diff --git a/moose-core/biophysics/CaConcBase.cpp b/moose-core/biophysics/CaConcBase.cpp
index 2d66b70940c9820f6b958d32594b64f220056b77..c484b24827292cb1d2f8b031c066eb2c6562de87 100644
--- a/moose-core/biophysics/CaConcBase.cpp
+++ b/moose-core/biophysics/CaConcBase.cpp
@@ -1,11 +1,11 @@
/**********************************************************************
-** This program is part of 'MOOSE', the
-** Messaging Object Oriented Simulation Environment.
-** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
-** It is made available under the terms of the
-** GNU Lesser General Public License version 2.1
-** See the file COPYING.LIB for the full notice.
-**********************************************************************/
+ ** This program is part of 'MOOSE', the
+ ** Messaging Object Oriented Simulation Environment.
+ ** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
+ ** It is made available under the terms of the
+ ** GNU Lesser General Public License version 2.1
+ ** See the file COPYING.LIB for the full notice.
+ **********************************************************************/
// #include <cfloat>
#include "header.h"
@@ -23,178 +23,178 @@
*/
// Static function.
SrcFinfo1< double >* CaConcBase::concOut() {
- static SrcFinfo1< double > concOut( "concOut",
- "Concentration of Ca in pool" );
- return &concOut;
+ static SrcFinfo1< double > concOut( "concOut",
+ "Concentration of Ca in pool" );
+ return &concOut;
}
const Cinfo* CaConcBase::initCinfo()
{
- ///////////////////////////////////////////////////////
- // Shared message definitions
- ///////////////////////////////////////////////////////
- static DestFinfo process( "process",
- "Handles process call",
- new ProcOpFunc< CaConcBase >( &CaConcBase::process ) );
- static DestFinfo reinit( "reinit",
- "Handles reinit call",
- new ProcOpFunc< CaConcBase >( &CaConcBase::reinit ) );
-
- static Finfo* processShared[] =
- {
- &process, &reinit
- };
-
- static SharedFinfo proc( "proc",
- "Shared message to receive Process message from scheduler",
- processShared, sizeof( processShared ) / sizeof( Finfo* ) );
+ ///////////////////////////////////////////////////////
+ // Shared message definitions
+ ///////////////////////////////////////////////////////
+ static DestFinfo process( "process",
+ "Handles process call",
+ new ProcOpFunc< CaConcBase >( &CaConcBase::process ) );
+ static DestFinfo reinit( "reinit",
+ "Handles reinit call",
+ new ProcOpFunc< CaConcBase >( &CaConcBase::reinit ) );
+
+ static Finfo* processShared[] =
+ {
+ &process, &reinit
+ };
+
+ static SharedFinfo proc( "proc",
+ "Shared message to receive Process message from scheduler",
+ processShared, sizeof( processShared ) / sizeof( Finfo* ) );
-///////////////////////////////////////////////////////
-// Field definitions
-///////////////////////////////////////////////////////
- static ElementValueFinfo< CaConcBase, double > Ca( "Ca",
- "Calcium concentration.",
- &CaConcBase::setCa,
- &CaConcBase::getCa
- );
- static ElementValueFinfo< CaConcBase, double > CaBasal( "CaBasal",
- "Basal Calcium concentration.",
- &CaConcBase::setCaBasal,
- &CaConcBase::getCaBasal
- );
- static ElementValueFinfo< CaConcBase, double > Ca_base( "Ca_base",
- "Basal Calcium concentration, synonym for CaBasal",
- &CaConcBase::setCaBasal,
- &CaConcBase::getCaBasal
- );
- static ElementValueFinfo< CaConcBase, double > tau( "tau",
- "Settling time for Ca concentration",
- &CaConcBase::setTau,
- &CaConcBase::getTau
- );
- static ElementValueFinfo< CaConcBase, double > B( "B",
- "Volume scaling factor. "
- "Deprecated. This is a legacy field from GENESIS and exposes "
- "internal calculations. Please do not use. \n"
- "B = 1/(vol * F) so that it obeys:\n"
- "dC/dt = B*I_Ca - C/tau",
- &CaConcBase::setB,
- &CaConcBase::getB
- );
- static ElementValueFinfo< CaConcBase, double > thick( "thick",
- "Thickness of Ca shell, assumed cylindrical. Legal range is "
- "between zero and the radius. If outside this range it is "
- "taken as the radius. Default zero, ie, the shell is the entire "
- "thickness of the cylinder",
- &CaConcBase::setThickness,
- &CaConcBase::getThickness
- );
- static ElementValueFinfo< CaConcBase, double > length( "length",
- "Length of Ca shell, assumed cylindrical",
- &CaConcBase::setLength,
- &CaConcBase::getLength
- );
- static ElementValueFinfo< CaConcBase, double > diameter( "diameter",
- "Diameter of Ca shell, assumed cylindrical",
- &CaConcBase::setDiameter,
- &CaConcBase::getDiameter
- );
- static ElementValueFinfo< CaConcBase, double > ceiling( "ceiling",
- "Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.",
- &CaConcBase::setCeiling,
- &CaConcBase::getCeiling
- );
- static ElementValueFinfo< CaConcBase, double > floor( "floor",
- "Floor value for Ca concentration. If Ca < floor, Ca = floor",
- &CaConcBase::setFloor,
- &CaConcBase::getFloor
- );
-
-///////////////////////////////////////////////////////
-// MsgDest definitions
-///////////////////////////////////////////////////////
-
- static DestFinfo current( "current",
- "Calcium Ion current, due to be converted to conc.",
- new EpFunc1< CaConcBase, double >( &CaConcBase::current )
- );
-
- static DestFinfo currentFraction( "currentFraction",
- "Fraction of total Ion current, that is carried by Ca2+.",
- new EpFunc2< CaConcBase, double, double >( &CaConcBase::currentFraction )
- );
-
- static DestFinfo increase( "increase",
- "Any input current that increases the concentration.",
- new EpFunc1< CaConcBase, double >( &CaConcBase::increase )
- );
-
- static DestFinfo decrease( "decrease",
- "Any input current that decreases the concentration.",
- new EpFunc1< CaConcBase, double >( &CaConcBase::decrease )
- );
-
- static DestFinfo basal( "basal",
- "Synonym for assignment of basal conc.",
- new EpFunc1< CaConcBase, double >( &CaConcBase::setCaBasal )
- );
-
- static Finfo* CaConcBaseFinfos[] =
- {
- &proc, // Shared
- concOut(), // Src
- &Ca, // Value
- &CaBasal, // Value
- &Ca_base, // Value
- &tau, // Value
- &B, // Value
- &thick, // Value
- &diameter, // Value
- &length, // Value
- &ceiling, // Value
- &floor, // Value
- ¤t, // Dest
- ¤tFraction, // Dest
- &increase, // Dest
- &decrease, // Dest
- &basal, // Dest
- };
-
- // We want the Ca updates before channel updates, so along with compts.
- // static SchedInfo schedInfo[] = { { process, 0, 0 } };
-
- static string doc[] =
- {
- "Name", "CaConcBase",
- "Author", "Upinder S. Bhalla, 2014, NCBS",
- "Description",
- "CaConcBase: Base class for Calcium concentration "
- "pool. Takes current from a channel and keeps track of "
- "calcium buildup and depletion by a "
- "single exponential process. ",
- };
+ ///////////////////////////////////////////////////////
+ // Field definitions
+ ///////////////////////////////////////////////////////
+ static ElementValueFinfo< CaConcBase, double > Ca( "Ca",
+ "Calcium concentration.",
+ &CaConcBase::setCa,
+ &CaConcBase::getCa
+ );
+ static ElementValueFinfo< CaConcBase, double > CaBasal( "CaBasal",
+ "Basal Calcium concentration.",
+ &CaConcBase::setCaBasal,
+ &CaConcBase::getCaBasal
+ );
+ static ElementValueFinfo< CaConcBase, double > Ca_base( "Ca_base",
+ "Basal Calcium concentration, synonym for CaBasal",
+ &CaConcBase::setCaBasal,
+ &CaConcBase::getCaBasal
+ );
+ static ElementValueFinfo< CaConcBase, double > tau( "tau",
+ "Settling time for Ca concentration",
+ &CaConcBase::setTau,
+ &CaConcBase::getTau
+ );
+ static ElementValueFinfo< CaConcBase, double > B( "B",
+ "Volume scaling factor. "
+ "Deprecated. This is a legacy field from GENESIS and exposes "
+ "internal calculations. Please do not use. \n"
+ "B = 1/(vol * F) so that it obeys:\n"
+ "dC/dt = B*I_Ca - C/tau",
+ &CaConcBase::setB,
+ &CaConcBase::getB
+ );
+ static ElementValueFinfo< CaConcBase, double > thick( "thick",
+ "Thickness of Ca shell, assumed cylindrical. Legal range is "
+ "between zero and the radius. If outside this range it is "
+ "taken as the radius. Default zero, ie, the shell is the entire "
+ "thickness of the cylinder",
+ &CaConcBase::setThickness,
+ &CaConcBase::getThickness
+ );
+ static ElementValueFinfo< CaConcBase, double > length( "length",
+ "Length of Ca shell, assumed cylindrical",
+ &CaConcBase::setLength,
+ &CaConcBase::getLength
+ );
+ static ElementValueFinfo< CaConcBase, double > diameter( "diameter",
+ "Diameter of Ca shell, assumed cylindrical",
+ &CaConcBase::setDiameter,
+ &CaConcBase::getDiameter
+ );
+ static ElementValueFinfo< CaConcBase, double > ceiling( "ceiling",
+ "Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.",
+ &CaConcBase::setCeiling,
+ &CaConcBase::getCeiling
+ );
+ static ElementValueFinfo< CaConcBase, double > floor( "floor",
+ "Floor value for Ca concentration. If Ca < floor, Ca = floor",
+ &CaConcBase::setFloor,
+ &CaConcBase::getFloor
+ );
+
+ ///////////////////////////////////////////////////////
+ // MsgDest definitions
+ ///////////////////////////////////////////////////////
+
+ static DestFinfo current( "current",
+ "Calcium Ion current, due to be converted to conc.",
+ new EpFunc1< CaConcBase, double >( &CaConcBase::current )
+ );
+
+ static DestFinfo currentFraction( "currentFraction",
+ "Fraction of total Ion current, that is carried by Ca2+.",
+ new EpFunc2< CaConcBase, double, double >( &CaConcBase::currentFraction )
+ );
+
+ static DestFinfo increase( "increase",
+ "Any input current that increases the concentration.",
+ new EpFunc1< CaConcBase, double >( &CaConcBase::increase )
+ );
+
+ static DestFinfo decrease( "decrease",
+ "Any input current that decreases the concentration.",
+ new EpFunc1< CaConcBase, double >( &CaConcBase::decrease )
+ );
+
+ static DestFinfo basal( "basal",
+ "Synonym for assignment of basal conc.",
+ new EpFunc1< CaConcBase, double >( &CaConcBase::setCaBasal )
+ );
+
+ static Finfo* CaConcBaseFinfos[] =
+ {
+ &proc, // Shared
+ concOut(), // Src
+ &Ca, // Value
+ &CaBasal, // Value
+ &Ca_base, // Value
+ &tau, // Value
+ &B, // Value
+ &thick, // Value
+ &diameter, // Value
+ &length, // Value
+ &ceiling, // Value
+ &floor, // Value
+ ¤t, // Dest
+ ¤tFraction, // Dest
+ &increase, // Dest
+ &decrease, // Dest
+ &basal, // Dest
+ };
+
+ // We want the Ca updates before channel updates, so along with compts.
+ // static SchedInfo schedInfo[] = { { process, 0, 0 } };
+
+ static string doc[] =
+ {
+ "Name", "CaConcBase",
+ "Author", "Upinder S. Bhalla, 2014, NCBS",
+ "Description",
+ "CaConcBase: Base class for Calcium concentration "
+ "pool. Takes current from a channel and keeps track of "
+ "calcium buildup and depletion by a "
+ "single exponential process. ",
+ };
- static ZeroSizeDinfo< int > dinfo;
-
- static Cinfo CaConcBaseCinfo(
- "CaConcBase",
- Neutral::initCinfo(),
- CaConcBaseFinfos,
- sizeof( CaConcBaseFinfos )/sizeof(Finfo *),
- &dinfo,
- doc,
- sizeof(doc)/sizeof(string)
- );
-
- return &CaConcBaseCinfo;
+ static ZeroSizeDinfo< int > dinfo;
+
+ static Cinfo CaConcBaseCinfo(
+ "CaConcBase",
+ Neutral::initCinfo(),
+ CaConcBaseFinfos,
+ sizeof( CaConcBaseFinfos )/sizeof(Finfo *),
+ &dinfo,
+ doc,
+ sizeof(doc)/sizeof(string)
+ );
+
+ return &CaConcBaseCinfo;
}
///////////////////////////////////////////////////
static const Cinfo* caConcCinfo = CaConcBase::initCinfo();
CaConcBase::CaConcBase()
- :
- thickness_( 0.0 )
+ :
+ thickness_( 0.0 )
{;}
///////////////////////////////////////////////////
@@ -203,98 +203,98 @@ CaConcBase::CaConcBase()
void CaConcBase::setCa( const Eref& e, double Ca )
{
- vSetCa( e, Ca );
+ vSetCa( e, Ca );
}
double CaConcBase::getCa( const Eref& e ) const
{
- return vGetCa( e );
+ return vGetCa( e );
}
void CaConcBase::setCaBasal( const Eref& e, double CaBasal )
{
- vSetCaBasal( e, CaBasal );
+ vSetCaBasal( e, CaBasal );
}
double CaConcBase::getCaBasal( const Eref& e ) const
{
- return vGetCaBasal( e );
+ return vGetCaBasal( e );
}
void CaConcBase::setTau( const Eref& e, double tau )
{
- vSetTau( e, tau );
+ vSetTau( e, tau );
}
double CaConcBase::getTau( const Eref& e ) const
{
- return vGetTau( e );
+ return vGetTau( e );
}
void CaConcBase::setB( const Eref& e, double B )
{
- vSetB( e, B );
+ vSetB( e, B );
}
double CaConcBase::getB( const Eref& e ) const
{
- return vGetB( e );
+ return vGetB( e );
}
void CaConcBase::setCeiling( const Eref& e, double ceiling )
{
- vSetCeiling( e, ceiling );
+ vSetCeiling( e, ceiling );
}
double CaConcBase::getCeiling( const Eref& e ) const
{
- return vGetCeiling( e );
+ return vGetCeiling( e );
}
void CaConcBase::setFloor( const Eref& e, double floor )
{
- vSetFloor( e, floor );
+ vSetFloor( e, floor );
}
double CaConcBase::getFloor( const Eref& e ) const
{
- return vGetFloor( e );
+ return vGetFloor( e );
}
void CaConcBase::updateDimensions( const Eref& e )
{
- double vol = PI * diameter_ * diameter_ * length_ * 0.25;
- if ( thickness_ > 0 && thickness_ < diameter_/2.0 ) {
- double coreRadius = diameter_ / 2.0 - thickness_;
- vol -= PI * coreRadius * coreRadius * length_;
- }
- double B = 1.0 / ( FaradayConst * vol );
- vSetB( e, B );
+ double vol = PI * diameter_ * diameter_ * length_ * 0.25;
+ if ( thickness_ > 0 && thickness_ < diameter_/2.0 ) {
+ double coreRadius = diameter_ / 2.0 - thickness_;
+ vol -= PI * coreRadius * coreRadius * length_;
+ }
+ double B = 1.0 / ( FaradayConst * vol );
+ vSetB( e, B );
}
void CaConcBase::setThickness( const Eref& e, double thickness )
{
- thickness_ = thickness;
- updateDimensions( e );
+ thickness_ = thickness;
+ updateDimensions( e );
}
double CaConcBase::getThickness( const Eref& e ) const
{
- return thickness_;
+ return thickness_;
}
void CaConcBase::setDiameter( const Eref& e, double diameter )
{
- diameter_ = diameter;
- updateDimensions( e );
+ diameter_ = diameter;
+ updateDimensions( e );
}
double CaConcBase::getDiameter( const Eref& e ) const
{
- return diameter_;
+ return diameter_;
}
void CaConcBase::setLength( const Eref& e, double length )
{
- length_ = length;
- updateDimensions( e );
+ length_ = length;
+ updateDimensions( e );
}
double CaConcBase::getLength( const Eref& e ) const
{
- return length_;
+ return length_;
}
///////////////////////////////////////////////////
@@ -303,32 +303,32 @@ double CaConcBase::getLength( const Eref& e ) const
void CaConcBase::reinit( const Eref& e, ProcPtr p )
{
- vReinit( e, p );
+ vReinit( e, p );
}
void CaConcBase::process( const Eref& e, ProcPtr p )
{
- vProcess( e, p );
+ vProcess( e, p );
}
void CaConcBase::current( const Eref& e, double I )
{
- vCurrent( e, I );
+ vCurrent( e, I );
}
void CaConcBase::currentFraction( const Eref& e, double I, double fraction )
{
- vCurrentFraction( e, I, fraction );
+ vCurrentFraction( e, I, fraction );
}
void CaConcBase::increase( const Eref& e, double I )
{
- vIncrease( e, I );
+ vIncrease( e, I );
}
void CaConcBase::decrease( const Eref& e, double I )
{
- vDecrease( e, I );
+ vDecrease( e, I );
}
/////////////////////////////////////////////////////
@@ -342,48 +342,48 @@ void CaConcBase::vSetSolver( const Eref& e, Id hsolve )
// static func
void CaConcBase::zombify( Element* orig, const Cinfo* zClass,
- Id hsolve )
+ Id hsolve )
{
- if ( orig->cinfo() == zClass )
- return;
- unsigned int start = orig->localDataStart();
- unsigned int num = orig->numLocalData();
- if ( num == 0 )
- return;
- vector< double > data( num * 9 );
-
- unsigned int j = 0;
- for ( unsigned int i = 0; i < num; ++i ) {
- Eref er( orig, i + start );
- const CaConcBase* cb =
- reinterpret_cast< const CaConcBase* >( er.data() );
- data[j + 0] = cb->getCa( er );
- data[j + 1] = cb->getCaBasal( er );
- data[j + 2] = cb->getTau( er );
- data[j + 3] = cb->getB( er );
- data[j + 4] = cb->getCeiling( er );
- data[j + 5] = cb->getFloor( er );
- data[j + 6] = cb->getThickness( er );
- data[j + 7] = cb->getLength( er );
- data[j + 8] = cb->getDiameter( er );
- j += 9;
- }
- orig->zombieSwap( zClass );
- j = 0;
- for ( unsigned int i = 0; i < num; ++i ) {
- Eref er( orig, i + start );
- CaConcBase* cb = reinterpret_cast< CaConcBase* >( er.data() );
- cb->vSetSolver( er, hsolve );
- cb->setCa( er, data[j + 0] );
- cb->setCaBasal( er, data[j + 1] );
- cb->setTau( er, data[j + 2] );
- cb->setB( er, data[j + 3] );
- cb->setCeiling( er, data[j + 4] );
- cb->setFloor( er, data[j + 5] );
- cb->setThickness( er, data[j + 6] );
- cb->setLength( er, data[j + 7] );
- cb->setDiameter( er, data[j + 8] );
- j += 7;
- }
+ if ( orig->cinfo() == zClass )
+ return;
+ unsigned int start = orig->localDataStart();
+ unsigned int num = orig->numLocalData();
+ if ( num == 0 )
+ return;
+ vector< double > data( num * 9 );
+
+ unsigned int j = 0;
+ for ( unsigned int i = 0; i < num; ++i ) {
+ Eref er( orig, i + start );
+ const CaConcBase* cb =
+ reinterpret_cast< const CaConcBase* >( er.data() );
+ data[j + 0] = cb->getCa( er );
+ data[j + 1] = cb->getCaBasal( er );
+ data[j + 2] = cb->getTau( er );
+ data[j + 3] = cb->getB( er );
+ data[j + 4] = cb->getCeiling( er );
+ data[j + 5] = cb->getFloor( er );
+ data[j + 6] = cb->getThickness( er );
+ data[j + 7] = cb->getLength( er );
+ data[j + 8] = cb->getDiameter( er );
+ j += 9;
+ }
+ orig->zombieSwap( zClass );
+ j = 0;
+ for ( unsigned int i = 0; i < num; ++i ) {
+ Eref er( orig, i + start );
+ CaConcBase* cb = reinterpret_cast< CaConcBase* >( er.data() );
+ cb->vSetSolver( er, hsolve );
+ cb->setCa( er, data[j + 0] );
+ cb->setCaBasal( er, data[j + 1] );
+ cb->setTau( er, data[j + 2] );
+ cb->setB( er, data[j + 3] );
+ cb->setCeiling( er, data[j + 4] );
+ cb->setFloor( er, data[j + 5] );
+ cb->setThickness( er, data[j + 6] );
+ cb->setLength( er, data[j + 7] );
+ cb->setDiameter( er, data[j + 8] );
+ j += 9; //was 7?
+ }
}