void DifShell::localProcess_0( const Eref & e, ProcPtr p )
{
/**
* Send ion concentration and thickness to adjacent DifShells. They will
* then compute their incoming fluxes.
*/
innerDifSourceOut()->send( e, C_, thickness_ );
outerDifSourceOut()->send( e, C_, thickness_ );
/**
* 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.
*/
concentrationOut()->send( e, C_ );
}
const Cinfo* DifShellBase::initCinfo()
{
static DestFinfo process( "process",
"Handles process call",
new ProcOpFunc< DifShellBase>(&DifShellBase::process ) );
static DestFinfo reinit( "reinit",
"Reinit happens only in stage 0",
new ProcOpFunc< DifShellBase>( &DifShellBase::reinit ));
static Finfo* processShared[] = {
&process, &reinit
};
static SharedFinfo proc(
"proc",
"Shared message to receive Process message from scheduler",
processShared, sizeof( processShared ) / sizeof( Finfo* ));
static DestFinfo reaction( "reaction",
"Here the DifShell receives reaction rates (forward and backward), and concentrations for the "
"free-buffer and bound-buffer molecules.",
new EpFunc4< DifShellBase, double, double, double, double >( &DifShellBase::buffer ));
static Finfo* bufferShared[] = {
DifShellBase::concentrationOut(), &reaction
};
static SharedFinfo buffer( "buffer",
"This is a shared message from a DifShell to a Buffer (FixBuffer or DifBuffer). " ,
bufferShared,
sizeof( bufferShared ) / sizeof( Finfo* ));
/////
static DestFinfo fluxFromOut( "fluxFromOut",
"Destination message",
new EpFunc2< DifShellBase, double, double > ( &DifShellBase::fluxFromOut ));
static Finfo* innerDifShared[] = {
&fluxFromOut, DifShellBase::innerDifSourceOut(),
};
static SharedFinfo innerDif( "innerDif",
"This shared message (and the next) is between DifShells: 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< DifShellBase, double, double> ( &DifShellBase::fluxFromIn ) );
static Finfo* outerDifShared[] = {
&fluxFromIn, DifShellBase::outerDifSourceOut(),
};
static SharedFinfo outerDif( "outerDif",
"Using this message, an outer shell sends to, and receives from its inner shell." ,
outerDifShared,
sizeof( outerDifShared ) / sizeof( Finfo* ));
static ElementValueFinfo< DifShellBase, double> C( "C",
"Concentration C",// is computed by the DifShell",
&DifShellBase::setC,
&DifShellBase::getC);
static ElementValueFinfo< DifShellBase, double> Ceq( "Ceq", "",
&DifShellBase::setCeq,
&DifShellBase::getCeq);
static ElementValueFinfo< DifShellBase, double> D( "D", "",
&DifShellBase::setD,
&DifShellBase::getD);
static ElementValueFinfo< DifShellBase, double> valence( "valence", "",
&DifShellBase::setValence,
&DifShellBase::getValence);
static ElementValueFinfo< DifShellBase, double> leak( "leak", "",
&DifShellBase::setLeak,
&DifShellBase::getLeak);
static ElementValueFinfo< DifShellBase, unsigned int> shapeMode( "shapeMode", "",
&DifShellBase::setShapeMode,
&DifShellBase::getShapeMode);
static ElementValueFinfo< DifShellBase, double> length( "length", "",
&DifShellBase::setLength,
&DifShellBase::getLength);
static ElementValueFinfo< DifShellBase, double> diameter( "diameter", "",
&DifShellBase::setDiameter,
&DifShellBase::getDiameter );
static ElementValueFinfo< DifShellBase, double> thickness( "thickness", "",
&DifShellBase::setThickness,
&DifShellBase::getThickness );
static ElementValueFinfo< DifShellBase, double> volume( "volume", "",
&DifShellBase::setVolume,
&DifShellBase::getVolume );
static ElementValueFinfo< DifShellBase, double> outerArea( "outerArea", "",
&DifShellBase::setOuterArea,
&DifShellBase::getOuterArea);
static ElementValueFinfo< DifShellBase, double> innerArea( "innerArea", "",
&DifShellBase::setInnerArea,
&DifShellBase::getInnerArea );
static DestFinfo mmPump( "mmPump", "Here DifShell receives pump outflux",
new EpFunc2< DifShellBase, double, double >( &DifShellBase::mmPump ) );
static DestFinfo influx( "influx", "",
new EpFunc1< DifShellBase, double > (&DifShellBase::influx ));
static DestFinfo outflux( "outflux", "",
new EpFunc1< DifShellBase, double >( &DifShellBase::influx ));
static DestFinfo fInflux( "fInflux", "",
new EpFunc2< DifShellBase, double, double >( &DifShellBase::fInflux ));
static DestFinfo fOutflux( "fOutflux", "",
new EpFunc2< DifShellBase, double, double> (&DifShellBase::fOutflux ));
static DestFinfo storeInflux( "storeInflux", "",
new EpFunc1< DifShellBase, double >( &DifShellBase::storeInflux ) );
static DestFinfo storeOutflux( "storeOutflux", "",
new EpFunc1< DifShellBase, double > ( &DifShellBase::storeOutflux ) );
static DestFinfo tauPump( "tauPump","",
new EpFunc2< DifShellBase, double, double >( &DifShellBase::tauPump ) );
static DestFinfo eqTauPump( "eqTauPump", "",
new EpFunc1< DifShellBase, double >( &DifShellBase::eqTauPump ) );
static DestFinfo hillPump( "hillPump", "",
new EpFunc3< DifShellBase, double, double, unsigned int >( &DifShellBase::hillPump ) );
static Finfo* difShellBaseFinfos[] = {
//////////////////////////////////////////////////////////////////
// Field definitions
//////////////////////////////////////////////////////////////////
&C,
&Ceq,
&D,
&valence,
&leak,
&shapeMode,
&length,
&diameter,
&thickness,
&volume,
&outerArea,
&innerArea,
//////////////////////////////////////////////////////////////////
// MsgSrc definitions
//////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////
// SharedFinfo definitions
//////////////////////////////////////////////////////////////////
&proc,
&buffer,
concentrationOut(),
innerDifSourceOut(),
outerDifSourceOut(),
&innerDif,
&outerDif,
//////////////////////////////////////////////////////////////////
// DestFinfo definitions
//////////////////////////////////////////////////////////////////
&influx,
&outflux,
&fInflux,
&fOutflux,
&storeInflux,
&storeOutflux,
&tauPump,
&eqTauPump,
&mmPump,
&hillPump,
};
static string doc[] =
{
"Name", "DifShellBase",
"Author", "Niraj Dudani. Ported to async13 by Subhasis Ray/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 ZeroSizeDinfo< int > dinfo;
//static Dinfo< DifShellBase> dinfo;
static Cinfo difShellBaseCinfo(
"DifShellBase",
Neutral::initCinfo(),
difShellBaseFinfos,
sizeof( difShellBaseFinfos ) / sizeof( Finfo* ),
&dinfo,
doc,
sizeof( doc ) / sizeof( string ));
return &difShellBaseCinfo;
}
const Cinfo* DifShell::initCinfo()
{
static DestFinfo process( "process",
"Handles process call",
new ProcOpFunc< DifShell >( &DifShell::process_0 ) );
static DestFinfo reinit( "reinit",
"Reinit happens only in stage 0",
new ProcOpFunc< DifShell >( &DifShell::reinit_0 ));
static Finfo* processShared_0[] = {
&process,
&reinit
};
static SharedFinfo process_0(
"process_0",
"Here we create 2 shared finfos to attach with the Ticks. This is because we want to perform DifShell "
"computations in 2 stages, much as in the Compartment object. "
"In the first stage we send out the concentration value to other DifShells and Buffer elements. We also "
"receive fluxes and currents and sum them up to compute ( dC / dt ). "
"In the second stage we find the new C value using an explicit integration method. "
"This 2-stage procedure eliminates the need to store and send prev_C values, as was common in GENESIS.",
processShared_0,
sizeof( processShared_0 ) / sizeof( Finfo* ));
static DestFinfo process1( "process",
"Handle process call",
new ProcOpFunc< DifShell >( &DifShell::process_1 ) );
static DestFinfo reinit1( "reinit",
"Reinit happens only in stage 0",
new ProcOpFunc< DifShell >( &DifShell::reinit_1)
);
static Finfo* processShared_1[] = {
&process1, &reinit1
};
static SharedFinfo process_1( "process_1",
"Second process call",
processShared_1,
sizeof( processShared_1 ) / sizeof( Finfo* ) );
static DestFinfo reaction( "reaction",
"Here the DifShell receives reaction rates (forward and backward), and concentrations for the "
"free-buffer and bound-buffer molecules.",
new OpFunc4< DifShell, double, double, double, double >( &DifShell::buffer ));
static Finfo* bufferShared[] = {
concentrationOut(), &reaction
};
static SharedFinfo buffer( "buffer",
"This is a shared message from a DifShell to a Buffer (FixBuffer or DifBuffer). "
"During stage 0:\n "
"- DifShell 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"
"During stage 1: \n"
"- DifShell advances concentration C \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 OpFunc2< DifShell, double, double > ( &DifShell::fluxFromOut ));
static Finfo* innerDifShared[] = {
innerDifSourceOut(),
&fluxFromOut
};
static SharedFinfo innerDif( "innerDif",
"This shared message (and the next) is between DifShells: 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 OpFunc2< DifShell, double, double> ( &DifShell::fluxFromIn ) );
static Finfo* outerDifShared[] = {
&fluxFromIn,
outerDifSourceOut(),
};
static SharedFinfo outerDif( "outerDif",
"Using this message, an outer shell sends to, and receives from its inner shell." ,
outerDifShared,
sizeof( outerDifShared ) / sizeof( Finfo* ));
static ReadOnlyValueFinfo< DifShell, double> C( "C",
"Concentration C is computed by the DifShell and is read-only",
&DifShell::getC);
static ValueFinfo< DifShell, double> Ceq( "Ceq", "",
&DifShell::setCeq,
&DifShell::getCeq);
static ValueFinfo< DifShell, double> D( "D", "",
&DifShell::setD,
&DifShell::getD);
static ValueFinfo< DifShell, double> valence( "valence", "",
&DifShell::setValence,
&DifShell::getValence);
static ValueFinfo< DifShell, double> leak( "leak", "",
&DifShell::setLeak,
&DifShell::getLeak);
static ValueFinfo< DifShell, unsigned int> shapeMode( "shapeMode", "",
&DifShell::setShapeMode,
&DifShell::getShapeMode);
static ValueFinfo< DifShell, double> length( "length", "",
&DifShell::setLength,
&DifShell::getLength);
static ValueFinfo< DifShell, double> diameter( "diameter", "",
&DifShell::setDiameter,
&DifShell::getDiameter );
static ValueFinfo< DifShell, double> thickness( "thickness", "",
&DifShell::setThickness,
&DifShell::getThickness );
static ValueFinfo< DifShell, double> volume( "volume", "",
&DifShell::setVolume,
&DifShell::getVolume );
static ValueFinfo< DifShell, double> outerArea( "outerArea", "",
&DifShell::setOuterArea,
&DifShell::getOuterArea);
static ValueFinfo< DifShell, double> innerArea( "innerArea", "",
&DifShell::setInnerArea,
&DifShell::getInnerArea );
static DestFinfo influx( "influx", "",
new OpFunc1< DifShell, double > (&DifShell::influx ));
static DestFinfo outflux( "outflux", "",
new OpFunc1< DifShell, double >( &DifShell::influx ));
static DestFinfo fInflux( "fInflux", "",
new OpFunc2< DifShell, double, double >( &DifShell::fInflux ));
static DestFinfo fOutflux( "fOutflux", "",
new OpFunc2< DifShell, double, double> (&DifShell::fOutflux ));
static DestFinfo storeInflux( "storeInflux", "",
new OpFunc1< DifShell, double >( &DifShell::storeInflux ) );
static DestFinfo storeOutflux( "storeOutflux", "",
new OpFunc1< DifShell, double > ( &DifShell::storeOutflux ) );
static DestFinfo tauPump( "tauPump","",
new OpFunc2< DifShell, double, double >( &DifShell::tauPump ) );
static DestFinfo eqTauPump( "eqTauPump", "",
new OpFunc1< DifShell, double >( &DifShell::eqTauPump ) );
static DestFinfo mmPump( "mmPump", "",
new OpFunc2< DifShell, double, double >( &DifShell::mmPump ) );
static DestFinfo hillPump( "hillPump", "",
new OpFunc3< DifShell, double, double, unsigned int >( &DifShell::hillPump ) );
static Finfo* difShellFinfos[] = {
//////////////////////////////////////////////////////////////////
// Field definitions
//////////////////////////////////////////////////////////////////
&C,
&Ceq,
&D,
&valence,
&leak,
&shapeMode,
&length,
&diameter,
&thickness,
&volume,
&outerArea,
&innerArea,
//////////////////////////////////////////////////////////////////
// MsgSrc definitions
//////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////
// SharedFinfo definitions
//////////////////////////////////////////////////////////////////
&process_0,
&process_1,
&buffer,
&innerDif,
&outerDif,
//////////////////////////////////////////////////////////////////
// DestFinfo definitions
//////////////////////////////////////////////////////////////////
&influx,
&outflux,
&fInflux,
&fOutflux,
&storeInflux,
&storeOutflux,
&tauPump,
&eqTauPump,
&mmPump,
&hillPump,
};
static string doc[] =
{
"Name", "DifShell",
"Author", "Niraj Dudani. Ported to async13 by Subhasis Ray.",
"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",
Neutral::initCinfo(),
difShellFinfos,
sizeof( difShellFinfos ) / sizeof( Finfo* ),
&dinfo,
doc,
sizeof( doc ) / sizeof( string ));
return &difShellCinfo;
}
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;
}