PoolBase Class Reference

#include <PoolBase.h>

Inheritance diagram for PoolBase:

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List of all members.

Public Member Functions
	PoolBase ()
virtual	~PoolBase ()
void	setN (const Eref &e, double v)
double	getN (const Eref &e) const
void	setNinit (const Eref &e, double v)
double	getNinit (const Eref &e) const
void	setDiffConst (const Eref &e, double v)
double	getDiffConst (const Eref &e) const
void	setMotorConst (const Eref &e, double v)
double	getMotorConst (const Eref &e) const
void	setConc (const Eref &e, double v)
double	getConc (const Eref &e) const
void	setConcInit (const Eref &e, double v)
double	getConcInit (const Eref &e) const
void	setVolume (const Eref &e, double v)
double	getVolume (const Eref &e) const
void	setSpecies (const Eref &e, SpeciesId v)
SpeciesId	getSpecies (const Eref &e) const
virtual void	vSetN (const Eref &e, double v)=0
virtual double	vGetN (const Eref &e) const =0
virtual void	vSetNinit (const Eref &e, double v)=0
virtual double	vGetNinit (const Eref &e) const =0
virtual void	vSetDiffConst (const Eref &e, double v)=0
virtual double	vGetDiffConst (const Eref &e) const =0
virtual void	vSetMotorConst (const Eref &e, double v)
	Dummy MotorConst field for most Pool subclasses.
virtual double	vGetMotorConst (const Eref &e) const
virtual void	vSetConc (const Eref &e, double v)=0
virtual double	vGetConc (const Eref &e) const =0
virtual void	vSetConcInit (const Eref &e, double v)=0
virtual double	vGetVolume (const Eref &e) const =0
virtual void	vSetVolume (const Eref &e, double v)=0
virtual void	vSetSpecies (const Eref &e, SpeciesId v)=0
virtual SpeciesId	vGetSpecies (const Eref &e) const =0
virtual void	vSetSolver (Id ksolve, Id dsolve)
void	process (const Eref &e, ProcPtr p)
void	reinit (const Eref &e, ProcPtr p)
void	reac (double A, double B)
void	handleMolWt (const Eref &e, double v)
virtual void	vProcess (const Eref &e, ProcPtr p)
virtual void	vReinit (const Eref &e, ProcPtr p)
virtual void	vReac (double A, double B)
virtual void	vHandleMolWt (const Eref &e, double v)
Static Public Member Functions
static void	zombify (Element *original, const Cinfo *zClass, Id ksolve, Id dsolve)
static const Cinfo *	initCinfo ()
Friends
void	testSyncArray (unsigned int size, unsigned int numThreads, unsigned int method)
void	checkVal (double time, const PoolBase *m, unsigned int size)
void	forceCheckVal (double time, Element *e, unsigned int size)

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Detailed Description

The PoolBase class is the base class for molecular pools. A pool is a set of molecules of a given species, in a uniform chemical context. Note that the same species might be present in other compartments, or be handled by other solvers. PoolBase is the base class for mass-action, single particle and other numerical variants of pools.

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Constructor & Destructor Documentation

PoolBase::PoolBase

(

)

PoolBase::~PoolBase

(

)

[virtual]

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Member Function Documentation

double PoolBase::getConc

(

const Eref &

e

)

const

References vGetConc().

Referenced by initCinfo().

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double PoolBase::getConcInit

(

const Eref &

e

)

const

Referenced by initCinfo(), and zombify().

double PoolBase::getDiffConst

(

const Eref &

e

)

const

References vGetDiffConst().

Referenced by initCinfo(), and zombify().

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double PoolBase::getMotorConst

(

const Eref &

e

)

const

References vGetMotorConst().

Referenced by initCinfo(), and zombify().

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double PoolBase::getN

(

const Eref &

e

)

const

References vGetN().

Referenced by initCinfo().

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double PoolBase::getNinit

(

const Eref &

e

)

const

References vGetNinit().

Referenced by initCinfo(), and Pool::vReinit().

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unsigned int PoolBase::getSpecies

(

const Eref &

e

)

const

References vGetSpecies().

Referenced by initCinfo(), and zombify().

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double PoolBase::getVolume

(

const Eref &

e

)

const

References vGetVolume().

Referenced by initCinfo().

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void PoolBase::handleMolWt	(	const Eref &	e,
		double	v
	)

References vHandleMolWt().

Referenced by initCinfo().

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const Cinfo * PoolBase::initCinfo

(

)

[static]

Reimplemented in BufPool, Pool, ZombieBufPool, and ZombiePool.

References getConc(), getConcInit(), getDiffConst(), getMotorConst(), getN(), getNinit(), getSpecies(), getVolume(), handleMolWt(), Neutral::initCinfo(), nOut, process(), reac(), reinit(), setConc(), setConcInit(), setDiffConst(), setMotorConst(), setN(), setNinit(), setSpecies(), and setVolume().

Referenced by getSlaveEnable(), ZombiePool::initCinfo(), and Pool::initCinfo().

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void PoolBase::process	(	const Eref &	e,
		ProcPtr	p
	)

References vProcess().

Referenced by initCinfo().

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void PoolBase::reac	(	double	A,
		double	B
	)

References vReac().

Referenced by initCinfo().

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void PoolBase::reinit	(	const Eref &	e,
		ProcPtr	p
	)

References vReinit().

Referenced by initCinfo().

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void PoolBase::setConc	(	const Eref &	e,
		double	v
	)

References vSetConc().

Referenced by initCinfo().

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void PoolBase::setConcInit	(	const Eref &	e,
		double	v
	)

References vSetConcInit().

Referenced by initCinfo(), and zombify().

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void PoolBase::setDiffConst	(	const Eref &	e,
		double	v
	)

References vSetDiffConst().

Referenced by initCinfo(), and zombify().

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void PoolBase::setMotorConst	(	const Eref &	e,
		double	v
	)

References vSetMotorConst().

Referenced by initCinfo(), and zombify().

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void PoolBase::setN	(	const Eref &	e,
		double	v
	)

References vSetN().

Referenced by initCinfo().

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void PoolBase::setNinit	(	const Eref &	e,
		double	v
	)

References lookupVolumeFromMesh(), NA, and vSetNinit().

Referenced by initCinfo().

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void PoolBase::setSpecies	(	const Eref &	e,
		SpeciesId	v
	)

References vSetSpecies().

Referenced by initCinfo(), and zombify().

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void PoolBase::setVolume	(	const Eref &	e,
		double	v
	)

Volume is usually volume, but we also permit areal density This is obtained by looking up the corresponding spatial mesh entry in the parent compartment. If the message isn't set then it defaults to 1.0.

References vSetVolume().

Referenced by initCinfo().

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virtual double PoolBase::vGetConc

(

const Eref &

e

)

const [pure virtual]

Implemented in Pool, and ZombiePool.

Referenced by getConc().

virtual double PoolBase::vGetDiffConst

(

const Eref &

e

)

const [pure virtual]

Implemented in Pool, and ZombiePool.

Referenced by getDiffConst().

double PoolBase::vGetMotorConst

(

const Eref &

e

)

const [virtual]

Reimplemented in Pool, and ZombiePool.

Referenced by getMotorConst().

virtual double PoolBase::vGetN

(

const Eref &

e

)

const [pure virtual]

Implemented in Pool, and ZombiePool.

Referenced by getN().

virtual double PoolBase::vGetNinit

(

const Eref &

e

)

const [pure virtual]

Implemented in Pool, and ZombiePool.

Referenced by getNinit().

virtual SpeciesId PoolBase::vGetSpecies

(

const Eref &

e

)

const [pure virtual]

Implemented in Pool, and ZombiePool.

Referenced by getSpecies().

virtual double PoolBase::vGetVolume

(

const Eref &

e

)

const [pure virtual]

Implemented in Pool, and ZombiePool.

Referenced by getVolume().

void PoolBase::vHandleMolWt	(	const Eref &	e,
		double	v
	)			[virtual]

Reimplemented in Pool.

Referenced by handleMolWt().

void PoolBase::vProcess	(	const Eref &	e,
		ProcPtr	p
	)			[virtual]

Reimplemented in BufPool, and Pool.

Referenced by process().

void PoolBase::vReac	(	double	A,
		double	B
	)			[virtual]

Reimplemented in Pool.

Referenced by reac().

void PoolBase::vReinit	(	const Eref &	e,
		ProcPtr	p
	)			[virtual]

Reimplemented in BufPool, and Pool.

Referenced by reinit().

virtual void PoolBase::vSetConc	(	const Eref &	e,
		double	v
	)			[pure virtual]

Implemented in BufPool, Pool, ZombieBufPool, and ZombiePool.

Referenced by setConc().

virtual void PoolBase::vSetConcInit	(	const Eref &	e,
		double	v
	)			[pure virtual]

Implemented in BufPool, Pool, ZombieBufPool, and ZombiePool.

Referenced by setConcInit().

virtual void PoolBase::vSetDiffConst	(	const Eref &	e,
		double	v
	)			[pure virtual]

Implemented in Pool, and ZombiePool.

Referenced by setDiffConst().

void PoolBase::vSetMotorConst	(	const Eref &	e,
		double	v
	)			[virtual]

Dummy MotorConst field for most Pool subclasses.

Reimplemented in Pool, and ZombiePool.

Referenced by setMotorConst().

virtual void PoolBase::vSetN	(	const Eref &	e,
		double	v
	)			[pure virtual]

Implemented in BufPool, Pool, ZombieBufPool, and ZombiePool.

Referenced by setN().

virtual void PoolBase::vSetNinit	(	const Eref &	e,
		double	v
	)			[pure virtual]

Implemented in BufPool, Pool, ZombieBufPool, and ZombiePool.

Referenced by setNinit().

void PoolBase::vSetSolver	(	Id	ksolve,
		Id	dsolve
	)			[virtual]

Assign whatever info is needed by the zombie based on the solver Element. Encapsulates some unpleasant field extraction, casting, and assignment. Default version of this function does nothing.

Reimplemented in ZombiePool.

Referenced by zombify().

virtual void PoolBase::vSetSpecies	(	const Eref &	e,
		SpeciesId	v
	)			[pure virtual]

Implemented in Pool, and ZombiePool.

Referenced by setSpecies().

virtual void PoolBase::vSetVolume	(	const Eref &	e,
		double	v
	)			[pure virtual]

Implemented in Pool, and ZombiePool.

Referenced by setVolume().

void PoolBase::zombify	(	Element *	original,
		const Cinfo *	zClass,
		Id	ksolve,
		Id	dsolve
	)			[static]

zombify is the base function for conversion between pool subclasses. This can be overridden, but should work for most things. This takes the original Element, and without touching its messaging, replaces it with a new data object of the specified zClass. It does the best it can with conversion of fields. Typically needs to be followed by rescheduling and possibly a class-specific function for assigning further zombie fields outside the ken of the PoolBase. The 'solver' argument specifies which objects handle the solver for this conversion. For the Pool this is either or both of a kinetic solver /ksolve/ and a diffusion solver /dsolve/. The term zombie arises because this operation was originally carried out to strip an object of independent function, and replace it with a solver-controlled facsimile.

References Element::cinfo(), Eref::data(), getConcInit(), getDiffConst(), getMotorConst(), getSpecies(), Element::localDataStart(), Element::numLocalData(), setConcInit(), setDiffConst(), setMotorConst(), setSpecies(), vSetSolver(), and Element::zombieSwap().

Referenced by Stoich::unZombifyPools().

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Friends And Related Function Documentation

void checkVal	(	double	time,
		const PoolBase *	m,
		unsigned int	size
	)			[friend]

void forceCheckVal	(	double	time,
		Element *	e,
		unsigned int	size
	)			[friend]

void testSyncArray	(	unsigned int	size,
		unsigned int	numThreads,
		unsigned int	method
	)			[friend]

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

• kinetics/PoolBase.h
• kinetics/PoolBase.cpp