diff --git a/moose-core/biophysics/DifBufferBase.cpp b/moose-core/biophysics/DifBufferBase.cpp
index 72725ac479b658a36f0dce6e396d86868d85569d..40628a21e44d95612293230d45824ccb52c1b638 100644
--- a/moose-core/biophysics/DifBufferBase.cpp
+++ b/moose-core/biophysics/DifBufferBase.cpp
@@ -41,12 +41,12 @@ const Cinfo * DifBufferBase::initCinfo()
};
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* ));
+ "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).",
@@ -74,8 +74,8 @@ const Cinfo * DifBufferBase::initCinfo()
new EpFunc2< DifBufferBase, double, double > ( &DifBufferBase::fluxFromOut ));
static Finfo* innerDifShared[] = {
- &fluxFromOut,
- DifBufferBase::innerDifSourceOut()
+ &fluxFromOut,
+ DifBufferBase::innerDifSourceOut()
};
@@ -104,60 +104,62 @@ const Cinfo * DifBufferBase::initCinfo()
// Field defs
////////////////////////////
static ElementValueFinfo<DifBufferBase, double> activation("activation",
- "Ion concentration from incoming conc message.",
- &DifBufferBase::setActivation,
- &DifBufferBase::getActivation);
+ "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);
+ "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);
+ "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 ReadOnlyElementValueFinfo<DifBufferBase, double> bFree("bFree",
- "Free buffer concentration",
- &DifBufferBase::getBFree);
- static ReadOnlyElementValueFinfo<DifBufferBase, double> bBound("bBound",
- "Bound buffer concentration",
- &DifBufferBase::getBBound);
+ "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);
+ "Total buffer concentration.",
+ &DifBufferBase::setBTot,
+ &DifBufferBase::getBTot);
static ElementValueFinfo<DifBufferBase, double> length("length",
- "Length of shell",
- &DifBufferBase::setLength,
- &DifBufferBase::getLength);
+ "Length of shell",
+ &DifBufferBase::setLength,
+ &DifBufferBase::getLength);
static ElementValueFinfo<DifBufferBase, double> diameter("diameter",
- "Diameter of shell",
- &DifBufferBase::setDiameter,
- &DifBufferBase::getDiameter);
+ "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);
+ "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);
+ "Thickness of shell",
+ &DifBufferBase::setThickness,
+ &DifBufferBase::getThickness);
static ElementValueFinfo<DifBufferBase, double> innerArea("innerArea",
- "Inner area of shell",
- &DifBufferBase::setInnerArea,
- &DifBufferBase::getInnerArea);
+ "Inner area of shell",
+ &DifBufferBase::setInnerArea,
+ &DifBufferBase::getInnerArea);
static ElementValueFinfo<DifBufferBase, double> outerArea("outerArea",
- "Outer area of shell",
- &DifBufferBase::setOuterArea,
- &DifBufferBase::getOuterArea);
+ "Outer area of shell",
+ &DifBufferBase::setOuterArea,
+ &DifBufferBase::getOuterArea);
static ElementValueFinfo< DifBufferBase, double> volume( "volume", "",
- &DifBufferBase::setVolume,
- &DifBufferBase::getVolume );
+ &DifBufferBase::setVolume,
+ &DifBufferBase::getVolume );
////
// DestFinfo
@@ -399,61 +401,61 @@ 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;
+ 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; //??
- }
+ 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; //??
+ }
}