PoolBase Class Reference

#include <PoolBase.h>

Inheritance diagram for PoolBase:

Collaboration diagram for PoolBase:

Public Member Functions
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 void	vDecrement (double val)
virtual double	vGetConc (const Eref &e) const =0
virtual double	vGetConcInit (const Eref &e) const
virtual double	vGetDiffConst (const Eref &e) const =0
virtual bool	vGetIsBuffered (const Eref &e) const =0
virtual double	vGetMotorConst (const Eref &e) const
virtual double	vGetN (const Eref &e) const =0
virtual double	vGetNinit (const Eref &e) const =0
virtual SpeciesId	vGetSpecies (const Eref &e) const =0
virtual double	vGetVolume (const Eref &e) const =0
virtual void	vHandleMolWt (const Eref &e, double v)
virtual void	vIncrement (double val)
virtual void	vnIn (double val)
virtual void	vProcess (const Eref &e, ProcPtr p)
virtual void	vReac (double A, double B)
virtual void	vReinit (const Eref &e, ProcPtr p)
virtual void	vSetConc (const Eref &e, double v)=0
virtual void	vSetConcInit (const Eref &e, double v)=0
virtual void	vSetDiffConst (const Eref &e, double v)=0
virtual void	vSetIsBuffered (const Eref &e, bool v)
	I put in a default empty function for vSetIsBuffered. More...
virtual void	vSetMotorConst (const Eref &e, double v)
	Dummy MotorConst field for most Pool subclasses. More...
virtual void	vSetN (const Eref &e, double v)=0
virtual void	vSetNinit (const Eref &e, double v)=0
virtual void	vSetSolver (Id ksolve, Id dsolve)
virtual void	vSetSpecies (const Eref &e, SpeciesId v)=0
virtual void	vSetVolume (const Eref &e, double v)=0
virtual	~PoolBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()
static void	zombify (Element *original, const Cinfo *zClass, Id ksolve, Id dsolve)

Private Attributes
double	concInit_

Friends
void	checkVal (double time, const PoolBase *m, unsigned int size)
void	forceCheckVal (double time, Element *e, unsigned int size)
void	testSyncArray (unsigned int size, unsigned int numThreads, unsigned int method)

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.

Definition at line 30 of file PoolBase.h.

Constructor & Destructor Documentation

PoolBase::PoolBase

(

)

Definition at line 228 of file PoolBase.cpp.

    : concInit_( 0.0 )
{;}

PoolBase::~PoolBase ( )

virtual

Definition at line 232 of file PoolBase.cpp.

{;}

Member Function Documentation

void PoolBase::decrement

(

double

val

)

Definition at line 254 of file PoolBase.cpp.

References vDecrement().

Referenced by initCinfo().

{
    vDecrement( val );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double PoolBase::getConc

(

const Eref &

e

)

const

Definition at line 331 of file PoolBase.cpp.

References vGetConc().

Referenced by initCinfo().

{
    return vGetConc( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double PoolBase::getConcInit

(

const Eref &

e

)

const

Definition at line 347 of file PoolBase.cpp.

References vGetConcInit().

Referenced by initCinfo(), and zombify().

{
    // return concInit_;
    return vGetConcInit( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double PoolBase::getDiffConst

(

const Eref &

e

)

const

Definition at line 358 of file PoolBase.cpp.

References vGetDiffConst().

Referenced by initCinfo(), Dsolve::setStoich(), and zombify().

{
    return vGetDiffConst( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

bool PoolBase::getIsBuffered

(

const Eref &

e

)

const

Definition at line 401 of file PoolBase.cpp.

References vGetIsBuffered().

Referenced by initCinfo().

{
    return vGetIsBuffered( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double PoolBase::getMotorConst

(

const Eref &

e

)

const

Definition at line 368 of file PoolBase.cpp.

References vGetMotorConst().

Referenced by initCinfo(), and zombify().

{
    return vGetMotorConst( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double PoolBase::getN

(

const Eref &

e

)

const

Definition at line 308 of file PoolBase.cpp.

References vGetN().

Referenced by initCinfo().

{
    return vGetN( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double PoolBase::getNinit

(

const Eref &

e

)

const

Definition at line 319 of file PoolBase.cpp.

References vGetNinit().

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

{
    return vGetNinit( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

unsigned int PoolBase::getSpecies

(

const Eref &

e

)

const

Definition at line 388 of file PoolBase.cpp.

References vGetSpecies().

Referenced by initCinfo(), and zombify().

{
    return vGetSpecies( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double PoolBase::getVolume

(

const Eref &

e

)

const

Definition at line 378 of file PoolBase.cpp.

References vGetVolume().

Referenced by initCinfo().

{
    return vGetVolume( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 269 of file PoolBase.cpp.

References vHandleMolWt().

Referenced by initCinfo().

{
    vHandleMolWt( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

void PoolBase::increment

(

double

val

)

Definition at line 249 of file PoolBase.cpp.

References vIncrement().

Referenced by initCinfo().

{
    vIncrement(val);
}

Here is the call graph for this function:

Here is the caller graph for this function:

const Cinfo * PoolBase::initCinfo ( )

static

Definition at line 19 of file PoolBase.cpp.

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

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

{
    // Field Definitions
    static ElementValueFinfo< PoolBase, double > n(
        "n",
        "Number of molecules in pool",
        &PoolBase::setN,
        &PoolBase::getN
    );

    static ElementValueFinfo< PoolBase, double > nInit(
        "nInit",
        "Initial value of number of molecules in pool",
        &PoolBase::setNinit,
        &PoolBase::getNinit
    );

    static ElementValueFinfo< PoolBase, double > diffConst(
        "diffConst",
        "Diffusion constant of molecule",
        &PoolBase::setDiffConst,
        &PoolBase::getDiffConst
    );

    static ElementValueFinfo< PoolBase, double > motorConst(
        "motorConst",
        "Motor transport rate molecule. + is away from soma, - is "
        "towards soma. Only relevant for ZombiePool subclasses.",
        &PoolBase::setMotorConst,
        &PoolBase::getMotorConst
    );

    static ElementValueFinfo< PoolBase, double > conc(
        "conc",
        "Concentration of molecules in this pool",
        &PoolBase::setConc,
        &PoolBase::getConc
    );

    static ElementValueFinfo< PoolBase, double > concInit(
        "concInit",
        "Initial value of molecular concentration in pool",
        &PoolBase::setConcInit,
        &PoolBase::getConcInit
    );

    static ElementValueFinfo< PoolBase, double > volume(
        "volume",
        "Volume of compartment. Units are SI. "
        "Utility field, the actual volume info is "
        "stored on a volume mesh entry in the parent compartment."
        "This mapping is implicit: the parent compartment must be "
        "somewhere up the element tree, and must have matching mesh "
        "entries. If the compartment isn't"
        "available the volume is just taken as 1",
        &PoolBase::setVolume,
        &PoolBase::getVolume
    );

    static ElementValueFinfo< PoolBase, unsigned int > speciesId(
        "speciesId",
        "Species identifier for this mol pool. Eventually link to ontology.",
        &PoolBase::setSpecies,
        &PoolBase::getSpecies
    );

    static ElementValueFinfo< PoolBase, bool > isBuffered(
        "isBuffered",
        "Flag: True if Pool is buffered. "
        "In the case of Pool and BufPool the field can be assigned, to "
        "change the type of the Pool object to BufPool, or vice versa. "
        "None of the messages are affected. "
        "This object class flip can only be done in the non-zombified "
        "form of the Pool/BufPool. In Zombies it is read-only.",
        &PoolBase::setIsBuffered,
        &PoolBase::getIsBuffered
    );

    // MsgDest Definitions
    static DestFinfo process( "process",
                              "Handles process call",
                              new ProcOpFunc< PoolBase >( &PoolBase::process ) );
    static DestFinfo reinit( "reinit",
                             "Handles reinit call",
                             new ProcOpFunc< PoolBase >( &PoolBase::reinit ) );

    static DestFinfo reacDest( "reacDest",
                               "Handles reaction input",
                               new OpFunc2< PoolBase, double, double >( &PoolBase::reac )
                             );

    static DestFinfo handleMolWt( "handleMolWt",
                                  "Separate finfo to assign molWt, and consequently diffusion const."
                                  "Should only be used in SharedMsg with species.",
                                  new EpFunc1< PoolBase, double >( &PoolBase::handleMolWt )
                                );
    // MsgDest Definitions: These three are used for non-reaction
    // calculations involving algebraically defined rate terms.
    static DestFinfo increment( "increment",
                                "Increments mol numbers by specified amount. Can be +ve or -ve",
                                new OpFunc1< PoolBase, double >( &PoolBase::increment )
                              );

    static DestFinfo decrement( "decrement",
                                "Decrements mol numbers by specified amount. Can be +ve or -ve",
                                new OpFunc1< PoolBase, double >( &PoolBase::decrement )
                              );

    static DestFinfo nIn( "nIn",
                          "Assigns the number of molecules in Pool to specified value",
                          new OpFunc1< PoolBase, double >( &PoolBase::nIn )
                        );

    // SrcFinfo Definitions

    static SrcFinfo1< double > nOut(
        "nOut",
        "Sends out # of molecules in pool on each timestep"
    );

    static SrcFinfo0 requestMolWt(
        "requestMolWt",
        "Requests Species object for mol wt"
    );

    // SharedMsg Definitions
    static Finfo* reacShared[] =
    {
        &reacDest, &nOut
    };
    static SharedFinfo reac( "reac",
                             "Connects to reaction",
                             reacShared, sizeof( reacShared ) / sizeof( const Finfo* )
                           );
    static Finfo* procShared[] =
    {
        &process, &reinit
    };
    static SharedFinfo proc( "proc",
                             "Shared message for process and reinit",
                             procShared, sizeof( procShared ) / sizeof( const Finfo* )
                           );

    static Finfo* speciesShared[] =
    {
        &requestMolWt, &handleMolWt
    };

    static SharedFinfo species( "species",
                                "Shared message for connecting to species objects",
                                speciesShared, sizeof( speciesShared ) / sizeof ( const Finfo* )
                              );

    static Finfo* poolFinfos[] =
    {
        &n,         // Value
        &nInit,     // Value
        &diffConst, // Value
        &motorConst,    // Value
        &conc,      // Value
        &concInit,  // Value
        &volume,    // Readonly Value
        &speciesId, // Value
        &isBuffered,    // Value
        &increment,         // DestFinfo
        &decrement,         // DestFinfo
        &nIn,               // DestFinfo
        &reac,              // SharedFinfo
        &proc,              // SharedFinfo
        &species,           // SharedFinfo
    };

    static string doc[] =
    {
        "Name", "PoolBase",
        "Author", "Upi Bhalla",
        "Description", "Abstract base class for pools."
    };
    static ZeroSizeDinfo< int > dinfo;
    static Cinfo poolCinfo (
        "PoolBase",
        Neutral::initCinfo(),
        poolFinfos,
        sizeof( poolFinfos ) / sizeof ( Finfo* ),
        &dinfo,
        doc,
        sizeof( doc )/sizeof( string ),
        true // Ban creation as this is an abstract base class.
    );

    return &poolCinfo;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void PoolBase::nIn

(

double

val

)

Definition at line 259 of file PoolBase.cpp.

References vnIn().

Referenced by initCinfo().

{
    vnIn(val);
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 239 of file PoolBase.cpp.

References vProcess().

Referenced by initCinfo().

{
    vProcess( e, p );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 264 of file PoolBase.cpp.

References vReac().

Referenced by initCinfo().

{
    vReac( A, B );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 244 of file PoolBase.cpp.

References vReinit().

Referenced by initCinfo().

{
    vReinit( e, p );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 325 of file PoolBase.cpp.

References vSetConc().

Referenced by initCinfo().

{
    vSetConc( e, c );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 336 of file PoolBase.cpp.

References concInit_, and vSetConcInit().

Referenced by initCinfo(), and zombify().

{
    concInit_ = c;
    vSetConcInit( e, c );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 353 of file PoolBase.cpp.

References vSetDiffConst().

Referenced by initCinfo(), and zombify().

{
    vSetDiffConst( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

void PoolBase::setIsBuffered	(	const Eref &	e,
		bool	v
	)

Functions to examine and change class between Pool and BufPool.

setIsBuffered is active only for Pool and BufPool. Otherwise ignored.

Definition at line 396 of file PoolBase.cpp.

References vSetIsBuffered().

Referenced by initCinfo().

{
    vSetIsBuffered( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 363 of file PoolBase.cpp.

References vSetMotorConst().

Referenced by initCinfo(), and zombify().

{
    vSetMotorConst( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 303 of file PoolBase.cpp.

References vSetN().

Referenced by initCinfo().

{
    vSetN( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 313 of file PoolBase.cpp.

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

Referenced by initCinfo().

{
    concInit_ =  v / ( NA * lookupVolumeFromMesh( e ) );
    vSetNinit( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Definition at line 383 of file PoolBase.cpp.

References vSetSpecies().

Referenced by initCinfo(), and zombify().

{
    vSetSpecies( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

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.

Definition at line 373 of file PoolBase.cpp.

References vSetVolume().

Referenced by initCinfo().

{
    vSetVolume( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

void PoolBase::vDecrement ( double  val )

virtual

Reimplemented in Pool.

Definition at line 293 of file PoolBase.cpp.

Referenced by decrement().

{;}

Here is the caller graph for this function:

virtual double PoolBase::vGetConc ( const Eref &  e ) const

pure virtual

Implemented in Pool, and ZombiePool.

Referenced by getConc().

Here is the caller graph for this function:

double PoolBase::vGetConcInit ( const Eref &  e ) const

virtual

Reimplemented in ZombiePool.

Definition at line 342 of file PoolBase.cpp.

References concInit_.

Referenced by getConcInit().

{
    return concInit_;
}

Here is the caller graph for this function:

virtual double PoolBase::vGetDiffConst ( const Eref &  e ) const

pure virtual

Implemented in Pool, and ZombiePool.

Referenced by getDiffConst().

Here is the caller graph for this function:

virtual bool PoolBase::vGetIsBuffered ( const Eref &  e ) const

pure virtual

Implemented in Pool, ZombiePool, and ZombieBufPool.

Referenced by getIsBuffered().

Here is the caller graph for this function:

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

virtual

Reimplemented in ZombiePool, and Pool.

Definition at line 414 of file PoolBase.cpp.

Referenced by getMotorConst().

{
    return 0.0;
}

Here is the caller graph for this function:

virtual double PoolBase::vGetN ( const Eref &  e ) const

pure virtual

Implemented in Pool, and ZombiePool.

Referenced by getN().

Here is the caller graph for this function:

virtual double PoolBase::vGetNinit ( const Eref &  e ) const

pure virtual

Implemented in Pool, and ZombiePool.

Referenced by getNinit().

Here is the caller graph for this function:

virtual SpeciesId PoolBase::vGetSpecies ( const Eref &  e ) const

pure virtual

Implemented in Pool, and ZombiePool.

Referenced by getSpecies().

Here is the caller graph for this function:

virtual double PoolBase::vGetVolume ( const Eref &  e ) const

pure virtual

Implemented in Pool, and ZombiePool.

Referenced by getVolume().

Here is the caller graph for this function:

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

virtual

Reimplemented in Pool.

Definition at line 287 of file PoolBase.cpp.

Referenced by handleMolWt().

{;}

Here is the caller graph for this function:

void PoolBase::vIncrement ( double  val )

virtual

Reimplemented in Pool.

Definition at line 290 of file PoolBase.cpp.

Referenced by increment().

{;}

Here is the caller graph for this function:

void PoolBase::vnIn ( double  val )

virtual

Reimplemented in Pool.

Definition at line 296 of file PoolBase.cpp.

Referenced by nIn().

{;}

Here is the caller graph for this function:

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

virtual

Reimplemented in Pool, and BufPool.

Definition at line 278 of file PoolBase.cpp.

Referenced by process().

{;}

Here is the caller graph for this function:

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

virtual

Reimplemented in Pool.

Definition at line 284 of file PoolBase.cpp.

Referenced by reac().

{;}

Here is the caller graph for this function:

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

virtual

Reimplemented in Pool, and BufPool.

Definition at line 281 of file PoolBase.cpp.

Referenced by reinit().

{;}

Here is the caller graph for this function:

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

pure virtual

Implemented in Pool, ZombiePool, BufPool, and ZombieBufPool.

Referenced by setConc().

Here is the caller graph for this function:

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

pure virtual

Implemented in Pool, ZombiePool, BufPool, and ZombieBufPool.

Referenced by setConcInit().

Here is the caller graph for this function:

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

pure virtual

Implemented in Pool, and ZombiePool.

Referenced by setDiffConst().

Here is the caller graph for this function:

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

virtual

I put in a default empty function for vSetIsBuffered.

Dummy default function for most pool subclasses.

Reimplemented in Pool.

Definition at line 420 of file PoolBase.cpp.

Referenced by setIsBuffered().

{;}

Here is the caller graph for this function:

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

virtual

Dummy MotorConst field for most Pool subclasses.

Reimplemented in ZombiePool, and Pool.

Definition at line 411 of file PoolBase.cpp.

Referenced by setMotorConst().

{;}

Here is the caller graph for this function:

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

pure virtual

Implemented in Pool, ZombiePool, BufPool, and ZombieBufPool.

Referenced by setN().

Here is the caller graph for this function:

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

pure virtual

Implemented in Pool, ZombiePool, BufPool, and ZombieBufPool.

Referenced by setNinit().

Here is the caller graph for this function:

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.

Definition at line 467 of file PoolBase.cpp.

Referenced by zombify().

{
    ;
}

Here is the caller graph for this function:

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

pure virtual

Implemented in Pool, and ZombiePool.

Referenced by setSpecies().

Here is the caller graph for this function:

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

pure virtual

Implemented in Pool, and ZombiePool.

Referenced by setVolume().

Here is the caller graph for this function:

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.

Definition at line 430 of file PoolBase.cpp.

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

Referenced by Dsolve::setPath(), Stoich::unZombifyPools(), and Stoich::zombifyModel().

{
    if ( orig->cinfo() == zClass )
        return;
    unsigned int start = orig->localDataStart();
    unsigned int num = orig->numLocalData();
    if ( num == 0 )
        return;
    vector< unsigned int > species( num, 0 );
    vector< double > concInit( num, 0.0 );
    vector< double > diffConst( num, 0.0 );
    vector< double > motorConst( num, 0.0 );
    for ( unsigned int i = 0; i < num; ++i )
    {
        Eref er( orig, i + start );
        const PoolBase* pb =
            reinterpret_cast< const PoolBase* >( er.data() );
        species[ i ] = pb->getSpecies( er );
        concInit[ i ] = pb->getConcInit( er );
        diffConst[ i ] = pb->getDiffConst( er );
        motorConst[ i ] = pb->getMotorConst( er );
    }
    orig->zombieSwap( zClass );
    for ( unsigned int i = 0; i < num; ++i )
    {
        Eref er( orig, i + start );
        PoolBase* pb = reinterpret_cast< PoolBase* >( er.data() );
        pb->vSetSolver( ksolve, dsolve );
        pb->setSpecies( er, species[i] );
        pb->setConcInit( er, concInit[i] );
        pb->setDiffConst( er, diffConst[i] );
        pb->setMotorConst( er, motorConst[i] );
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

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

Member Data Documentation

double PoolBase::concInit_

private

Definition at line 157 of file PoolBase.h.

Referenced by setConcInit(), setNinit(), and vGetConcInit().

---

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

• moose-core/kinetics/PoolBase.h
• moose-core/kinetics/PoolBase.cpp