#include <Pool.h>

Inheritance diagram for Pool:

Collaboration diagram for Pool:

Public Member Functions
	Pool ()

void	vDecrement (double val)

double	vGetConc (const Eref &e) const

double	vGetDiffConst (const Eref &e) const

bool	vGetIsBuffered (const Eref &e) const

double	vGetMotorConst (const Eref &e) const

double	vGetN (const Eref &e) const

double	vGetNinit (const Eref &e) const

SpeciesId	vGetSpecies (const Eref &e) const

double	vGetVolume (const Eref &e) const

void	vHandleMolWt (const Eref &e, double v)

void	vIncrement (double val)

void	vnIn (double val)

void	vProcess (const Eref &e, ProcPtr p)

void	vReac (double A, double B)

void	vReinit (const Eref &e, ProcPtr p)

void	vSetConc (const Eref &e, double v)

void	vSetConcInit (const Eref &e, double v)

void	vSetDiffConst (const Eref &e, double v)

void	vSetIsBuffered (const Eref &e, bool v)

void	vSetMotorConst (const Eref &e, double v)
	Dummy MotorConst field for most Pool subclasses. More...

void	vSetN (const Eref &e, double v)

void	vSetNinit (const Eref &e, double v)

void	vSetSpecies (const Eref &e, SpeciesId v)

void	vSetVolume (const Eref &e, double v)

	~Pool ()

Public Member Functions inherited from PoolBase
void	decrement (double val)

double	getConc (const Eref &e) const

double	getConcInit (const Eref &e) const

double	getDiffConst (const Eref &e) const

bool	getIsBuffered (const Eref &e) const

double	getMotorConst (const Eref &e) const

double	getN (const Eref &e) const

double	getNinit (const Eref &e) const

SpeciesId	getSpecies (const Eref &e) const

double	getVolume (const Eref &e) const

void	handleMolWt (const Eref &e, double v)

void	increment (double val)

void	nIn (double val)

	PoolBase ()

void	process (const Eref &e, ProcPtr p)

void	reac (double A, double B)

void	reinit (const Eref &e, ProcPtr p)

void	setConc (const Eref &e, double v)

void	setConcInit (const Eref &e, double v)

void	setDiffConst (const Eref &e, double v)

void	setIsBuffered (const Eref &e, bool v)

void	setMotorConst (const Eref &e, double v)

void	setN (const Eref &e, double v)

void	setNinit (const Eref &e, double v)

void	setSpecies (const Eref &e, SpeciesId v)

void	setVolume (const Eref &e, double v)

virtual double	vGetConcInit (const Eref &e) const

virtual void	vSetSolver (Id ksolve, Id dsolve)

virtual	~PoolBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from PoolBase
static const Cinfo *	initCinfo ()

static void	zombify (Element original, const Cinfo zClass, Id ksolve, Id dsolve)

Private Attributes
double	A_
	Motor transport constant. More...

double	B_
	Internal state variables, used only in explict mode. More...

double	diffConst_
	initial number of molecules. More...

double	motorConst_
	Diffusion constant. More...

double	n_

double	nInit_
	Number of molecules in pool. More...

unsigned int	species_

Detailed Description

The Pool class is a molecular pool. This 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.

Definition at line 19 of file Pool.h.

Constructor & Destructor Documentation

Pool::Pool ( )

Definition at line 52 of file Pool.cpp.

     : n_( 0.0 ), nInit_( 0.0 ), diffConst_( 0.0 ), motorConst_( 0.0 ),
       A_( 0.0 ), B_( 0.0 ), species_( 0 )
 {;}

Pool::~Pool ( )

Definition at line 57 of file Pool.cpp.

58 {;}

Member Function Documentation

const Cinfo * Pool::initCinfo ( )

static

Definition at line 18 of file Pool.cpp.

References PoolBase::initCinfo(), and poolCinfo.

Referenced by BufPool::initCinfo(), and Dsolve::setPath().

 {
     // Field Definitions: All inherited from PoolBase.
     // MsgDest Definitions: All inherited
     // SrcFinfo Definitions: All inherited.
     // SharedMsg Definitions: All inherited.
     static Dinfo< Pool > dinfo;
     static Cinfo poolCinfo (
         "Pool",
         PoolBase::initCinfo(),
         0,
         0,
         &dinfo
     );
 
     return &poolCinfo;
 }

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void Pool::vDecrement ( double val )

virtual

Reimplemented from PoolBase.

Definition at line 141 of file Pool.cpp.

References A_, and B_.

 {
     if ( val < 0 )
         A_ -= val;
     else
         B_ += val;
 }

double Pool::vGetConc ( const Eref & e ) const

virtual

Implements PoolBase.

Definition at line 192 of file Pool.cpp.

References lookupVolumeFromMesh(), n_, and NA.

 {
     return (n_ / NA) / lookupVolumeFromMesh( e );
 }

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double Pool::vGetDiffConst ( const Eref & e ) const

virtual

Implements PoolBase.

Definition at line 207 of file Pool.cpp.

References diffConst_.

 {
     return diffConst_;
 }

bool Pool::vGetIsBuffered ( const Eref & e ) const

virtual

We need this explicit check because when the moose class is flipped, the internal C++ class isn't. Inherited by BufPool.

Implements PoolBase.

Definition at line 83 of file Pool.cpp.

References Element::cinfo(), Eref::element(), and Cinfo::name().

Referenced by vSetIsBuffered().

 {
     return e.element()->cinfo()->name() == "BufPool";
 }

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double Pool::vGetMotorConst ( const Eref & e ) const

virtual

Reimplemented from PoolBase.

Definition at line 217 of file Pool.cpp.

References motorConst_.

 {
     return motorConst_;
 }

double Pool::vGetN ( const Eref & e ) const

virtual

Implements PoolBase.

Definition at line 170 of file Pool.cpp.

References n_.

 {
     return n_;
 }

double Pool::vGetNinit ( const Eref & e ) const

virtual

Implements PoolBase.

Definition at line 180 of file Pool.cpp.

References nInit_.

 {
     return nInit_;
 }

SpeciesId Pool::vGetSpecies ( const Eref & e ) const

virtual

Implements PoolBase.

Definition at line 237 of file Pool.cpp.

References species_.

 {
     return species_;
 }

double Pool::vGetVolume ( const Eref & e ) const

virtual

Implements PoolBase.

Definition at line 227 of file Pool.cpp.

References lookupVolumeFromMesh().

 {
     return lookupVolumeFromMesh( e );
 }

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void Pool::vHandleMolWt	(	const Eref &	e,
		double	v
	)

virtual

Reimplemented from PoolBase.

Definition at line 156 of file Pool.cpp.

 {
     ; // Here I should update DiffConst too.
 }

void Pool::vIncrement ( double val )

virtual

Reimplemented from PoolBase.

Definition at line 133 of file Pool.cpp.

References A_, and B_.

 {
     if ( val > 0 )
         A_ += val;
     else
         B_ -= val;
 }

void Pool::vnIn ( double val )

virtual

Reimplemented from PoolBase.

Definition at line 149 of file Pool.cpp.

References A_, B_, and n_.

 {
     n_ = val;
     B_ = 0;
     A_ = 0;
 }

void Pool::vProcess	(	const Eref &	e,
		ProcPtr	p
	)

virtual

Reimplemented from PoolBase.

Definition at line 97 of file Pool.cpp.

References A_, B_, ProcInfo::dt, EPSILON, n_, and SrcFinfo1< T >::send().

 {
     // double A = e.sumBuf( aSlot );
     // double B = e.sumBuf( bSlot );
 
     if ( n_ > EPSILON && B_ > EPSILON )
     {
         double C = exp( -B_ * p->dt / n_ );
         n_ *= C + (A_ / B_ ) * ( 1.0 - C );
     }
     else
     {
         n_ += ( A_ - B_ ) * p->dt;
         if ( n_ < 0.0 )
             n_ = 0.0;
     }
 
     A_ = B_ = 0.0;
 
     nOut.send( e, n_ );
 }

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void Pool::vReac	(	double	A,
		double	B
	)

virtual

Reimplemented from PoolBase.

Definition at line 127 of file Pool.cpp.

References A_, and B_.

 {
     A_ += A;
     B_ += B;
 }

void Pool::vReinit	(	const Eref &	e,
		ProcPtr	p
	)

virtual

Reimplemented from PoolBase.

Definition at line 119 of file Pool.cpp.

References A_, B_, PoolBase::getNinit(), n_, and SrcFinfo1< T >::send().

Referenced by BufPool::vProcess(), and BufPool::vReinit().

 {
     A_ = B_ = 0.0;
     n_ = getNinit( e );
 
     nOut.send( e, n_ );
 }

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void Pool::vSetConc	(	const Eref &	e,
		double	v
	)

virtual

Implements PoolBase.

Definition at line 186 of file Pool.cpp.

References lookupVolumeFromMesh(), n_, and NA.

 {
     n_ = NA * c * lookupVolumeFromMesh( e );
 }

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void Pool::vSetConcInit	(	const Eref &	e,
		double	v
	)

virtual

Implements PoolBase.

Definition at line 197 of file Pool.cpp.

References lookupVolumeFromMesh(), NA, and nInit_.

 {
     nInit_ = NA * c * lookupVolumeFromMesh( e );
 }

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void Pool::vSetDiffConst	(	const Eref &	e,
		double	v
	)

virtual

Implements PoolBase.

Definition at line 202 of file Pool.cpp.

References diffConst_.

 {
     diffConst_ = v;
 }

void Pool::vSetIsBuffered	(	const Eref &	e,
		bool	v
	)

virtual

Functions to examine and change class between Pool and BufPool.

setIsBuffered is a really nasty operation, made possible only because BufPool is derived from Pool and has no other fields. It uses a low-level replaceCinfo call to just change the identity of the Cinfo used, leaving everything else as is.

Reimplemented from PoolBase.

Definition at line 68 of file Pool.cpp.

References bufPoolCinfo, Eref::element(), Cinfo::find(), Element::replaceCinfo(), and vGetIsBuffered().

 {
     static const Cinfo* bufPoolCinfo = Cinfo::find( "BufPool" );
     if (vGetIsBuffered( e ) == v)
         return;
     if (v)
     {
         e.element()->replaceCinfo( bufPoolCinfo );
     }
     else
     {
         e.element()->replaceCinfo( poolCinfo );
     }
 }

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void Pool::vSetMotorConst	(	const Eref &	e,
		double	v
	)

virtual

Dummy MotorConst field for most Pool subclasses.

Reimplemented from PoolBase.

Definition at line 212 of file Pool.cpp.

References motorConst_.

 {
     motorConst_ = v;
 }

void Pool::vSetN	(	const Eref &	e,
		double	v
	)

virtual

Implements PoolBase.

Definition at line 165 of file Pool.cpp.

References n_.

Referenced by BufPool::vSetN().

 {
     n_ = v;
 }

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void Pool::vSetNinit	(	const Eref &	e,
		double	v
	)

virtual

Implements PoolBase.

Definition at line 175 of file Pool.cpp.

References nInit_.

Referenced by BufPool::vSetN().

 {
     nInit_ = v;
 }

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void Pool::vSetSpecies	(	const Eref &	e,
		SpeciesId	v
	)

virtual

Implements PoolBase.

Definition at line 232 of file Pool.cpp.

References species_.

 {
     species_ = v;
 }

void Pool::vSetVolume	(	const Eref &	e,
		double	v
	)

virtual

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.

Implements PoolBase.

Definition at line 222 of file Pool.cpp.

 {
     cout << "Warning: Pool::vSetVolume: Operation not permitted. Ignored\n";
 }

Member Data Documentation

double Pool::A_

private

Motor transport constant.

Definition at line 87 of file Pool.h.

Referenced by vDecrement(), vIncrement(), vnIn(), vProcess(), vReac(), and vReinit().

double Pool::B_

private

Internal state variables, used only in explict mode.

Definition at line 88 of file Pool.h.

Referenced by vDecrement(), vIncrement(), vnIn(), vProcess(), vReac(), and vReinit().

double Pool::diffConst_

private

initial number of molecules.

Definition at line 85 of file Pool.h.

Referenced by vGetDiffConst(), and vSetDiffConst().

double Pool::motorConst_

private

Diffusion constant.

Definition at line 86 of file Pool.h.

Referenced by vGetMotorConst(), and vSetMotorConst().

double Pool::n_

private

Definition at line 83 of file Pool.h.

Referenced by vGetConc(), vGetN(), vnIn(), vProcess(), vReinit(), vSetConc(), and vSetN().

double Pool::nInit_

private

Number of molecules in pool.

Definition at line 84 of file Pool.h.

Referenced by vGetNinit(), vSetConcInit(), and vSetNinit().

unsigned int Pool::species_

private

System wide identifier for all mol pools that are chemically the same species.

Definition at line 94 of file Pool.h.

Referenced by vGetSpecies(), and vSetSpecies().

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

moose-core/kinetics/Pool.h
moose-core/kinetics/Pool.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation