VoxelPoolsBase Class Reference

#include <VoxelPoolsBase.h>

Inheritance diagram for VoxelPoolsBase:

Collaboration diagram for VoxelPoolsBase:

Public Member Functions
	VoxelPoolsBase ()
virtual	~VoxelPoolsBase ()
void	resizeArrays (unsigned int totNumPools)
unsigned int	size () const
const double *	S () const
vector< double > &	Svec ()
	Returns a handle to the mol # vector.
double *	varS ()
const double *	Sinit () const
double *	varSinit ()
void	reinit ()
void	setVolume (double vol)
	Just assigns the volume without any cascading to other values.
double	getVolume () const
	Return the volume of the voxel.
virtual void	setVolumeAndDependencies (double vol)
void	setN (unsigned int i, double v)
double	getN (unsigned int) const
void	setNinit (unsigned int, double v)
double	getNinit (unsigned int) const
void	setDiffConst (unsigned int, double v)
double	getDiffConst (unsigned int) const
virtual void	updateAllRateTerms (const vector< RateTerm * > &rates, unsigned int numCoreRates)=0
virtual void	updateRateTerms (const vector< RateTerm * > &rates, unsigned int numCoreRates, unsigned int index)=0
void	filterCrossRateTerms (const vector< Id > &offSolverReacs, const vector< pair< Id, Id > > &offSolverReacCompts)
void	xferIn (const vector< unsigned int > &poolIndex, const vector< double > &values, const vector< double > &lastValues, unsigned int voxelIndex)
void	xferInOnlyProxies (const vector< unsigned int > &poolIndex, const vector< double > &values, unsigned int numProxyPools, unsigned int voxelIndex)
void	xferOut (unsigned int voxelIndex, vector< double > &values, const vector< unsigned int > &poolIndex)
	Assembles data values for sending out for x-compt reacs.
void	addProxyVoxy (unsigned int comptIndex, Id comptId, unsigned int voxel)
	Adds the index of a voxel to which proxy data should go.
void	addProxyTransferIndex (unsigned int comptIndex, unsigned int transferIndex)
bool	hasXfer (unsigned int comptIndex) const
	True when this voxel has data to be transferred.
bool	isVoxelJunctionPresent (Id i1, Id i2) const
void	resetXreacScale (unsigned int size)
void	forwardReacVolumeFactor (unsigned int i, double volume)
void	backwardReacVolumeFactor (unsigned int i, double volume)
double	getXreacScaleSubstrates (unsigned int i) const
double	getXreacScaleProducts (unsigned int i) const
void	scaleVolsBufsRates (double ratio, const Stoich *stoichPtr)
void	print () const
	Debugging utility.
Protected Attributes
const Stoich *	stoichPtr_
vector< RateTerm * >	rates_

Constructor & Destructor Documentation

VoxelPoolsBase::VoxelPoolsBase ( )

VoxelPoolsBase::~VoxelPoolsBase ( ) [virtual]

Member Function Documentation

void VoxelPoolsBase::addProxyTransferIndex	(	unsigned int	comptIndex,
		unsigned int	transferIndex
	)

void VoxelPoolsBase::addProxyVoxy	(	unsigned int	comptIndex,
		Id	comptId,
		unsigned int	voxel
	)

Adds the index of a voxel to which proxy data should go.

void VoxelPoolsBase::backwardReacVolumeFactor	(	unsigned int	i,
		double	volume
	)

Multiply in scale factor for different cross-reac volumes, to be applied to specified RateTerm in the rates_ vector. Applies to backward reaction terms

References getVolume().

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void VoxelPoolsBase::filterCrossRateTerms	(	const vector< Id > &	offSolverReacs,
		const vector< pair< Id, Id > > &	offSolverReacCompts
	)

Changes cross rate terms to zero if there is no junction

void VoxelPoolsBase::forwardReacVolumeFactor	(	unsigned int	i,
		double	volume
	)

Multiply in scale factor for different cross-reac volumes, to be applied to specified RateTerm in the rates_ vector. Applies to forward reaction terms

References getVolume().

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double VoxelPoolsBase::getDiffConst ( unsigned int i ) const

double VoxelPoolsBase::getN ( unsigned int i ) const

double VoxelPoolsBase::getNinit ( unsigned int i ) const

double VoxelPoolsBase::getVolume ( ) const

Return the volume of the voxel.

Referenced by backwardReacVolumeFactor(), forwardReacVolumeFactor(), and scaleVolsBufsRates().

double VoxelPoolsBase::getXreacScaleProducts ( unsigned int i ) const

Return scale factor for specified entry on rate terms. Index is # of cross-compartment rate term.

Referenced by scaleVolsBufsRates().

double VoxelPoolsBase::getXreacScaleSubstrates ( unsigned int i ) const

Return scale factor for specified entry on rate terms. Index is # of cross-compartment rate term.

Referenced by scaleVolsBufsRates().

bool VoxelPoolsBase::hasXfer ( unsigned int comptIndex ) const

True when this voxel has data to be transferred.

Assigns the Id and volume of the specified x-reac coupled compartment void setComptVolume( unsigned int comptIndex, Id id, double vol );

References size().

Referenced by ZombiePoolInterface::assignXferVoxels().

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bool VoxelPoolsBase::isVoxelJunctionPresent	(	Id	i1,
		Id	i2
	)			const

True when there is a junction. i1 must match, and if i2 is non-zero then it too must match.

void VoxelPoolsBase::print ( ) const

Debugging utility.

Reimplemented in VoxelPools.

void VoxelPoolsBase::reinit ( )

Assigns S = Sinit and sets up initial dt.

Referenced by VoxelPools::reinit(), GssaVoxelPools::reinit(), and VoxelPools::setStoich().

void VoxelPoolsBase::resetXreacScale ( unsigned int size )

Initialize/reset the vector xReacScaling_ for scale factors for each cross reaction in this voxel.

void VoxelPoolsBase::resizeArrays ( unsigned int totNumPools )

Allocate # of pools

Using the computed array sizes, now allocate space for them.

const double * VoxelPoolsBase::S ( ) const

Returns the array of doubles of current mol s at the specified mesh index

Referenced by GssaVoxelPools::refreshAtot().

void VoxelPoolsBase::scaleVolsBufsRates	(	double	ratio,
		const Stoich *	stoichPtr
	)

References Stoich::getNumCoreRates(), Stoich::getRateTerms(), getVolume(), getXreacScaleProducts(), getXreacScaleSubstrates(), and rates_.

Referenced by Stoich::scaleBufsAndRates().

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void VoxelPoolsBase::setDiffConst	(	unsigned int	i,
		double	v
	)

void VoxelPoolsBase::setN	(	unsigned int	i,
		double	v
	)

void VoxelPoolsBase::setNinit	(	unsigned int	i,
		double	v
	)

void VoxelPoolsBase::setVolume ( double vol )

Just assigns the volume without any cascading to other values.

Referenced by ZombiePoolInterface::setCompartment(), and SteadyState::setStoich().

void VoxelPoolsBase::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 in GssaVoxelPools, and VoxelPools.

const double * VoxelPoolsBase::Sinit ( ) const

Returns the array of doubles of initial mol s at the specified mesh index

unsigned int VoxelPoolsBase::size ( ) const

Returns # of pools

Referenced by hasXfer().

vector< double > & VoxelPoolsBase::Svec ( )

Returns a handle to the mol # vector.

Referenced by GssaVoxelPools::advance().

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

Reassign entire rate vector.

Implemented in GssaVoxelPools, and VoxelPools.

virtual void VoxelPoolsBase::updateRateTerms	(	const vector< RateTerm * > &	rates,
		unsigned int	numCoreRates,
		unsigned int	index
	)			`[pure 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.

Implemented in GssaVoxelPools, and VoxelPools.

double * VoxelPoolsBase::varS ( )

Returns the array of doubles of current mol s at the specified mesh index. Dangerous, allows one to modify the values.

Referenced by VoxelPools::advance(), GssaVoxelPools::advance(), GssaVoxelPools::reinit(), GssaVoxelPools::updateDependentMathExpn(), and GssaVoxelPools::xferIn().

double * VoxelPoolsBase::varSinit ( )

Returns the array of doubles of initial mol s at the specified mesh index, as a writable array.

void VoxelPoolsBase::xferIn	(	const vector< unsigned int > &	poolIndex,
		const vector< double > &	values,
		const vector< double > &	lastValues,
		unsigned int	voxelIndex
	)

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

void VoxelPoolsBase::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 in GssaVoxelPools.

void VoxelPoolsBase::xferOut	(	unsigned int	voxelIndex,
		vector< double > &	values,
		const vector< unsigned int > &	poolIndex
	)

Assembles data values for sending out for x-compt reacs.

Member Data Documentation

vector< RateTerm* > VoxelPoolsBase::rates_ [protected]

Referenced by GssaVoxelPools::getReacVelocity(), VoxelPools::print(), scaleVolsBufsRates(), VoxelPools::updateRates(), GssaVoxelPools::~GssaVoxelPools(), and VoxelPools::~VoxelPools().

const Stoich* VoxelPoolsBase::stoichPtr_ [protected]

Referenced by VoxelPools::gslFunc(), VoxelPools::print(), VoxelPools::setStoich(), GssaVoxelPools::setStoich(), VoxelPools::setVolumeAndDependencies(), GssaVoxelPools::setVolumeAndDependencies(), and VoxelPools::updateRates().

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

ksolve/VoxelPoolsBase.h
ksolve/VoxelPoolsBase.cpp

VoxelPoolsBase Class Reference

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation