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Commit 08f2e43a authored by Asia Jędrzejewska-Szmek's avatar Asia Jędrzejewska-Szmek
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1 merge request!205DifShell and DifBuffer implementation
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moose-core/biophysics/DifBufferBase.cpp
+ 106
− 104
View file @ 08f2e43a
...@@ -41,12 +41,12 @@ const Cinfo * DifBufferBase::initCinfo() ...@@ -41,12 +41,12 @@ const Cinfo * DifBufferBase::initCinfo()
}; };
static SharedFinfo proc( static SharedFinfo proc(
"proc", "proc",
"Here we create 2 shared finfos to attach with the Ticks. This is because we want to perform DifBufferBase " "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. " "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", "In the first stage we send out the concentration value to other DifBufferBases and Buffer elements. We also",
processShared, processShared,
sizeof( processShared ) / sizeof( Finfo* )); sizeof( processShared ) / sizeof( Finfo* ));
static DestFinfo concentration("concentration", static DestFinfo concentration("concentration",
"Receives concentration (from DifShell).", "Receives concentration (from DifShell).",
...@@ -74,8 +74,8 @@ const Cinfo * DifBufferBase::initCinfo() ...@@ -74,8 +74,8 @@ const Cinfo * DifBufferBase::initCinfo()
new EpFunc2< DifBufferBase, double, double > ( &DifBufferBase::fluxFromOut )); new EpFunc2< DifBufferBase, double, double > ( &DifBufferBase::fluxFromOut ));
static Finfo* innerDifShared[] = { static Finfo* innerDifShared[] = {
&fluxFromOut, &fluxFromOut,
DifBufferBase::innerDifSourceOut() DifBufferBase::innerDifSourceOut()
}; };
...@@ -104,60 +104,62 @@ const Cinfo * DifBufferBase::initCinfo() ...@@ -104,60 +104,62 @@ const Cinfo * DifBufferBase::initCinfo()
// Field defs // Field defs
//////////////////////////// ////////////////////////////
static ElementValueFinfo<DifBufferBase, double> activation("activation", static ElementValueFinfo<DifBufferBase, double> activation("activation",
"Ion concentration from incoming conc message.", "Ion concentration from incoming conc message.",
&DifBufferBase::setActivation, &DifBufferBase::setActivation,
&DifBufferBase::getActivation); &DifBufferBase::getActivation);
static ElementValueFinfo<DifBufferBase, double> kf("kf", static ElementValueFinfo<DifBufferBase, double> kf("kf",
"Forward rate constant of buffer molecules 1/mM/s (?)", "Forward rate constant of buffer molecules 1/mM/s (?)",
&DifBufferBase::setKf, &DifBufferBase::setKf,
&DifBufferBase::getKf); &DifBufferBase::getKf);
static ElementValueFinfo<DifBufferBase, double> kb("kb", static ElementValueFinfo<DifBufferBase, double> kb("kb",
"Backward rate constant of buffer molecules. 1/s", "Backward rate constant of buffer molecules. 1/s",
&DifBufferBase::setKb, &DifBufferBase::setKb,
&DifBufferBase::getKb); &DifBufferBase::getKb);
static ElementValueFinfo<DifBufferBase, double> D("D", static ElementValueFinfo<DifBufferBase, double> D("D",
"Diffusion constant of buffer molecules. m^2/s", "Diffusion constant of buffer molecules. m^2/s",
&DifBufferBase::setD, &DifBufferBase::setD,
&DifBufferBase::getD); &DifBufferBase::getD);
static ReadOnlyElementValueFinfo<DifBufferBase, double> bFree("bFree", static ElementValueFinfo<DifBufferBase, double> bFree("bFree",
"Free buffer concentration", "Free buffer concentration",
&DifBufferBase::getBFree); &DifBufferBase::setBFree,
static ReadOnlyElementValueFinfo<DifBufferBase, double> bBound("bBound", &DifBufferBase::getBFree);
"Bound buffer concentration", static ElementValueFinfo<DifBufferBase, double> bBound("bBound",
&DifBufferBase::getBBound); "Bound buffer concentration",
&DifBufferBase::setBBound,
&DifBufferBase::getBBound);
static ElementValueFinfo<DifBufferBase, double> bTot("bTot", static ElementValueFinfo<DifBufferBase, double> bTot("bTot",
"Total buffer concentration.", "Total buffer concentration.",
&DifBufferBase::setBTot, &DifBufferBase::setBTot,
&DifBufferBase::getBTot); &DifBufferBase::getBTot);
static ElementValueFinfo<DifBufferBase, double> length("length", static ElementValueFinfo<DifBufferBase, double> length("length",
"Length of shell", "Length of shell",
&DifBufferBase::setLength, &DifBufferBase::setLength,
&DifBufferBase::getLength); &DifBufferBase::getLength);
static ElementValueFinfo<DifBufferBase, double> diameter("diameter", static ElementValueFinfo<DifBufferBase, double> diameter("diameter",
"Diameter of shell", "Diameter of shell",
&DifBufferBase::setDiameter, &DifBufferBase::setDiameter,
&DifBufferBase::getDiameter); &DifBufferBase::getDiameter);
static ElementValueFinfo<DifBufferBase, unsigned int> shapeMode("shapeMode", static ElementValueFinfo<DifBufferBase, unsigned int> shapeMode("shapeMode",
"shape of the shell: SHELL=0, SLICE=SLAB=1, USERDEF=3", "shape of the shell: SHELL=0, SLICE=SLAB=1, USERDEF=3",
&DifBufferBase::setShapeMode, &DifBufferBase::setShapeMode,
&DifBufferBase::getShapeMode); &DifBufferBase::getShapeMode);
static ElementValueFinfo<DifBufferBase, double> thickness("thickness", static ElementValueFinfo<DifBufferBase, double> thickness("thickness",
"Thickness of shell", "Thickness of shell",
&DifBufferBase::setThickness, &DifBufferBase::setThickness,
&DifBufferBase::getThickness); &DifBufferBase::getThickness);
static ElementValueFinfo<DifBufferBase, double> innerArea("innerArea", static ElementValueFinfo<DifBufferBase, double> innerArea("innerArea",
"Inner area of shell", "Inner area of shell",
&DifBufferBase::setInnerArea, &DifBufferBase::setInnerArea,
&DifBufferBase::getInnerArea); &DifBufferBase::getInnerArea);
static ElementValueFinfo<DifBufferBase, double> outerArea("outerArea", static ElementValueFinfo<DifBufferBase, double> outerArea("outerArea",
"Outer area of shell", "Outer area of shell",
&DifBufferBase::setOuterArea, &DifBufferBase::setOuterArea,
&DifBufferBase::getOuterArea); &DifBufferBase::getOuterArea);
static ElementValueFinfo< DifBufferBase, double> volume( "volume", "", static ElementValueFinfo< DifBufferBase, double> volume( "volume", "",
&DifBufferBase::setVolume, &DifBufferBase::setVolume,
&DifBufferBase::getVolume ); &DifBufferBase::getVolume );
//// ////
// DestFinfo // DestFinfo
...@@ -399,61 +401,61 @@ void DifBufferBase::vSetSolver( const Eref& e, Id hsolve ) ...@@ -399,61 +401,61 @@ void DifBufferBase::vSetSolver( const Eref& e, Id hsolve )
{;} {;}
void DifBufferBase::zombify( Element* orig, const Cinfo* zClass, void DifBufferBase::zombify( Element* orig, const Cinfo* zClass,
Id hsolve ) Id hsolve )
{ {
if ( orig->cinfo() == zClass ) if ( orig->cinfo() == zClass )
return; return;
unsigned int start = orig->localDataStart(); unsigned int start = orig->localDataStart();
unsigned int num = orig->numLocalData(); unsigned int num = orig->numLocalData();
if ( num == 0 ) if ( num == 0 )
return; return;
unsigned int len = 14; unsigned int len = 14;
vector< double > data( num * len ); vector< double > data( num * len );
unsigned int j = 0; unsigned int j = 0;
for ( unsigned int i = 0; i < num; ++i ) { for ( unsigned int i = 0; i < num; ++i ) {
Eref er( orig, i + start ); Eref er( orig, i + start );
const DifBufferBase* ds = const DifBufferBase* ds =
reinterpret_cast< const DifBufferBase* >( er.data() ); reinterpret_cast< const DifBufferBase* >( er.data() );
data[j + 0] = ds->getActivation( er ); data[j + 0] = ds->getActivation( er );
data[j + 1] = ds->getBFree( er ); data[j + 1] = ds->getBFree( er );
data[j + 2] = ds->getBBound( er ); data[j + 2] = ds->getBBound( er );
data[j + 3] = ds->getBTot( er ); data[j + 3] = ds->getBTot( er );
data[j + 4] = ds->getKf( er ); data[j + 4] = ds->getKf( er );
data[j + 5] = ds->getKb( er ); data[j + 5] = ds->getKb( er );
data[j + 6] = ds->getD( er ); data[j + 6] = ds->getD( er );
data[j + 7] = ds->getShapeMode( er ); data[j + 7] = ds->getShapeMode( er );
data[j + 8] = ds->getLength( er ); data[j + 8] = ds->getLength( er );
data[j + 9] = ds->getDiameter( er ); data[j + 9] = ds->getDiameter( er );
data[j + 10] = ds->getThickness( er ); data[j + 10] = ds->getThickness( er );
data[j + 11] = ds->getVolume( er ); data[j + 11] = ds->getVolume( er );
data[j + 12] = ds->getOuterArea( er ); data[j + 12] = ds->getOuterArea( er );
data[j + 13] = ds->getInnerArea( er ); data[j + 13] = ds->getInnerArea( er );
j += len; j += len;
} }
orig->zombieSwap( zClass ); orig->zombieSwap( zClass );
j = 0; j = 0;
for ( unsigned int i = 0; i < num; ++i ) { for ( unsigned int i = 0; i < num; ++i ) {
Eref er( orig, i + start ); Eref er( orig, i + start );
DifBufferBase* ds = DifBufferBase* ds =
reinterpret_cast< DifBufferBase* >( er.data() ); reinterpret_cast< DifBufferBase* >( er.data() );
ds->vSetSolver(er,hsolve); ds->vSetSolver(er,hsolve);
ds->setActivation(er, data[j+0]); ds->setActivation(er, data[j+0]);
ds->setBFree(er, data[j + 1]); ds->setBFree(er, data[j + 1]);
ds->setBBound(er, data[j + 2]); ds->setBBound(er, data[j + 2]);
ds->setBTot(er, data[j + 3]); ds->setBTot(er, data[j + 3]);
ds->setKf(er, data[j + 4]); ds->setKf(er, data[j + 4]);
ds->setKb(er, data[j + 5]); ds->setKb(er, data[j + 5]);
ds->setD(er, data[j + 6]); ds->setD(er, data[j + 6]);
ds->setShapeMode(er, data[j + 7]); ds->setShapeMode(er, data[j + 7]);
ds->setLength(er, data[j + 8]); ds->setLength(er, data[j + 8]);
ds->setDiameter(er, data[j + 9]); ds->setDiameter(er, data[j + 9]);
ds->setThickness(er, data[j + 10]); ds->setThickness(er, data[j + 10]);
ds->setVolume(er, data[j + 11]); ds->setVolume(er, data[j + 11]);
ds->setOuterArea(er, data[j + 12]); ds->setOuterArea(er, data[j + 12]);
ds->setInnerArea(er, data[j + 13]); ds->setInnerArea(er, data[j + 13]);
j += len; //?? j += len; //??
} }
} }
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