ZombiePoolInterface Class Reference

#include <ZombiePoolInterface.h>

Inheritance diagram for ZombiePoolInterface:

Collaboration diagram for ZombiePoolInterface:

Public Member Functions
	ZombiePoolInterface ()
virtual void	setNinit (const Eref &e, double val)=0
	Set initial # of molecules in given pool and voxel. Bdry cond.
virtual double	getNinit (const Eref &e) const =0
	get initial # of molecules in given pool and voxel. Bdry cond.
virtual void	setN (const Eref &e, double val)=0
	Set # of molecules in given pool and voxel. Varies with time.
virtual double	getN (const Eref &e) const =0
	Get # of molecules in given pool and voxel. Varies with time.
virtual void	setDiffConst (const Eref &e, double val)=0
	Diffusion constant: Only one per pool, voxel number is ignored.
virtual double	getDiffConst (const Eref &e) const =0
	Diffusion constant: Only one per pool, voxel number is ignored.
virtual void	setMotorConst (const Eref &e, double val)
virtual void	setNumPools (unsigned int num)=0
	Specifies number of pools (species) handled by system.
virtual unsigned int	getNumPools () const =0
	gets number of pools (species) handled by system.
virtual void	setNumAllVoxels (unsigned int numVoxels)=0
	Assign number of voxels (size of pools_ vector ).
virtual unsigned int	getNumLocalVoxels () const =0
	Number of voxels here. pools_.size() == getNumLocalVoxels.
virtual VoxelPoolsBase *	pools (unsigned int i)=0
	Return a pointer to the specified VoxelPool.
virtual double	volume (unsigned int i) const =0
	Return volume of voxel i.
virtual void	getBlock (vector< double > &values) const =0
virtual void	setBlock (const vector< double > &values)=0
virtual void	setStoich (Id stoich)=0
virtual void	setDsolve (Id dsolve)=0
	Assigns the diffusion solver. Used by the reac solvers.
virtual void	setCompartment (Id compartment)
	Assigns compartment.
Id	getCompartment () const
void	setupCrossSolverReacs (const map< Id, vector< Id > > &xr, Id otherStoich)
	Sets up cross-solver reactions.
void	setupCrossSolverReacVols (const vector< vector< Id > > &subCompts, const vector< vector< Id > > &prdCompts)
void	filterCrossRateTerms (const vector< Id > &xreacs, const vector< pair< Id, Id > > &xrt)
virtual void	updateRateTerms (unsigned int index=~0U)=0
virtual unsigned int	getPoolIndex (const Eref &er) const =0
	Return pool index, using Stoich ptr to do lookup.
void	xComptIn (const Eref &e, Id srcZombiePoolInterface, vector< double > values)
void	assignXferVoxels (unsigned int xferCompt)
void	assignXferIndex (unsigned int numProxyMols, unsigned int xferCompt, const vector< vector< unsigned int > > &voxy)
void	setupXfer (Id myZombiePoolInterface, Id otherZombiePoolInterface, unsigned int numProxyMols, const vector< VoxelJunction > &vj)
unsigned int	assignProxyPools (const map< Id, vector< Id > > &xr, Id myZombiePoolInterface, Id otherZombiePoolInterface, Id otherComptId)
void	matchJunctionVols (vector< double > &vols, Id otherComptId) const
Protected Attributes
Id	stoich_
Id	compartment_
	Id of Chem compartment used to figure out volumes of voxels.
vector< XferInfo >	xfer_
bool	isBuilt_
	Flag: True when solver setup has been completed.

Detailed Description

This pure virtual base class is for solvers that want to talk to the zombie pool. The Eref specifies both the pool identity and the voxel number within the pool.

Constructor & Destructor Documentation

ZombiePoolInterface::ZombiePoolInterface ( )

Member Function Documentation

unsigned int ZombiePoolInterface::assignProxyPools	(	const map< Id, vector< Id > > &	xr,
		Id	myZombiePoolInterface,
		Id	otherZombiePoolInterface,
		Id	otherComptId
	)

Reimplemented in Ksolve.

void ZombiePoolInterface::assignXferIndex	(	unsigned int	numProxyMols,
		unsigned int	xferCompt,
		const vector< vector< unsigned int > > &	voxy
	)

Reimplemented in Ksolve.

void ZombiePoolInterface::assignXferVoxels ( unsigned int xferCompt )

Figures out which voxels are involved in cross-compt reactions. Stores in the appropriate xfer_ entry.

Reimplemented in Ksolve.

References getNumLocalVoxels(), VoxelPoolsBase::hasXfer(), pools(), and xfer_.

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void ZombiePoolInterface::filterCrossRateTerms	(	const vector< Id > &	xreacs,
		const vector< pair< Id, Id > > &	xrt
	)

Referenced by Stoich::filterXreacs().

virtual void ZombiePoolInterface::getBlock ( vector< double > & values ) const [pure virtual]

Gets block of data. The first 4 entries are passed in on the 'values' vector: the start voxel, numVoxels, start pool#, numPools. These are followed by numVoxels * numPools of data values which are filled in by the function. We assert that the entire requested block is present in this ZombiePoolInterface. The block is organized as an array of arrays of voxels; values[pool#][voxel#]

Note that numVoxels and numPools are the number in the current block, not the upper limit of the block. So values.size() == 4 + numPools * numVoxels.

Implemented in Gsolve, and Ksolve.

Referenced by Ksolve::process(), and Gsolve::process().

Id ZombiePoolInterface::getCompartment ( ) const

Reimplemented in Gsolve.

References compartment_.

Referenced by Ksolve::initCinfo().

virtual double ZombiePoolInterface::getDiffConst ( const Eref & e ) const [pure virtual]

Diffusion constant: Only one per pool, voxel number is ignored.

Implemented in Gsolve, and Ksolve.

virtual double ZombiePoolInterface::getN ( const Eref & e ) const [pure virtual]

Get # of molecules in given pool and voxel. Varies with time.

Implemented in Gsolve, and Ksolve.

Referenced by ZombiePool::vGetN().

virtual double ZombiePoolInterface::getNinit ( const Eref & e ) const [pure virtual]

get initial # of molecules in given pool and voxel. Bdry cond.

Implemented in Gsolve, and Ksolve.

Referenced by ZombiePool::vGetNinit().

virtual unsigned int ZombiePoolInterface::getNumLocalVoxels ( ) const [pure virtual]

Number of voxels here. pools_.size() == getNumLocalVoxels.

Implemented in Gsolve, and Ksolve.

Referenced by assignXferVoxels().

virtual unsigned int ZombiePoolInterface::getNumPools ( ) const [pure virtual]

gets number of pools (species) handled by system.

Implemented in Gsolve, and Ksolve.

virtual unsigned int ZombiePoolInterface::getPoolIndex ( const Eref & er ) const [pure virtual]

Return pool index, using Stoich ptr to do lookup.

Implemented in Gsolve, and Ksolve.

void ZombiePoolInterface::matchJunctionVols	(	vector< double > &	vols,
		Id	otherComptId
	)			const

Reimplemented in Ksolve.

virtual VoxelPoolsBase* ZombiePoolInterface::pools ( unsigned int i ) [pure virtual]

Return a pointer to the specified VoxelPool.

Implemented in Gsolve, and Ksolve.

Referenced by assignXferVoxels(), Stoich::scaleBufsAndRates(), and setCompartment().

virtual void ZombiePoolInterface::setBlock ( const vector< double > & values ) [pure virtual]

Sets block of data. The first 4 entries on the 'values' vector are the start voxel, numVoxels, start pool#, numPools. These are followed by numVoxels * numPools of data values.

Implemented in Gsolve, and Ksolve.

Referenced by Ksolve::process(), and Gsolve::process().

void ZombiePoolInterface::setCompartment ( Id compartment ) [virtual]

Assigns compartment.

Reimplemented in Gsolve.

References Element::cinfo(), compartment_, Id::element(), Cinfo::isA(), isBuilt_, pools(), setNumAllVoxels(), and VoxelPoolsBase::setVolume().

Referenced by Ksolve::initCinfo().

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virtual void ZombiePoolInterface::setDiffConst	(	const Eref &	e,
		double	val
	)			`[pure virtual]`

Diffusion constant: Only one per pool, voxel number is ignored.

Implemented in Gsolve, and Ksolve.

Referenced by ZombiePool::vSetDiffConst().

virtual void ZombiePoolInterface::setDsolve ( Id dsolve ) [pure virtual]

Assigns the diffusion solver. Used by the reac solvers.

Implemented in Gsolve, and Ksolve.

virtual void ZombiePoolInterface::setMotorConst	(	const Eref &	e,
		double	val
	)			`[inline, virtual]`

Motor constant: Only one per pool, voxel number is ignored. Used only in Dsolves, so here I put in a dummy.

Referenced by ZombiePool::vSetMotorConst().

virtual void ZombiePoolInterface::setN	(	const Eref &	e,
		double	val
	)			`[pure virtual]`

Set # of molecules in given pool and voxel. Varies with time.

Implemented in Gsolve, and Ksolve.

Referenced by ZombiePool::vSetN().

virtual void ZombiePoolInterface::setNinit	(	const Eref &	e,
		double	val
	)			`[pure virtual]`

Set initial # of molecules in given pool and voxel. Bdry cond.

Implemented in Gsolve, and Ksolve.

Referenced by ZombiePool::vSetNinit().

virtual void ZombiePoolInterface::setNumAllVoxels ( unsigned int numVoxels ) [pure virtual]

Assign number of voxels (size of pools_ vector ).

Implemented in Gsolve, and Ksolve.

Referenced by setCompartment().

virtual void ZombiePoolInterface::setNumPools ( unsigned int num ) [pure virtual]

Specifies number of pools (species) handled by system.

Implemented in Gsolve, and Ksolve.

Referenced by Stoich::resizeArrays().

virtual void ZombiePoolInterface::setStoich ( Id stoich ) [pure virtual]

Informs the ZPI about the stoich, used during subsequent computations. Called to wrap up the model building. The Stoich does this call after it has set up its own path.

Implemented in Gsolve, and Ksolve.

void ZombiePoolInterface::setupCrossSolverReacs	(	const map< Id, vector< Id > > &	xr,
		Id	otherStoich
	)

Sets up cross-solver reactions.

Referenced by Stoich::buildXreacs().

void ZombiePoolInterface::setupCrossSolverReacVols	(	const vector< vector< Id > > &	subCompts,
		const vector< vector< Id > > &	prdCompts
	)

Referenced by Stoich::setupCrossSolverReacVols().

void ZombiePoolInterface::setupXfer	(	Id	myZombiePoolInterface,
		Id	otherZombiePoolInterface,
		unsigned int	numProxyMols,
		const vector< VoxelJunction > &	vj
	)

Reimplemented in Ksolve.

virtual void ZombiePoolInterface::updateRateTerms ( unsigned int index = ~0U ) [pure virtual]

Informs the solver that the rate terms or volumes have changed and that the parameters must be updated. The index specifies which rateTerm to change, and if it is ~0U it means update all of them.

Implemented in Gsolve, and Ksolve.

Referenced by Stoich::setEnzK1(), Stoich::setEnzK2(), Stoich::setEnzK3(), Stoich::setMMenzKcat(), Stoich::setMMenzKm(), Stoich::setReacKb(), and Stoich::setReacKf().

virtual double ZombiePoolInterface::volume ( unsigned int i ) const [pure virtual]

Return volume of voxel i.

Implemented in Gsolve, and Ksolve.