#include <DifShell.h>

Inheritance diagram for DifShell:

Collaboration diagram for DifShell:

Public Member Functions
void	calculateVolumeArea (const Eref &e)

	DifShell ()
	Faraday's constant (Coulomb / Mole) More...

void	vBuffer (const Eref &e, double kf, double kb, double bFree, double bBound)

void	vEqTauPump (const Eref &e, double kP)

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

void	vFluxFromIn (const Eref &e, double innerC, double innerThickness)

void	vFluxFromOut (const Eref &e, double outerC, double outerThickness)

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

double	vGetC (const Eref &e) const

double	vGetCeq (const Eref &e) const

double	vGetD (const Eref &e) const

double	vGetDiameter (const Eref &e) const

double	vGetInnerArea (const Eref &e) const

double	vGetLeak (const Eref &e) const

double	vGetLength (const Eref &e) const

double	vGetOuterArea (const Eref &e) const

unsigned int	vGetShapeMode (const Eref &e) const

double	vGetThickness (const Eref &e) const

double	vGetValence (const Eref &e) const

double	vGetVolume (const Eref &e) const

void	vHillPump (const Eref &e, double vMax, double Kd, unsigned int hill)

void	vInflux (const Eref &e, double I)

void	vMMPump (const Eref &e, double vMax, double Kd)

void	vOutflux (const Eref &e, double I)

void	vProcess (const Eref &e, ProcPtr p)

void	vReinit (const Eref &e, ProcPtr p)

void	vSetC (const Eref &e, double C)
	C is a read-only field. More...

void	vSetCeq (const Eref &e, double Ceq)

void	vSetD (const Eref &e, double D)

void	vSetDiameter (const Eref &e, double diameter)

void	vSetInnerArea (const Eref &e, double innerArea)

void	vSetLeak (const Eref &e, double leak)

void	vSetLength (const Eref &e, double length)

void	vSetOuterArea (const Eref &e, double outerArea)

void	vSetShapeMode (const Eref &e, unsigned int shapeMode)

void	vSetThickness (const Eref &e, double thickness)

void	vSetValence (const Eref &e, double valence)

void	vSetVolume (const Eref &e, double volume)

void	vStoreInflux (const Eref &e, double flux)

void	vStoreOutflux (const Eref &e, double flux)

void	vTauPump (const Eref &e, double kP, double Ceq)

Public Member Functions inherited from DifShellBase
void	buffer (const Eref &e, double kf, double kb, double bFree, double bBound)

	DifShellBase ()

void	eqTauPump (const Eref &e, double kP)

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

void	fluxFromIn (const Eref &e, double innerC, double innerThickness)

void	fluxFromOut (const Eref &e, double outerC, double outerThickness)

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

double	getC (const Eref &e) const

double	getCeq (const Eref &e) const

double	getD (const Eref &e) const

double	getDiameter (const Eref &e) const

double	getInnerArea (const Eref &e) const

double	getLeak (const Eref &e) const

double	getLength (const Eref &e) const

double	getOuterArea (const Eref &e) const

unsigned int	getShapeMode (const Eref &e) const

double	getThickness (const Eref &e) const

double	getValence (const Eref &e) const

double	getVolume (const Eref &e) const

void	hillPump (const Eref &e, double vMax, double Kd, unsigned int hill)

void	influx (const Eref &e, double I)

void	mmPump (const Eref &e, double vMax, double Kd)

void	outflux (const Eref &e, double I)

void	process (const Eref &e, ProcPtr p)

void	reinit (const Eref &e, ProcPtr p)

void	setC (const Eref &e, double C)

void	setCeq (const Eref &e, double Ceq)

void	setD (const Eref &e, double D)

void	setDiameter (const Eref &e, double diameter)

void	setInnerArea (const Eref &e, double innerArea)

void	setLeak (const Eref &e, double leak)

void	setLength (const Eref &e, double length)

void	setOuterArea (const Eref &e, double outerArea)

void	setShapeMode (const Eref &e, unsigned int shapeMode)

void	setThickness (const Eref &e, double thickness)

void	setValence (const Eref &e, double valence)

void	setVolume (const Eref &e, double volume)

void	storeInflux (const Eref &e, double flux)

void	storeOutflux (const Eref &e, double flux)

void	tauPump (const Eref &e, double kP, double Ceq)

Static Public Member Functions
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from DifShellBase
static SrcFinfo1< double > *	concentrationOut ()

static const Cinfo *	initCinfo ()

static SrcFinfo2< double, double > *	innerDifSourceOut ()

static SrcFinfo2< double, double > *	outerDifSourceOut ()

Private Member Functions
double	integrate (double state, double dt, double A, double B)

Private Attributes
double	C_

double	Ceq_

double	Cmultiplier_

double	D_

double	dCbyDt_

double	diameter_

double	innerArea_

double	leak_

double	length_

double	outerArea_

double	prevC_

unsigned int	shapeMode_

double	thickness_

double	valence_

double	volume_

Static Private Attributes
static const double	EPSILON = 1.0e-10

static const double	F = 96485.3415
	Faraday's constant (Coulomb / Mole) More...

Detailed Description

Definition at line 14 of file DifShell.h.

Constructor & Destructor Documentation

DifShell::DifShell ( )

Faraday's constant (Coulomb / Mole)

Definition at line 56 of file DifShell.cpp.

                    :
   dCbyDt_( 0.0 ),
   Cmultiplier_(0.0),
   C_( 0.0 ),
   Ceq_( 0.0 ),
   prevC_(0.0),
   D_( 0.0 ),
   valence_( 0.0 ),
   leak_( 0.0 ),
   shapeMode_(0),
   length_(0),
   diameter_(0),
   thickness_(0),
   volume_(0),
   outerArea_(0),
   innerArea_(0)
 { ; }

Member Function Documentation

void DifShell::calculateVolumeArea ( const Eref & e )

Definition at line 285 of file DifShell.cpp.

References diameter_, innerArea_, length_, M_PI, outerArea_, shapeMode_, thickness_, and volume_.

Referenced by vReinit(), vSetDiameter(), vSetLength(), vSetShapeMode(), and vSetThickness().

 {
 double rOut = diameter_/2.;
 
   double rIn = rOut - thickness_;
 
   if (rIn <0)
       rIn = 0.;
 
   switch ( shapeMode_ )
     {
       /*
        * Onion Shell
        */
     case 0:
       if ( length_ == 0.0 ) { // Spherical shell
     volume_ = 4./3.* M_PI * ( rOut * rOut * rOut - rIn * rIn * rIn );
     outerArea_ = 4*M_PI * rOut * rOut;
     innerArea_ = 4*M_PI * rIn * rIn;
       } else { // Cylindrical shell
     volume_ = ( M_PI * length_  ) * ( rOut * rOut - rIn * rIn );
     outerArea_ = 2*M_PI * rOut * length_;
     innerArea_ = 2*M_PI * rIn * length_;
       }
 
       break;
 
       /*
        * Cylindrical Slice
        */
     case 1:
       volume_ = M_PI * diameter_ * diameter_ * thickness_ / 4.0;
       outerArea_ = M_PI * diameter_ * diameter_ / 4.0;
       innerArea_ = outerArea_;
       break;
 
       /*
        * User defined
        */
     case 3:
       // Nothing to be done here. Volume and inner-, outer areas specified by
       // user.
       break;
 
     default:
       assert( 0 );
     }
 }

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const Cinfo * DifShell::initCinfo ( )

static

Definition at line 19 of file DifShell.cpp.

References difShellCinfo, and DifShellBase::initCinfo().

 {
 
 
   static string doc[] =
     {
       "Name", "DifShell",
       "Author", "Niraj Dudani. Ported to async13 by Subhasis Ray. Rewritten by Asia Jedrzejewska-Szmek",
       "Description", "DifShell object: Models diffusion of an ion (typically calcium) within an "
       "electric compartment. A DifShell is an iso-concentration region with respect to "
       "the ion. Adjoining DifShells exchange flux of this ion, and also keep track of "
       "changes in concentration due to pumping, buffering and channel currents, by "
       "talking to the appropriate objects.",
     };
   static Dinfo< DifShell > dinfo;
   static Cinfo difShellCinfo(
                  "DifShell",
                  DifShellBase::initCinfo(),
                  0,
                  0,
                  &dinfo,
                  doc,
                  sizeof( doc ) / sizeof( string ));
 
   return &difShellCinfo;
 }

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double DifShell::integrate	(	double	state,
		double	dt,
		double	A,
		double	B
	)

private

Definition at line 275 of file DifShell.cpp.

References EPSILON.

Referenced by vProcess().

 {
     if ( B > EPSILON ) {
         double x = exp( -B * dt );
         return state * x + ( A / B ) * ( 1 - x );
     }
 
     return state + A * dt ;
 }

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void DifShell::vBuffer	(	const Eref &	e,
		double	kf,
		double	kb,
		double	bFree,
		double	bBound
	)

virtual

Implements DifShellBase.

Definition at line 376 of file DifShell.cpp.

References Cmultiplier_, and dCbyDt_.

 {
   dCbyDt_ += kb * bBound;
   Cmultiplier_ += kf * bFree;
 }

void DifShell::vEqTauPump	(	const Eref &	e,
		double	kP
	)

virtual

Same as tauPump, except that we use the v value of Ceq.

Implements DifShellBase.

Definition at line 459 of file DifShell.cpp.

References Ceq_, Cmultiplier_, and dCbyDt_.

 {
   dCbyDt_ += kP*Ceq_;
   Cmultiplier_ -= kP;
 }

void DifShell::vFInflux	(	const Eref &	e,
		double	I,
		double	fraction
	)

virtual

Implements DifShellBase.

Definition at line 429 of file DifShell.cpp.

References dCbyDt_, F, valence_, and volume_.

 {
   dCbyDt_ += fraction * I / ( F * valence_ * volume_ );
 }

void DifShell::vFluxFromIn	(	const Eref &	e,
		double	innerC,
		double	innerThickness
	)

virtual

Implements DifShellBase.

Definition at line 400 of file DifShell.cpp.

References Cmultiplier_, D_, dCbyDt_, innerArea_, thickness_, and volume_.

 {
   //influx from inner shell
   //double dx = ( innerThickness + thickness_ ) / 2.0;
   double diff = 2.* D_/volume_ * innerArea_ / (innerThickness + thickness_);
 
   dCbyDt_ +=  diff *  innerC ;
   Cmultiplier_ += diff ;
 }

void DifShell::vFluxFromOut	(	const Eref &	e,
		double	outerC,
		double	outerThickness
	)

virtual

We could pre-compute ( D / Volume ), but let us leave the optimizations for the solver.

Implements DifShellBase.

Definition at line 386 of file DifShell.cpp.

References Cmultiplier_, D_, dCbyDt_, outerArea_, thickness_, and volume_.

 {
   double diff =2.*  D_ /volume_ *  outerArea_ / (outerThickness + thickness_) ;
   //influx from outer shell
   dCbyDt_ +=  diff * outerC;
   Cmultiplier_ += diff ;
 
 }

void DifShell::vFOutflux	(	const Eref &	e,
		double	I,
		double	fraction
	)

virtual

Implements DifShellBase.

Definition at line 434 of file DifShell.cpp.

References dCbyDt_, F, valence_, and volume_.

 {
   dCbyDt_ -= fraction * I / ( F * valence_ * volume_ );
 }

double DifShell::vGetC ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 90 of file DifShell.cpp.

References C_.

 {
   return C_;
 }

double DifShell::vGetCeq ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 107 of file DifShell.cpp.

References Ceq_.

 {
   return Ceq_;
 }

double DifShell::vGetD ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 122 of file DifShell.cpp.

References D_.

 {
   return D_;
 }

double DifShell::vGetDiameter ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 195 of file DifShell.cpp.

References diameter_.

 {
   return diameter_;
 }

double DifShell::vGetInnerArea ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 265 of file DifShell.cpp.

References innerArea_.

 {
   return innerArea_;
 }

double DifShell::vGetLeak ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 147 of file DifShell.cpp.

References leak_.

 {
   return leak_;
 }

double DifShell::vGetLength ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 179 of file DifShell.cpp.

References length_.

 {
   return length_;
 }

double DifShell::vGetOuterArea ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 247 of file DifShell.cpp.

References outerArea_.

 {
   return outerArea_;
 }

unsigned int DifShell::vGetShapeMode ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 163 of file DifShell.cpp.

References shapeMode_.

 {
   return shapeMode_;
 }

double DifShell::vGetThickness ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 211 of file DifShell.cpp.

References thickness_.

 {
   return thickness_;
 }

double DifShell::vGetValence ( const Eref & e ) const

virtual

Implements DifShellBase.

Definition at line 137 of file DifShell.cpp.

References valence_.

 {
   return valence_;
 }

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

virtual

Implements DifShellBase.

Definition at line 229 of file DifShell.cpp.

References volume_.

 {
   return volume_;
 }

void DifShell::vHillPump	(	const Eref &	e,
		double	vMax,
		double	Kd,
		unsigned int	hill
	)

virtual

Implements DifShellBase.

Definition at line 471 of file DifShell.cpp.

References C_, dCbyDt_, and volume_.

 {
   //This needs fixing
   double ch;
   switch( hill )
     {
     case 0:
       ch = 1.0;
       break;
     case 1:
       ch = C_;
       break;
     case 2:
       ch = C_ * C_;
       break;
     case 3:
       ch = C_ * C_ * C_;
       break;
     case 4:
       ch = C_ * C_;
       ch = ch * ch;
       break;
     default:
       ch = pow( C_, static_cast< double >( hill ) );
     };
 
   dCbyDt_ += -( vMax / volume_ ) * ( ch / ( ch + Kd ) );
 }

void DifShell::vInflux	(	const Eref &	e,
		double	I
	)

virtual

I: Amperes F_: Faraday's constant: Coulomb / mole valence_: charge on ion: dimensionless

Implements DifShellBase.

Definition at line 410 of file DifShell.cpp.

References dCbyDt_, F, valence_, and volume_.

 {
   dCbyDt_ += I / ( F * valence_ * volume_ );
 
 }

void DifShell::vMMPump	(	const Eref &	e,
		double	vMax,
		double	Kd
	)

virtual

Implements DifShellBase.

Definition at line 465 of file DifShell.cpp.

References C_, Cmultiplier_, and volume_.

 {
   Cmultiplier_ += ( vMax / volume_ )  / ( C_ + Kd ) ;
 
 }

void DifShell::vOutflux	(	const Eref &	e,
		double	I
	)

virtual

Same as influx, except subtracting.

Implements DifShellBase.

Definition at line 424 of file DifShell.cpp.

References dCbyDt_, F, valence_, and volume_.

 {
   dCbyDt_ -= I / ( F * valence_ * volume_ );
 }

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

virtual

Send ion concentration and thickness to adjacent DifShells. They will then compute their incoming fluxes.

Send ion concentration to ion buffers. They will send back information on the reaction (forward / backward rates ; free / bound buffer concentration) immediately, which this DifShell will use to find amount of ion captured or released in the current time-step.

Implements DifShellBase.

Definition at line 348 of file DifShell.cpp.

References C_, Cmultiplier_, DifShellBase::concentrationOut(), dCbyDt_, ProcInfo::dt, DifShellBase::innerDifSourceOut(), integrate(), leak_, DifShellBase::outerDifSourceOut(), prevC_, and thickness_.

 {
   C_ = integrate(C_,p->dt,dCbyDt_,Cmultiplier_);
 
   dCbyDt_ = leak_;
   Cmultiplier_ = 0;
   prevC_ = C_;
 
   innerDifSourceOut()->send( e, prevC_, thickness_ );
   outerDifSourceOut()->send( e, prevC_, thickness_ );
 
   concentrationOut()->send( e, C_ );
 
 }

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

virtual

Implements DifShellBase.

Definition at line 334 of file DifShell.cpp.

References C_, calculateVolumeArea(), Ceq_, Cmultiplier_, DifShellBase::concentrationOut(), dCbyDt_, DifShellBase::innerDifSourceOut(), leak_, DifShellBase::outerDifSourceOut(), prevC_, and thickness_.

 {
   dCbyDt_ = leak_;
   Cmultiplier_ = 0;
   calculateVolumeArea(e);
 
   C_= Ceq_;
   prevC_ = Ceq_;
   concentrationOut()->send( e, C_ );
   innerDifSourceOut()->send( e, prevC_, thickness_ );
   outerDifSourceOut()->send( e, prevC_, thickness_ );
 
 }

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void DifShell::vSetC	(	const Eref &	e,
		double	C
	)

virtual

C is a read-only field.

Implements DifShellBase.

Definition at line 80 of file DifShell.cpp.

References C_, and prevC_.

 {
   if ( C < 0.0 ) {
     cerr << "Error: DifShell: C cannot be negative!\n";
     return;
   }
 
   C_ = C;
   prevC_ = C_;
 }

void DifShell::vSetCeq	(	const Eref &	e,
		double	Ceq
	)

virtual

Implements DifShellBase.

Definition at line 95 of file DifShell.cpp.

References C_, Ceq_, and prevC_.

 {
   if ( Ceq < 0.0 ) {
     cerr << "Error: DifShell: Ceq cannot be negative!\n";
     return;
   }
 
   Ceq_ = Ceq;
   prevC_ = Ceq;
   C_ = Ceq;
 }

void DifShell::vSetD	(	const Eref &	e,
		double	D
	)

virtual

Implements DifShellBase.

Definition at line 112 of file DifShell.cpp.

References D_.

 {
   if ( D < 0.0 ) {
     cerr << "Error: DifShell: D cannot be negative!\n";
     return;
   }
 
   D_ = D;
 }

void DifShell::vSetDiameter	(	const Eref &	e,
		double	diameter
	)

virtual

Implements DifShellBase.

Definition at line 184 of file DifShell.cpp.

References calculateVolumeArea(), and diameter_.

 {
   if ( diameter < 0.0 ) {
     cerr << "Error: DifShell: diameter cannot be negative!\n";
     return;
   }
 
   diameter_ = diameter;
   calculateVolumeArea(e);
 }

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void DifShell::vSetInnerArea	(	const Eref &	e,
		double	innerArea
	)

virtual

Implements DifShellBase.

Definition at line 252 of file DifShell.cpp.

References innerArea_, and shapeMode_.

 {
   if ( shapeMode_ != 3 )
     cerr << "Warning: DifShell: Trying to set innerArea, when shapeMode is not USER-DEFINED\n";
 
   if ( innerArea < 0.0 ) {
     cerr << "Error: DifShell: innerArea cannot be negative!\n";
     return;
   }
 
   innerArea_ = innerArea;
 }

void DifShell::vSetLeak	(	const Eref &	e,
		double	leak
	)

virtual

Implements DifShellBase.

Definition at line 142 of file DifShell.cpp.

References leak_.

 {
   leak_ = leak;
 }

void DifShell::vSetLength	(	const Eref &	e,
		double	length
	)

virtual

Implements DifShellBase.

Definition at line 168 of file DifShell.cpp.

References calculateVolumeArea(), and length_.

 {
   if ( length < 0.0 ) {
     cerr << "Error: DifShell: length cannot be negative!\n";
     return;
   }
 
   length_ = length;
   calculateVolumeArea(e);
 }

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void DifShell::vSetOuterArea	(	const Eref &	e,
		double	outerArea
	)

virtual

Implements DifShellBase.

Definition at line 234 of file DifShell.cpp.

References outerArea_, and shapeMode_.

 {
   if (shapeMode_ != 3 )
     cerr << "Warning: DifShell: Trying to set outerArea, when shapeMode is not USER-DEFINED\n";
 
   if ( outerArea < 0.0 ) {
     cerr << "Error: DifShell: outerArea cannot be negative!\n";
     return;
   }
 
   outerArea_ = outerArea;
 }

void DifShell::vSetShapeMode	(	const Eref &	e,
		unsigned int	shapeMode
	)

virtual

Implements DifShellBase.

Definition at line 153 of file DifShell.cpp.

References calculateVolumeArea(), and shapeMode_.

 {
   if ( shapeMode != 0 && shapeMode != 1 && shapeMode != 3 ) {
     cerr << "Error: DifShell: I only understand shapeModes 0, 1 and 3.\n";
     return;
   }
   shapeMode_ = shapeMode;
   calculateVolumeArea(e);
 }

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void DifShell::vSetThickness	(	const Eref &	e,
		double	thickness
	)

virtual

Implements DifShellBase.

Definition at line 200 of file DifShell.cpp.

References calculateVolumeArea(), and thickness_.

 {
   if ( thickness < 0.0 ) {
     cerr << "Error: DifShell: thickness cannot be negative!\n";
     return;
   }
 
   thickness_ = thickness;
   calculateVolumeArea(e);
 }

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void DifShell::vSetValence	(	const Eref &	e,
		double	valence
	)

virtual

Implements DifShellBase.

Definition at line 127 of file DifShell.cpp.

References valence_.

 {
   if ( valence < 0.0 ) {
     cerr << "Error: DifShell: valence cannot be negative!\n";
     return;
   }
 
   valence_ = valence;
 }

void DifShell::vSetVolume	(	const Eref &	e,
		double	volume
	)

virtual

Implements DifShellBase.

Definition at line 216 of file DifShell.cpp.

References shapeMode_, and volume_.

 {
   if ( shapeMode_ != 3 )
     cerr << "Warning: DifShell: Trying to set volume, when shapeMode is not USER-DEFINED\n";
 
   if ( volume < 0.0 ) {
     cerr << "Error: DifShell: volume cannot be negative!\n";
     return;
   }
 
   volume_ = volume;
 }

void DifShell::vStoreInflux	(	const Eref &	e,
		double	flux
	)

virtual

Implements DifShellBase.

Definition at line 439 of file DifShell.cpp.

References dCbyDt_, and volume_.

 {
   dCbyDt_ += flux / volume_;
 }

void DifShell::vStoreOutflux	(	const Eref &	e,
		double	flux
	)

virtual

Implements DifShellBase.

Definition at line 444 of file DifShell.cpp.

References dCbyDt_, and volume_.

 {
   dCbyDt_ -= flux / volume_;
 }

void DifShell::vTauPump	(	const Eref &	e,
		double	kP,
		double	Ceq
	)

virtual

Implements DifShellBase.

Definition at line 449 of file DifShell.cpp.

References Cmultiplier_, and dCbyDt_.

 {
   //dCbyDt_ += -kP * ( C_ - Ceq );
   dCbyDt_ += kP*Ceq;
   Cmultiplier_ -= kP;
 }

Member Data Documentation

double DifShell::C_

private

Definition at line 88 of file DifShell.h.

Referenced by vGetC(), vHillPump(), vMMPump(), vProcess(), vReinit(), vSetC(), and vSetCeq().

double DifShell::Ceq_

private

Definition at line 89 of file DifShell.h.

Referenced by vEqTauPump(), vGetCeq(), vReinit(), and vSetCeq().

double DifShell::Cmultiplier_

private

Definition at line 87 of file DifShell.h.

Referenced by vBuffer(), vEqTauPump(), vFluxFromIn(), vFluxFromOut(), vMMPump(), vProcess(), vReinit(), and vTauPump().

double DifShell::D_

private

Definition at line 91 of file DifShell.h.

Referenced by vFluxFromIn(), vFluxFromOut(), vGetD(), and vSetD().

double DifShell::dCbyDt_

private

Definition at line 86 of file DifShell.h.

Referenced by vBuffer(), vEqTauPump(), vFInflux(), vFluxFromIn(), vFluxFromOut(), vFOutflux(), vHillPump(), vInflux(), vOutflux(), vProcess(), vReinit(), vStoreInflux(), vStoreOutflux(), and vTauPump().

double DifShell::diameter_

private

Definition at line 96 of file DifShell.h.

Referenced by calculateVolumeArea(), vGetDiameter(), and vSetDiameter().

const double DifShell::EPSILON = 1.0e-10

staticprivate

Definition at line 102 of file DifShell.h.

Referenced by integrate().

const double DifShell::F = 96485.3415

staticprivate

Faraday's constant (Coulomb / Mole)

Definition at line 104 of file DifShell.h.

Referenced by vFInflux(), vFOutflux(), vInflux(), and vOutflux().

double DifShell::innerArea_

private

Definition at line 100 of file DifShell.h.

Referenced by calculateVolumeArea(), vFluxFromIn(), vGetInnerArea(), and vSetInnerArea().

double DifShell::leak_

private

Definition at line 93 of file DifShell.h.

Referenced by vGetLeak(), vProcess(), vReinit(), and vSetLeak().

double DifShell::length_

private

Definition at line 95 of file DifShell.h.

Referenced by calculateVolumeArea(), vGetLength(), and vSetLength().

double DifShell::outerArea_

private

Definition at line 99 of file DifShell.h.

Referenced by calculateVolumeArea(), vFluxFromOut(), vGetOuterArea(), and vSetOuterArea().

double DifShell::prevC_

private

Definition at line 90 of file DifShell.h.

Referenced by vProcess(), vReinit(), vSetC(), and vSetCeq().

unsigned int DifShell::shapeMode_

private

Definition at line 94 of file DifShell.h.

Referenced by calculateVolumeArea(), vGetShapeMode(), vSetInnerArea(), vSetOuterArea(), vSetShapeMode(), and vSetVolume().

double DifShell::thickness_

private

Definition at line 97 of file DifShell.h.

Referenced by calculateVolumeArea(), vFluxFromIn(), vFluxFromOut(), vGetThickness(), vProcess(), vReinit(), and vSetThickness().

double DifShell::valence_

private

Definition at line 92 of file DifShell.h.

Referenced by vFInflux(), vFOutflux(), vGetValence(), vInflux(), vOutflux(), and vSetValence().

double DifShell::volume_

private

Definition at line 98 of file DifShell.h.

Referenced by calculateVolumeArea(), vFInflux(), vFluxFromIn(), vFluxFromOut(), vFOutflux(), vGetVolume(), vHillPump(), vInflux(), vMMPump(), vOutflux(), vSetVolume(), vStoreInflux(), and vStoreOutflux().

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

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

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