#include <DifBuffer.h>

Inheritance diagram for DifBuffer:

Collaboration diagram for DifBuffer:

Public Member Functions
void	calculateVolumeArea (const Eref &e)

	DifBuffer ()

void	vBuffer (const Eref &e, double C)

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

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

double	vGetActivation (const Eref &e) const

double	vGetBBound (const Eref &e) const

double	vGetBFree (const Eref &e) const

double	vGetBTot (const Eref &e) const

double	vGetD (const Eref &e) const

double	vGetDiameter (const Eref &e) const

double	vGetInnerArea (const Eref &e) const

double	vGetKb (const Eref &e) const

double	vGetKf (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	vGetVolume (const Eref &e) const

void	vProcess (const Eref &e, ProcPtr p)

void	vReinit (const Eref &e, ProcPtr p)

void	vSetActivation (const Eref &e, double value)

void	vSetBBound (const Eref &e, double value)

void	vSetBFree (const Eref &e, double value)

void	vSetBTot (const Eref &e, double value)

void	vSetD (const Eref &e, double value)

void	vSetDiameter (const Eref &e, double diameter)

void	vSetInnerArea (const Eref &e, double innerArea)

void	vSetKb (const Eref &e, double value)

void	vSetKf (const Eref &e, double value)

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	vSetVolume (const Eref &e, double volume)

Public Member Functions inherited from DifBufferBase
void	buffer (const Eref &e, double C)

	DifBufferBase ()

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

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

double	getActivation (const Eref &e) const

double	getBBound (const Eref &e) const

double	getBFree (const Eref &e) const

double	getBTot (const Eref &e) const

double	getD (const Eref &e) const

double	getDiameter (const Eref &e) const

double	getInnerArea (const Eref &e) const

double	getKb (const Eref &e) const

double	getKf (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	getVolume (const Eref &e) const

void	process (const Eref &e, ProcPtr p)

void	reinit (const Eref &e, ProcPtr p)

void	setActivation (const Eref &e, double value)

void	setBBound (const Eref &e, double value)

void	setBFree (const Eref &e, double value)

void	setBTot (const Eref &e, double value)

void	setD (const Eref &e, double value)

void	setDiameter (const Eref &e, double value)

void	setInnerArea (const Eref &e, double innerArea)

void	setKb (const Eref &e, double value)

void	setKf (const Eref &e, double value)

void	setLength (const Eref &e, double value)

void	setOuterArea (const Eref &e, double outerArea)

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

void	setThickness (const Eref &e, double value)

void	setVolume (const Eref &e, double volume)

Static Public Member Functions
static const Cinfo *	initCinfo ()

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

static SrcFinfo2< double, double > *	innerDifSourceOut ()

static SrcFinfo2< double, double > *	outerDifSourceOut ()

static SrcFinfo4< double, double, double, double > *	reactionOut ()

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

Private Attributes
double	activation_

double	Af_

double	bBound_

double	Bf_

double	bFree_

double	bTot_

double	D_

double	diameter_

double	innerArea_

double	kb_

double	kf_

double	length_

double	outerArea_

double	prevBound_

double	prevFree_

unsigned int	shapeMode_

double	thickness_

double	volume_

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

Detailed Description

Definition at line 13 of file DifBuffer.h.

Constructor & Destructor Documentation

DifBuffer::DifBuffer ( )

Definition at line 86 of file DifBuffer.cpp.

                      :
   activation_(0),
   Af_(0),
   Bf_(0),
   bFree_(0),
   bBound_(0),
   prevFree_(0),
   prevBound_(0),
   bTot_(0),
   kf_(0),
   kb_(0),
   D_(0),
   shapeMode_(0),
   length_(0),
   diameter_(0),
   thickness_(0),
   volume_(0),
   outerArea_(0),
   innerArea_(0)
 
 {}

Member Function Documentation

void DifBuffer::calculateVolumeArea ( const Eref & e )

Definition at line 367 of file DifBuffer.cpp.

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

Referenced by 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 * DifBuffer::initCinfo ( )

static

Definition at line 57 of file DifBuffer.cpp.

References difBufferCinfo, and DifBufferBase::initCinfo().

 {
 
   static string doc[] = {
     "Name", "DifBuffer",
     "Author", "Subhasis Ray (ported from GENESIS2)",
     "Description", "Models diffusible buffer where total concentration is constant. It is"
     " coupled with a DifShell.",
   };
   static Dinfo<DifBuffer> dinfo;
   static Cinfo difBufferCinfo(
                   "DifBuffer",
                   DifBufferBase::initCinfo(),
                   0,
                   0,
                   &dinfo,
                   doc,
                   sizeof(doc)/sizeof(string));
 
   return &difBufferCinfo;
 }

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

private

Definition at line 359 of file DifBuffer.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 DifBuffer::vBuffer	(	const Eref &	e,
		double	C
	)

virtual

Implements DifBufferBase.

Definition at line 351 of file DifBuffer.cpp.

References activation_.

 {
   activation_ = C;
   //cout<<"Buffer"<< C<<" ";
 }

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

virtual

Implements DifBufferBase.

Definition at line 506 of file DifBuffer.cpp.

References Af_, Bf_, D_, innerArea_, thickness_, and volume_.

 {
   double dif = 2 * D_  / volume_* innerArea_ / (thickness_ + innerThickness);
   Af_ += dif * innerC;
   Bf_ += dif;
 }

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

virtual

Implements DifBufferBase.

Definition at line 513 of file DifBuffer.cpp.

References Af_, Bf_, D_, outerArea_, thickness_, and volume_.

 {
   double dif = 2 * D_  / volume_* outerArea_ / (thickness_ + outerThickness);
   Af_ += dif * outerC;
   Bf_ += dif;
 }

double DifBuffer::vGetActivation ( const Eref & e ) const

virtual

Implements DifBufferBase.

Definition at line 111 of file DifBuffer.cpp.

References activation_.

 {
   return activation_;
 }

double DifBuffer::vGetBBound ( const Eref & e ) const

virtual

Implements DifBufferBase.

Definition at line 147 of file DifBuffer.cpp.

References bBound_.

 {
   return bBound_;
 }

double DifBuffer::vGetBFree ( const Eref & e ) const

virtual

Implements DifBufferBase.

Definition at line 126 of file DifBuffer.cpp.

References bFree_.

 {
   return bFree_;
 }

double DifBuffer::vGetBTot ( const Eref & e ) const

virtual

Implements DifBufferBase.

Definition at line 169 of file DifBuffer.cpp.

References bTot_.

 {
   return bTot_;
 }

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

virtual

Implements DifBufferBase.

Definition at line 215 of file DifBuffer.cpp.

References D_.

 {
   return D_;
 }

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

virtual

Implements DifBufferBase.

Definition at line 273 of file DifBuffer.cpp.

References diameter_.

 {
   return diameter_;
 }

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

virtual

Implements DifBufferBase.

Definition at line 343 of file DifBuffer.cpp.

References innerArea_.

 {
   return innerArea_;
 }

double DifBuffer::vGetKb ( const Eref & e ) const

virtual

Implements DifBufferBase.

Definition at line 201 of file DifBuffer.cpp.

References kb_.

 {
   return kb_;
 }

double DifBuffer::vGetKf ( const Eref & e ) const

virtual

Implements DifBufferBase.

Definition at line 186 of file DifBuffer.cpp.

References kf_.

 {
   return kf_;
 }

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

virtual

Implements DifBufferBase.

Definition at line 257 of file DifBuffer.cpp.

References length_.

 {
   return length_;
 }

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

virtual

Implements DifBufferBase.

Definition at line 325 of file DifBuffer.cpp.

References outerArea_.

 {
   return outerArea_;
 }

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

virtual

Implements DifBufferBase.

Definition at line 241 of file DifBuffer.cpp.

References shapeMode_.

 {
   return shapeMode_;
 }

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

virtual

Implements DifBufferBase.

Definition at line 289 of file DifBuffer.cpp.

References thickness_.

 {
   return thickness_;
 }

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

virtual

Implements DifBufferBase.

Definition at line 307 of file DifBuffer.cpp.

References volume_.

 {
   return volume_;
 }

void DifBuffer::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 DifBufferBase.

Definition at line 416 of file DifBuffer.cpp.

References activation_, Af_, bBound_, Bf_, bFree_, bTot_, ProcInfo::dt, DifBufferBase::innerDifSourceOut(), integrate(), kb_, kf_, DifBufferBase::outerDifSourceOut(), prevBound_, prevFree_, DifBufferBase::reactionOut(), and thickness_.

 {
   Af_ += kb_ * bBound_;
   Bf_ += kf_ * activation_;
 
   bFree_ = integrate(bFree_,p->dt,Af_,Bf_);
   bBound_ = bTot_ - bFree_;
   prevFree_ = bFree_;
   prevBound_ = bBound_;
 
   innerDifSourceOut()->send( e, prevFree_, thickness_ );
   outerDifSourceOut()->send( e, prevFree_, thickness_ );
   reactionOut()->send(e,kf_,kb_,bFree_,bBound_);
   Af_ = 0;
   Bf_= 0;
 
 }

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

virtual

Implements DifBufferBase.

Definition at line 447 of file DifBuffer.cpp.

References activation_, Af_, bBound_, Bf_, bFree_, bTot_, diameter_, innerArea_, DifBufferBase::innerDifSourceOut(), kb_, kf_, length_, M_PI, outerArea_, DifBufferBase::outerDifSourceOut(), prevBound_, prevFree_, shapeMode_, thickness_, and volume_.

 {
 
   Af_ = 0;
   Bf_= 0;
   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 );
     }
 
   bFree_ = bTot_/(1+activation_*kf_/kb_);
   prevFree_ = bFree_;
   bBound_ = bTot_ - bFree_;
   prevBound_ = bBound_;
   innerDifSourceOut()->send( e, prevFree_, thickness_ );
   outerDifSourceOut()->send( e, prevFree_, thickness_ );
 
 }

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void DifBuffer::vSetActivation	(	const Eref &	e,
		double	value
	)

virtual

Implements DifBufferBase.

Definition at line 116 of file DifBuffer.cpp.

References activation_, and value.

 {
   if ( value  < 0.0 ) {
     cerr << "Error: DifBuffer: Activation cannot be negative!\n";
     return;
   }
   activation_ = value;
 }

void DifBuffer::vSetBBound	(	const Eref &	e,
		double	value
	)

virtual

Implements DifBufferBase.

Definition at line 152 of file DifBuffer.cpp.

References bBound_, bFree_, bTot_, prevBound_, prevFree_, and value.

 {
   if ( value  < 0.0 ) {
     cerr << "Error: DifBuffer: Bound Buffer cannot be negative!\n";
     return;
   }
   if (value > bTot_){
     cerr << "Error: DifBuffer: Bound Buffer cannot exceed total buffer!\n";
     return;
   }
   bBound_ = value;
   bFree_ = bTot_ - bBound_;
   prevFree_= bFree_;
   prevBound_ = bBound_;
 }

void DifBuffer::vSetBFree	(	const Eref &	e,
		double	value
	)

virtual

Implements DifBufferBase.

Definition at line 130 of file DifBuffer.cpp.

References bBound_, bFree_, bTot_, prevBound_, prevFree_, and value.

 {
   if ( value  < 0.0 ) {
     cerr << "Error: DifBuffer: Free Buffer cannot be negative!\n";
     return;
   }
   if (value > bTot_){
     cerr << "Error: DifBuffer: Free Buffer cannot exceed total buffer!\n";
     return;
   }
   bFree_ = value;
   bBound_ = bTot_ - bFree_;
   prevFree_= bFree_;
   prevBound_ = bBound_;
 
 }

void DifBuffer::vSetBTot	(	const Eref &	e,
		double	value
	)

virtual

Implements DifBufferBase.

Definition at line 174 of file DifBuffer.cpp.

References bBound_, bFree_, bTot_, and value.

 {
   if ( value  < 0.0 ) {
     cerr << "Error: DifBuffer: Total buffer concentration cannot be negative!\n";
     return;
   }
   bTot_ = value;
   bFree_ = bTot_;
   bBound_ = 0;
 }

void DifBuffer::vSetD	(	const Eref &	e,
		double	value
	)

virtual

Implements DifBufferBase.

Definition at line 220 of file DifBuffer.cpp.

References D_, and value.

 {
 
   if ( value  < 0.0 ) {
     cerr << " Error: DifBuffer: Diffusion constant, D, cannot be negative!\n";
     return;
   }
   D_ = value;
 }

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

virtual

Implements DifBufferBase.

Definition at line 262 of file DifBuffer.cpp.

References calculateVolumeArea(), and diameter_.

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

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

virtual

Implements DifBufferBase.

Definition at line 330 of file DifBuffer.cpp.

References innerArea_, and shapeMode_.

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

void DifBuffer::vSetKb	(	const Eref &	e,
		double	value
	)

virtual

Implements DifBufferBase.

Definition at line 206 of file DifBuffer.cpp.

References kb_, and value.

 {
   if ( value  < 0.0 ) {
     cerr << "Error: DifBuffer: Kb cannot be negative!\n";
     return;
   }
   kb_ = value;
 }

void DifBuffer::vSetKf	(	const Eref &	e,
		double	value
	)

virtual

Implements DifBufferBase.

Definition at line 191 of file DifBuffer.cpp.

References kf_, and value.

 {
   if ( value  < 0.0 ) {
     cerr << "Error: DifBuffer: Kf cannot be negative!\n";
     return;
   }
   kf_ = value;
 }

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

virtual

Implements DifBufferBase.

Definition at line 246 of file DifBuffer.cpp.

References calculateVolumeArea(), and length_.

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

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

virtual

Implements DifBufferBase.

Definition at line 312 of file DifBuffer.cpp.

References outerArea_, and shapeMode_.

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

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

virtual

Implements DifBufferBase.

Definition at line 231 of file DifBuffer.cpp.

References calculateVolumeArea(), and shapeMode_.

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

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

virtual

Implements DifBufferBase.

Definition at line 278 of file DifBuffer.cpp.

References calculateVolumeArea(), and thickness_.

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

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

virtual

Implements DifBufferBase.

Definition at line 294 of file DifBuffer.cpp.

References shapeMode_, and volume_.

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