACTOR, and updateReacVelocities().

Referenced by advance(), reinit(), and xferIn().

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void GssaVoxelPools::reinit

(

const GssaSystem *

g

)

Builds the gssa system as needed.

References Stoich::getNumVarPools(), mtrand(), refreshAtot(), VoxelPoolsBase::reinit(), GssaSystem::stoich, Stoich::updateFuncs(), GssaSystem::useRandInit, and VoxelPoolsBase::varS().

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void GssaVoxelPools::setNumReac

(

unsigned int

n

)

void GssaVoxelPools::setStoich

(

const Stoich *

stoichPtr

)

References VoxelPoolsBase::stoichPtr_.

void GssaVoxelPools::setVolumeAndDependencies

(

double

vol

)

[virtual]

Assign the volume, and handle the cascading effects by scaling all the dependent values of nInit and rates if applicable.

Reimplemented from VoxelPoolsBase.

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

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

Reassign entire rate vector.

Implements VoxelPoolsBase.

Referenced by setVolumeAndDependencies().

void GssaVoxelPools::updateDependentMathExpn	(	const GssaSystem *	g,
		unsigned int	rindex
	)

References GssaSystem::dependentMathExpn, FuncTerm::evalPool(), Stoich::funcs(), GssaSystem::stoich, and VoxelPoolsBase::varS().

Referenced by advance().

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void GssaVoxelPools::updateDependentRates	(	const vector< unsigned int > &	deps,
		const Stoich *	stoich
	)

Referenced by advance().

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

Update specified index on rate terms. The entire rates vector is passed in for the source values, the index specifies which entry on the local rate vector is to be updated.

Implements VoxelPoolsBase.

void GssaVoxelPools::updateReacVelocities	(	const GssaSystem *	g,
		const double *	s,
		vector< double > &	v
	)			const

Referenced by refreshAtot().

void GssaVoxelPools::xferIn	(	XferInfo &	xf,
		unsigned int	voxelIndex,
		const GssaSystem *	g
	)

Digests incoming data values for cross-compt reactions. Sums the changes in the values onto the specified pools.

References XferInfo::lastValues, refreshAtot(), XferInfo::subzero, XferInfo::values, VoxelPoolsBase::varS(), and XferInfo::xferPoolIdx.

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void GssaVoxelPools::xferInOnlyProxies	(	const vector< unsigned int > &	poolIndex,
		const vector< double > &	values,
		unsigned int	numProxyPools,
		unsigned int	voxelIndex
	)

Used during initialization: Takes only the proxy pool values from the incoming transfer data, and assigns it to the proxy pools on current solver

Reimplemented from VoxelPoolsBase.

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

• ksolve/GssaVoxelPools.h
• ksolve/GssaVoxelPools.cpp