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Asia Jędrzejewska-Szmek authored08f2e43a
DifBufferBase.cpp 13.54 KiB
#include "header.h"
#include "DifBufferBase.h"
#include "ElementValueFinfo.h"
#include "../utility/numutil.h"
#include <cmath>
SrcFinfo4< double, double, double, double >* DifBufferBase::reactionOut()
{
static SrcFinfo4< double, double, double, double > reactionOut(
"reactionOut",
"Sends out reaction rates (forward and backward), and concentrations"
" (free-buffer and bound-buffer molecules).");
return &reactionOut;
}
SrcFinfo2< double, double >* DifBufferBase::innerDifSourceOut(){
static SrcFinfo2< double, double > sourceOut("innerDifSourceOut",
"Sends out source information.");
return &sourceOut;
}
SrcFinfo2< double, double >* DifBufferBase::outerDifSourceOut(){
static SrcFinfo2< double, double > sourceOut("outerDifSourceOut",
"Sends out source information.");
return &sourceOut;
}
const Cinfo * DifBufferBase::initCinfo()
{
static DestFinfo process( "process",
"Handles process call",
new ProcOpFunc< DifBufferBase >( &DifBufferBase::process) );
static DestFinfo reinit( "reinit",
"Reinit happens only in stage 0",
new ProcOpFunc< DifBufferBase >( &DifBufferBase::reinit));
static Finfo* processShared[] = {
&process,
&reinit
};
static SharedFinfo proc(
"proc",
"Here we create 2 shared finfos to attach with the Ticks. This is because we want to perform DifBufferBase "
"computations in 2 stages, much as in the Compartment object. "
"In the first stage we send out the concentration value to other DifBufferBases and Buffer elements. We also",
processShared,
sizeof( processShared ) / sizeof( Finfo* ));
static DestFinfo concentration("concentration",
"Receives concentration (from DifShell).",
new EpFunc1<DifBufferBase, double>(&DifBufferBase::buffer));
static Finfo* bufferShared[] = {
&concentration, DifBufferBase::reactionOut()
};
static SharedFinfo buffer( "buffer",
"This is a shared message with DifShell. "
"During stage 0:\n "
" - DifBufferBase sends ion concentration\n"
" - Buffer updates buffer concentration and sends it back immediately using a call-back.\n"
" - DifShell updates the time-derivative ( dC / dt ) \n"
"\n"
"During stage 1: \n"
" - DifShell advances concentration C \n\n"
"This scheme means that the Buffer does not need to be scheduled, and it does its computations when "
"it receives a cue from the DifShell. May not be the best idea, but it saves us from doing the above "
"computations in 3 stages instead of 2." ,
bufferShared,
sizeof( bufferShared ) / sizeof( Finfo* ));
static DestFinfo fluxFromOut( "fluxFromOut",
"Destination message",
new EpFunc2< DifBufferBase, double, double > ( &DifBufferBase::fluxFromOut ));
static Finfo* innerDifShared[] = {
&fluxFromOut,
DifBufferBase::innerDifSourceOut()
};
static SharedFinfo innerDif( "innerDif",
"This shared message (and the next) is between DifBufferBases: adjoining shells exchange information to "
"find out the flux between them. "
"Using this message, an inner shell sends to, and receives from its outer shell." ,
innerDifShared,
sizeof( innerDifShared ) / sizeof( Finfo* ));
static DestFinfo fluxFromIn( "fluxFromIn", "",
new EpFunc2< DifBufferBase, double, double> ( &DifBufferBase::fluxFromIn) );
static Finfo* outerDifShared[] = {
&fluxFromIn,
DifBufferBase::outerDifSourceOut(),
};
static SharedFinfo outerDif( "outerDif",
"Using this message, an outer shell sends to, and receives from its inner shell." ,
outerDifShared,
sizeof( outerDifShared ) / sizeof( Finfo* ));
////////////////////////////
// Field defs
////////////////////////////
static ElementValueFinfo<DifBufferBase, double> activation("activation",
"Ion concentration from incoming conc message.",
&DifBufferBase::setActivation,
&DifBufferBase::getActivation);
static ElementValueFinfo<DifBufferBase, double> kf("kf",
"Forward rate constant of buffer molecules 1/mM/s (?)",
&DifBufferBase::setKf,
&DifBufferBase::getKf);
static ElementValueFinfo<DifBufferBase, double> kb("kb",
"Backward rate constant of buffer molecules. 1/s",
&DifBufferBase::setKb,
&DifBufferBase::getKb);
static ElementValueFinfo<DifBufferBase, double> D("D",
"Diffusion constant of buffer molecules. m^2/s",
&DifBufferBase::setD,
&DifBufferBase::getD);
static ElementValueFinfo<DifBufferBase, double> bFree("bFree",
"Free buffer concentration",
&DifBufferBase::setBFree,
&DifBufferBase::getBFree);
static ElementValueFinfo<DifBufferBase, double> bBound("bBound",
"Bound buffer concentration",
&DifBufferBase::setBBound,
&DifBufferBase::getBBound);
static ElementValueFinfo<DifBufferBase, double> bTot("bTot",
"Total buffer concentration.",
&DifBufferBase::setBTot,
&DifBufferBase::getBTot);
static ElementValueFinfo<DifBufferBase, double> length("length",
"Length of shell",
&DifBufferBase::setLength,
&DifBufferBase::getLength);
static ElementValueFinfo<DifBufferBase, double> diameter("diameter",
"Diameter of shell",
&DifBufferBase::setDiameter, &DifBufferBase::getDiameter);
static ElementValueFinfo<DifBufferBase, unsigned int> shapeMode("shapeMode",
"shape of the shell: SHELL=0, SLICE=SLAB=1, USERDEF=3",
&DifBufferBase::setShapeMode,
&DifBufferBase::getShapeMode);
static ElementValueFinfo<DifBufferBase, double> thickness("thickness",
"Thickness of shell",
&DifBufferBase::setThickness,
&DifBufferBase::getThickness);
static ElementValueFinfo<DifBufferBase, double> innerArea("innerArea",
"Inner area of shell",
&DifBufferBase::setInnerArea,
&DifBufferBase::getInnerArea);
static ElementValueFinfo<DifBufferBase, double> outerArea("outerArea",
"Outer area of shell",
&DifBufferBase::setOuterArea,
&DifBufferBase::getOuterArea);
static ElementValueFinfo< DifBufferBase, double> volume( "volume", "",
&DifBufferBase::setVolume,
&DifBufferBase::getVolume );
////
// DestFinfo
////
static Finfo * difBufferFinfos[] = {
//////////////////////////////////////////////////////////////////
// Field definitions
//////////////////////////////////////////////////////////////////
&activation,
&D,
&bFree,
&bBound,
&bTot,
&kf,
&kb,
//&prevFree,
//&prevBound,
&length,
&diameter,
&shapeMode,
&thickness,
&innerArea,
&outerArea,
&volume,
//////////////////////////////////////////////////////////////////
// SharedFinfo definitions
/////////////////////////////////////////////////////////////////
&proc,
&buffer,
&innerDif,
&outerDif,
//
reactionOut(),
innerDifSourceOut(),
outerDifSourceOut(),
//////////////////////////////////////////////////////////////////
// DestFinfo definitions
//////////////////////////////////////////////////////////////////
&concentration,
};
static string doc[] = {
"Name", "DifBufferBase",
"Author", "Subhasis Ray (ported from GENESIS2)",
"Description", "Models diffusible buffer where total concentration is constant. It is"
" coupled with a DifShell.",
}; static ZeroSizeDinfo<int> dinfo;
static Cinfo difBufferCinfo(
"DifBufferBase",
Neutral::initCinfo(),
difBufferFinfos,
sizeof(difBufferFinfos)/sizeof(Finfo*),
&dinfo,
doc,
sizeof(doc)/sizeof(string));
return &difBufferCinfo;
}
static const Cinfo * difBufferCinfo = DifBufferBase::initCinfo();
////////////////////////////////////////////////////////////////////////////////
// Class functions
////////////////////////////////////////////////////////////////////////////////
DifBufferBase::DifBufferBase()
{ ; }
double DifBufferBase::getActivation(const Eref& e) const
{
return vGetActivation(e);
}
void DifBufferBase::setActivation(const Eref& e,double value)
{
vSetActivation(e,value);
}
double DifBufferBase::getBFree(const Eref& e) const
{
return vGetBFree(e);
}
void DifBufferBase::setBFree(const Eref& e,double value)
{
vSetBFree(e,value);
}
double DifBufferBase::getBBound(const Eref& e) const
{
return vGetBBound(e);
}
void DifBufferBase::setBBound(const Eref& e,double value)
{
vSetBBound(e,value);
}
double DifBufferBase::getBTot(const Eref& e) const
{
return vGetBTot(e);
}
void DifBufferBase::setBTot(const Eref& e,double value)
{
vSetBTot(e,value);
}
double DifBufferBase::getKf(const Eref& e) const
{
return vGetKf(e);
}
void DifBufferBase::setKf(const Eref& e,double value)
{
vSetKf(e,value);
}
double DifBufferBase::getKb(const Eref& e) const
{
return vGetKb(e);
}
void DifBufferBase::setKb(const Eref& e,double value)
{
vSetKb(e,value);
}
double DifBufferBase::getD(const Eref& e) const
{
return vGetD(e);
}
void DifBufferBase::setD(const Eref& e,double value)
{
vSetD(e,value);
}
void DifBufferBase::setShapeMode(const Eref& e, unsigned int shapeMode )
{
vSetShapeMode(e,shapeMode);
}
unsigned int DifBufferBase::getShapeMode(const Eref& e) const
{
return vGetShapeMode(e);
}
void DifBufferBase::setLength(const Eref& e, double length )
{
vSetLength(e,length);
}
double DifBufferBase::getLength(const Eref& e ) const
{
return vGetLength(e);
}
void DifBufferBase::setDiameter(const Eref& e, double diameter )
{
vSetDiameter(e,diameter);
}
double DifBufferBase::getDiameter(const Eref& e ) const
{
return vGetDiameter(e);
}
void DifBufferBase::setThickness( const Eref& e, double thickness )
{
vSetThickness(e,thickness);
}
double DifBufferBase::getThickness(const Eref& e) const
{
return vGetThickness(e);
}
void DifBufferBase::setVolume(const Eref& e, double volume )
{
vSetVolume(e,volume);
}
double DifBufferBase::getVolume(const Eref& e ) const
{
return vGetVolume(e);
}
void DifBufferBase::setOuterArea(const Eref& e, double outerArea )
{
vSetOuterArea(e,outerArea);
}
double DifBufferBase::getOuterArea(const Eref& e ) const
{
return vGetOuterArea(e);
}
void DifBufferBase::setInnerArea(const Eref& e, double innerArea )
{
vSetInnerArea(e,innerArea);
}
double DifBufferBase::getInnerArea(const Eref& e) const
{
return vGetInnerArea(e);
}
void DifBufferBase::buffer(const Eref& e,double C)
{
vBuffer(e,C);
}
void DifBufferBase::reinit( const Eref& e, ProcPtr p )
{
vReinit( e, p );
}
void DifBufferBase::process( const Eref& e, ProcPtr p )
{
vProcess( e, p );
}
void DifBufferBase:: fluxFromOut(const Eref& e,double outerC, double outerThickness )
{
vFluxFromOut(e,outerC,outerThickness);
}
void DifBufferBase:: fluxFromIn(const Eref& e,double innerC, double innerThickness )
{
vFluxFromIn(e,innerC,innerThickness);
}
void DifBufferBase::vSetSolver( const Eref& e, Id hsolve )
{;}
void DifBufferBase::zombify( Element* orig, const Cinfo* zClass,
Id hsolve )
{
if ( orig->cinfo() == zClass )
return;
unsigned int start = orig->localDataStart();
unsigned int num = orig->numLocalData();
if ( num == 0 )
return;
unsigned int len = 14;
vector< double > data( num * len );
unsigned int j = 0;
for ( unsigned int i = 0; i < num; ++i ) {
Eref er( orig, i + start );
const DifBufferBase* ds =
reinterpret_cast< const DifBufferBase* >( er.data() ); data[j + 0] = ds->getActivation( er );
data[j + 1] = ds->getBFree( er );
data[j + 2] = ds->getBBound( er );
data[j + 3] = ds->getBTot( er );
data[j + 4] = ds->getKf( er );
data[j + 5] = ds->getKb( er );
data[j + 6] = ds->getD( er );
data[j + 7] = ds->getShapeMode( er );
data[j + 8] = ds->getLength( er );
data[j + 9] = ds->getDiameter( er );
data[j + 10] = ds->getThickness( er );
data[j + 11] = ds->getVolume( er );
data[j + 12] = ds->getOuterArea( er );
data[j + 13] = ds->getInnerArea( er );
j += len;
}
orig->zombieSwap( zClass );
j = 0;
for ( unsigned int i = 0; i < num; ++i ) {
Eref er( orig, i + start );
DifBufferBase* ds =
reinterpret_cast< DifBufferBase* >( er.data() );
ds->vSetSolver(er,hsolve);
ds->setActivation(er, data[j+0]);
ds->setBFree(er, data[j + 1]);
ds->setBBound(er, data[j + 2]);
ds->setBTot(er, data[j + 3]);
ds->setKf(er, data[j + 4]);
ds->setKb(er, data[j + 5]);
ds->setD(er, data[j + 6]);
ds->setShapeMode(er, data[j + 7]);
ds->setLength(er, data[j + 8]);
ds->setDiameter(er, data[j + 9]);
ds->setThickness(er, data[j + 10]);
ds->setVolume(er, data[j + 11]);
ds->setOuterArea(er, data[j + 12]);
ds->setInnerArea(er, data[j + 13]);
j += len; //??
}
}