#include <CaConcBase.h>

Inheritance diagram for CaConcBase:

Collaboration diagram for CaConcBase:

Public Member Functions
	CaConcBase ()

void	current (const Eref &e, double I)

void	currentFraction (const Eref &e, double I, double fraction)

void	decrease (const Eref &e, double I)

double	getB (const Eref &e) const

double	getCa (const Eref &e) const

double	getCaBasal (const Eref &e) const

double	getCeiling (const Eref &e) const

double	getDiameter (const Eref &e) const

double	getFloor (const Eref &e) const

double	getLength (const Eref &e) const

double	getTau (const Eref &e) const

double	getThickness (const Eref &e) const

void	increase (const Eref &e, double I)

void	process (const Eref &, ProcPtr info)

void	reinit (const Eref &, ProcPtr info)

void	setB (const Eref &e, double val)

void	setCa (const Eref &e, double val)

void	setCaBasal (const Eref &e, double val)

void	setCeiling (const Eref &e, double val)

void	setDiameter (const Eref &e, double val)

void	setFloor (const Eref &e, double val)

void	setLength (const Eref &e, double val)

void	setTau (const Eref &e, double val)

void	setThickness (const Eref &e, double val)

void	updateDimensions (const Eref &e)

virtual void	vCurrent (const Eref &e, double I)=0

virtual void	vCurrentFraction (const Eref &e, double I, double fraction)=0

virtual void	vDecrease (const Eref &e, double I)=0

virtual double	vGetB (const Eref &e) const =0

virtual double	vGetCa (const Eref &e) const =0

virtual double	vGetCaBasal (const Eref &e) const =0

virtual double	vGetCeiling (const Eref &e) const =0

virtual double	vGetFloor (const Eref &e) const =0

virtual double	vGetTau (const Eref &e) const =0

virtual void	vIncrease (const Eref &e, double I)=0

virtual void	vProcess (const Eref &, ProcPtr info)=0

virtual void	vReinit (const Eref &, ProcPtr info)=0

virtual void	vSetB (const Eref &e, double val)=0

virtual void	vSetCa (const Eref &e, double val)=0

virtual void	vSetCaBasal (const Eref &e, double val)=0

virtual void	vSetCeiling (const Eref &e, double val)=0

virtual void	vSetFloor (const Eref &e, double val)=0

virtual void	vSetSolver (const Eref &e, Id hsolve)
	Used to set up the solver. Dummy for regular classes. More...

virtual void	vSetTau (const Eref &e, double val)=0

Static Public Member Functions
static SrcFinfo1< double > *	concOut ()

static const Cinfo *	initCinfo ()

static void	zombify (Element orig, const Cinfo zClass, Id hsolve)

Private Attributes
double	diameter_

double	length_

double	thickness_

Detailed Description

This is the base class for CaConc. It handles calcium current influx, conversion to calcium concentration, buffering, and pumps. It obeys the equation:

dC/dt = B*Ik - C/tau where Ca = Ca_base + C.

From the GENESIS notes: In SI units, where concentration is moles/m^3 (milli-moles/liter) and current is in amperes, theory gives B = 5.2e-6/(shell volume). In practice, B is a parameter to be fitted or estimated from experiment, as buffering, non-uniform distribution of Ca, etc., will modify this value. If thick = 0, the readcell routine calculates B by dividing the "density" parameter in the cell parameter file by the volume of the compartment. Otherwise, it scales as a true shell, with the volume of a shell having thickness thick. A negative value of the "density" parameter may be used to indicate that it should be taken as an absolute value of B, without scaling.

This is a base class to provide the interface functions.

Definition at line 38 of file CaConcBase.h.

Constructor & Destructor Documentation

CaConcBase::CaConcBase ( )

Definition at line 194 of file CaConcBase.cpp.

   :
   thickness_( 0.0 )
 {;}

Member Function Documentation

SrcFinfo1< double > * CaConcBase::concOut ( )

static

Definition at line 25 of file CaConcBase.cpp.

Referenced by initCinfo(), HSolveActive::sendValues(), CaConc::vProcess(), and CaConc::vReinit().

                                          {
   static SrcFinfo1< double > concOut( "concOut",
                       "Concentration of Ca in pool" );
   return &concOut;
 }

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void CaConcBase::current	(	const Eref &	e,
		double	I
	)

Definition at line 313 of file CaConcBase.cpp.

References vCurrent().

Referenced by initCinfo().

 {
   vCurrent( e, I );
 }

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void CaConcBase::currentFraction	(	const Eref &	e,
		double	I,
		double	fraction
	)

Definition at line 318 of file CaConcBase.cpp.

References vCurrentFraction().

Referenced by initCinfo().

 {
   vCurrentFraction( e, I, fraction );
 }

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void CaConcBase::decrease	(	const Eref &	e,
		double	I
	)

Definition at line 328 of file CaConcBase.cpp.

References vDecrease().

Referenced by initCinfo().

 {
   vDecrease( e, I );
 }

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double CaConcBase::getB ( const Eref & e ) const

Definition at line 234 of file CaConcBase.cpp.

References vGetB().

Referenced by initCinfo(), and zombify().

 {
   return vGetB( e );
 }

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double CaConcBase::getCa ( const Eref & e ) const

Definition at line 207 of file CaConcBase.cpp.

References vGetCa().

Referenced by initCinfo(), and zombify().

 {
   return vGetCa( e );
 }

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double CaConcBase::getCaBasal ( const Eref & e ) const

Definition at line 216 of file CaConcBase.cpp.

References vGetCaBasal().

Referenced by initCinfo(), and zombify().

 {
   return vGetCaBasal( e );
 }

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double CaConcBase::getCeiling ( const Eref & e ) const

Definition at line 242 of file CaConcBase.cpp.

References vGetCeiling().

Referenced by initCinfo(), and zombify().

 {
   return vGetCeiling( e );
 }

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double CaConcBase::getDiameter ( const Eref & e ) const

Definition at line 284 of file CaConcBase.cpp.

References diameter_.

Referenced by initCinfo(), and zombify().

 {
   return diameter_;
 }

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double CaConcBase::getFloor ( const Eref & e ) const

Definition at line 251 of file CaConcBase.cpp.

References vGetFloor().

Referenced by initCinfo(), and zombify().

 {
   return vGetFloor( e );
 }

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double CaConcBase::getLength ( const Eref & e ) const

Definition at line 294 of file CaConcBase.cpp.

References length_.

Referenced by initCinfo(), and zombify().

 {
   return length_;
 }

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double CaConcBase::getTau ( const Eref & e ) const

Definition at line 225 of file CaConcBase.cpp.

References vGetTau().

Referenced by initCinfo(), and zombify().

 {
   return vGetTau( e );
 }

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double CaConcBase::getThickness ( const Eref & e ) const

Definition at line 273 of file CaConcBase.cpp.

References thickness_.

Referenced by initCinfo(), and zombify().

 {
   return thickness_;
 }

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void CaConcBase::increase	(	const Eref &	e,
		double	I
	)

Definition at line 323 of file CaConcBase.cpp.

References vIncrease().

Referenced by initCinfo().

 {
   vIncrease( e, I );
 }

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const Cinfo * CaConcBase::initCinfo ( )

static

Definition at line 31 of file CaConcBase.cpp.

References concOut(), current(), currentFraction(), decrease(), getB(), getCa(), getCaBasal(), getCeiling(), getDiameter(), getFloor(), getLength(), getTau(), getThickness(), increase(), Neutral::initCinfo(), process(), reinit(), setB(), setCa(), setCaBasal(), setCeiling(), setDiameter(), setFloor(), setLength(), setTau(), and setThickness().

Referenced by ZombieCaConc::initCinfo(), and CaConc::initCinfo().

 {
   // Shared message definitions
   static DestFinfo process( "process",
                 "Handles process call",
                 new ProcOpFunc< CaConcBase >( &CaConcBase::process ) );
   static DestFinfo reinit( "reinit",
                "Handles reinit call",
                new ProcOpFunc< CaConcBase >( &CaConcBase::reinit ) );
 
   static Finfo* processShared[] =
     {
       &process, &reinit
     };
 
   static SharedFinfo proc( "proc",
                "Shared message to receive Process message from scheduler",
                processShared, sizeof( processShared ) / sizeof( Finfo* ) );
 
   // Field definitions
   static ElementValueFinfo< CaConcBase, double > Ca( "Ca",
                              "Calcium concentration.",
                              &CaConcBase::setCa,
                              &CaConcBase::getCa
                              );
   static ElementValueFinfo< CaConcBase, double > CaBasal( "CaBasal",
                               "Basal Calcium concentration.",
                               &CaConcBase::setCaBasal,
                               &CaConcBase::getCaBasal
                               );
   static ElementValueFinfo< CaConcBase, double > Ca_base( "Ca_base",
                               "Basal Calcium concentration, synonym for CaBasal",
                               &CaConcBase::setCaBasal,
                               &CaConcBase::getCaBasal
                               );
   static ElementValueFinfo< CaConcBase, double > tau( "tau",
                               "Settling time for Ca concentration",
                               &CaConcBase::setTau,
                               &CaConcBase::getTau
                               );
   static ElementValueFinfo< CaConcBase, double > B( "B",
                             "Volume scaling factor. "
                             "Deprecated. This is a legacy field from GENESIS and exposes "
                             "internal calculations. Please do not use. \n"
                             "B = 1/(vol * F) so that it obeys:\n"
                             "dC/dt = B*I_Ca - C/tau",
                             &CaConcBase::setB,
                             &CaConcBase::getB
                             );
   static ElementValueFinfo< CaConcBase, double > thick( "thick",
                             "Thickness of Ca shell, assumed cylindrical. Legal range is between 0 \n"
                             "and the radius. If outside this range it is taken as the radius. \n"
                             " Default zero, ie, the shell is the entire thickness of the cylinder \n",
                             &CaConcBase::setThickness,
                             &CaConcBase::getThickness
                             );
   static ElementValueFinfo< CaConcBase, double > length( "length",
                              "Length of Ca shell, assumed cylindrical",
                              &CaConcBase::setLength,
                              &CaConcBase::getLength
                              );
   static ElementValueFinfo< CaConcBase, double > diameter( "diameter",
                                "Diameter of Ca shell, assumed cylindrical",
                                &CaConcBase::setDiameter,
                                &CaConcBase::getDiameter
                                );
   static ElementValueFinfo< CaConcBase, double > ceiling( "ceiling",
                               "Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. \n"
                 "If ceiling <= 0.0, there is no upper limit on Ca concentration value.",
                               &CaConcBase::setCeiling,
                               &CaConcBase::getCeiling
                               );
   static ElementValueFinfo< CaConcBase, double > floor( "floor",
                             "Floor value for Ca concentration. If Ca < floor, Ca = floor",
                             &CaConcBase::setFloor,
                             &CaConcBase::getFloor
                             );
 
   // MsgDest definitions
 
   static DestFinfo current( "current",
                 "Calcium Ion current, due to be converted to conc.",
                 new EpFunc1< CaConcBase, double >( &CaConcBase::current )
                 );
 
   static DestFinfo currentFraction( "currentFraction",
                     "Fraction of total Ion current, that is carried by Ca2+.",
                     new EpFunc2< CaConcBase, double, double >( &CaConcBase::currentFraction )
                     );
 
   static DestFinfo increase( "increase",
                  "Any input current that increases the concentration.",
                  new EpFunc1< CaConcBase, double >( &CaConcBase::increase )
                  );
 
   static DestFinfo decrease( "decrease",
                  "Any input current that decreases the concentration.",
                  new EpFunc1< CaConcBase, double >( &CaConcBase::decrease )
                  );
 
   static DestFinfo basal( "basal",
               "Synonym for assignment of basal conc.",
               new EpFunc1< CaConcBase, double >( &CaConcBase::setCaBasal )
               );
 
   static Finfo* CaConcBaseFinfos[] =
     {
       &proc,        // Shared
       concOut(),    // Src
       &Ca,      // Value
       &CaBasal, // Value
       &Ca_base, // Value
       &tau,     // Value
       &B,           // Value
       &thick,       // Value
       &diameter,    // Value
       &length,  // Value
       &ceiling, // Value
       &floor,       // Value
       &current, // Dest
       &currentFraction, // Dest
       &increase,    // Dest
       &decrease,    // Dest
       &basal,       // Dest
     };
 
   // We want the Ca updates before channel updates, so along with compts.
   // static SchedInfo schedInfo[] = { { process, 0, 0 } };
 
   static string doc[] =
     {
       "Name", "CaConcBase",
       "Author", "Upinder S. Bhalla, 2014, NCBS",
       "Description",
       "CaConcBase: Base class for Calcium concentration pool. \n"
       "Takes current from a channel and keeps track of calcium buildup and \n"
       " depletion by a single exponential process. ",
     };
 
   static ZeroSizeDinfo< int > dinfo;
 
   static Cinfo CaConcBaseCinfo(
                    "CaConcBase",
                    Neutral::initCinfo(),
                    CaConcBaseFinfos,
                    sizeof( CaConcBaseFinfos )/sizeof(Finfo *),
                    &dinfo,
                    doc,
                    sizeof(doc)/sizeof(string)
                    );
 
   return &CaConcBaseCinfo;
 }

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void CaConcBase::process	(	const Eref &	e,
		ProcPtr	info
	)

Definition at line 308 of file CaConcBase.cpp.

References vProcess().

Referenced by initCinfo().

 {
   vProcess( e, p );
 }

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void CaConcBase::reinit	(	const Eref &	e,
		ProcPtr	info
	)

Definition at line 303 of file CaConcBase.cpp.

References vReinit().

Referenced by initCinfo().

 {
   vReinit( e, p );
 }

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void CaConcBase::setB	(	const Eref &	e,
		double	val
	)

Definition at line 230 of file CaConcBase.cpp.

References vSetB().

Referenced by initCinfo(), and zombify().

 {
   vSetB( e, B );
 }

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void CaConcBase::setCa	(	const Eref &	e,
		double	val
	)

Definition at line 203 of file CaConcBase.cpp.

References vSetCa().

Referenced by initCinfo(), and zombify().

 {
   vSetCa( e, Ca );
 }

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void CaConcBase::setCaBasal	(	const Eref &	e,
		double	val
	)

Definition at line 212 of file CaConcBase.cpp.

References vSetCaBasal().

Referenced by initCinfo(), and zombify().

 {
   vSetCaBasal( e, CaBasal );
 }

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void CaConcBase::setCeiling	(	const Eref &	e,
		double	val
	)

Definition at line 238 of file CaConcBase.cpp.

References vSetCeiling().

Referenced by initCinfo(), and zombify().

 {
   vSetCeiling( e, ceiling );
 }

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void CaConcBase::setDiameter	(	const Eref &	e,
		double	val
	)

Definition at line 278 of file CaConcBase.cpp.

References diameter_, and updateDimensions().

Referenced by initCinfo(), and zombify().

 {
   diameter_ = diameter;
   updateDimensions( e );
 }

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void CaConcBase::setFloor	(	const Eref &	e,
		double	val
	)

Definition at line 247 of file CaConcBase.cpp.

References vSetFloor().

Referenced by initCinfo(), and zombify().

 {
   vSetFloor( e, floor );
 }

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void CaConcBase::setLength	(	const Eref &	e,
		double	val
	)

Definition at line 289 of file CaConcBase.cpp.

References length_, and updateDimensions().

Referenced by initCinfo(), and zombify().

 {
   length_ = length;
   updateDimensions( e );
 }

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void CaConcBase::setTau	(	const Eref &	e,
		double	val
	)

Definition at line 221 of file CaConcBase.cpp.

References vSetTau().

Referenced by initCinfo(), and zombify().

 {
   vSetTau( e, tau );
 }

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void CaConcBase::setThickness	(	const Eref &	e,
		double	val
	)

Definition at line 267 of file CaConcBase.cpp.

References thickness_, and updateDimensions().

Referenced by initCinfo(), and zombify().

 {
   thickness_ = thickness;
   updateDimensions( e );
 }

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void CaConcBase::updateDimensions ( const Eref & e )

Definition at line 256 of file CaConcBase.cpp.

References diameter_, FaradayConst, length_, PI, thickness_, and vSetB().

Referenced by setDiameter(), setLength(), and setThickness().

 {
   double vol = PI * diameter_ * diameter_ * length_ * 0.25;
   if ( thickness_ > 0 && thickness_ < diameter_/2.0 ) {
     double coreRadius = diameter_ / 2.0 - thickness_;
     vol -= PI * coreRadius * coreRadius * length_;
   }
   double B = 1.0 / ( FaradayConst * vol );
   vSetB( e, B );
 }

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virtual void CaConcBase::vCurrent	(	const Eref &	e,
		double	I
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by current().

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virtual void CaConcBase::vCurrentFraction	(	const Eref &	e,
		double	I,
		double	fraction
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by currentFraction().

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virtual void CaConcBase::vDecrease	(	const Eref &	e,
		double	I
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by decrease().

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virtual double CaConcBase::vGetB ( const Eref & e ) const

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by getB().

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virtual double CaConcBase::vGetCa ( const Eref & e ) const

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by getCa().

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virtual double CaConcBase::vGetCaBasal ( const Eref & e ) const

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by getCaBasal().

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virtual double CaConcBase::vGetCeiling ( const Eref & e ) const

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by getCeiling().

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virtual double CaConcBase::vGetFloor ( const Eref & e ) const

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by getFloor().

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virtual double CaConcBase::vGetTau ( const Eref & e ) const

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by getTau().

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virtual void CaConcBase::vIncrease	(	const Eref &	e,
		double	I
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by increase().

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virtual void CaConcBase::vProcess	(	const Eref &	,
		ProcPtr	info
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by process().

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virtual void CaConcBase::vReinit	(	const Eref &	,
		ProcPtr	info
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by reinit().

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virtual void CaConcBase::vSetB	(	const Eref &	e,
		double	val
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by setB(), and updateDimensions().

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virtual void CaConcBase::vSetCa	(	const Eref &	e,
		double	val
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by setCa().

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virtual void CaConcBase::vSetCaBasal	(	const Eref &	e,
		double	val
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by setCaBasal().

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virtual void CaConcBase::vSetCeiling	(	const Eref &	e,
		double	val
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by setCeiling().

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virtual void CaConcBase::vSetFloor	(	const Eref &	e,
		double	val
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by setFloor().

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void CaConcBase::vSetSolver	(	const Eref &	e,
		Id	hsolve
	)

virtual

Used to set up the solver. Dummy for regular classes.

Reimplemented in ZombieCaConc.

Definition at line 339 of file CaConcBase.cpp.

Referenced by zombify().

340 {;}

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virtual void CaConcBase::vSetTau	(	const Eref &	e,
		double	val
	)

pure virtual

Implemented in CaConc, and ZombieCaConc.

Referenced by setTau().

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void CaConcBase::zombify	(	Element *	orig,
		const Cinfo *	zClass,
		Id	hsolve
	)

static

Swaps Cinfos in order to make Zombies.

Definition at line 343 of file CaConcBase.cpp.

References Element::cinfo(), Eref::data(), getB(), getCa(), getCaBasal(), getCeiling(), getDiameter(), getFloor(), getLength(), getTau(), getThickness(), Element::localDataStart(), Element::numLocalData(), setB(), setCa(), setCaBasal(), setCeiling(), setDiameter(), setFloor(), setLength(), setTau(), setThickness(), vSetSolver(), and Element::zombieSwap().

Referenced by HSolve::unzombify(), and HSolve::zombify().

 {
   if ( orig->cinfo() == zClass )
     return;
   unsigned int start = orig->localDataStart();
   unsigned int num = orig->numLocalData();
   if ( num == 0 )
     return;
   vector< double > data( num * 9 );
 
   unsigned int j = 0;
   for ( unsigned int i = 0; i < num; ++i ) {
     Eref er( orig, i + start );
     const CaConcBase* cb =
       reinterpret_cast< const CaConcBase* >( er.data() );
     data[j + 0] = cb->getCa( er );
     data[j + 1] = cb->getCaBasal( er );
     data[j + 2] = cb->getTau( er );
     data[j + 3] = cb->getB( er );
     data[j + 4] = cb->getCeiling( er );
     data[j + 5] = cb->getFloor( er );
     data[j + 6] = cb->getThickness( er );
     data[j + 7] = cb->getLength( er );
     data[j + 8] = cb->getDiameter( er );
     j += 9;
   }
   orig->zombieSwap( zClass );
   j = 0;
   for ( unsigned int i = 0; i < num; ++i ) {
     Eref er( orig, i + start );
     CaConcBase* cb = reinterpret_cast< CaConcBase* >( er.data() );
     cb->vSetSolver( er, hsolve );
     cb->setCa( er, data[j + 0] );
     cb->setCaBasal( er, data[j + 1] );
     cb->setTau( er, data[j + 2] );
     cb->setB( er, data[j + 3] );
     cb->setCeiling( er, data[j + 4] );
     cb->setFloor( er, data[j + 5] );
     cb->setThickness( er, data[j + 6] );
     cb->setLength( er, data[j + 7] );
     cb->setDiameter( er, data[j + 8] );
     j += 9; //was 7?
   }
 }

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Member Data Documentation

double CaConcBase::diameter_

private

Definition at line 123 of file CaConcBase.h.

Referenced by getDiameter(), setDiameter(), and updateDimensions().

double CaConcBase::length_

private

Definition at line 124 of file CaConcBase.h.

Referenced by getLength(), setLength(), and updateDimensions().

double CaConcBase::thickness_

private

Definition at line 122 of file CaConcBase.h.

Referenced by getThickness(), setThickness(), and updateDimensions().

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

moose-core/biophysics/CaConcBase.h
moose-core/biophysics/CaConcBase.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation