Implementation of MMPump

moose-core/biophysics/MMPump.cpp

+#include "header.h"
+#include "MMPump.h"
+#include "ElementValueFinfo.h"
+#include "../utility/numutil.h"
+#include <cmath>
+
+SrcFinfo2< double,double >* MMPump::PumpOut()
+{
+  static SrcFinfo2< double,double > pumpOut( "PumpOut",
+				    "Sends out MMPump parameters.");
+  return &pumpOut;
+}
+
+const Cinfo * MMPump::initCinfo()
+{
+  static DestFinfo process( "process",
+			    "Handles process call",
+			    new ProcOpFunc< MMPump>(&MMPump::process ) );
+  static DestFinfo reinit( "reinit",
+			   "Reinit happens only in stage 0",
+			   new ProcOpFunc< MMPump>( &MMPump::reinit ));
+    
+  static Finfo* processShared[] = {
+    &process, &reinit
+  };
+
+  static SharedFinfo proc(
+			  "proc", 
+			  "Shared message to receive Process message from scheduler",
+			  processShared, sizeof( processShared ) / sizeof( Finfo* ));
+    
+
+  ////////////////////////////
+  // Field defs
+  ////////////////////////////
+  
+
+  
+  static ElementValueFinfo<MMPump, double> Vmax("Vmax",
+						  "maximum pump velocity, scaled by mebrane"
+						    "surface area. i.e., max ion flux in moles/sec",
+						  &MMPump::setVmax,
+						  &MMPump::getVmax);
+ 
+  static ElementValueFinfo<MMPump, double> Kd("Kd",
+						 "half-maximal activating concentration in mM",
+						 &MMPump::setKd,
+						 &MMPump::getKd);
+  
+  ////
+  // DestFinfo
+  ////
+  static Finfo * difBufferFinfos[] = {
+    //////////////////////////////////////////////////////////////////
+    // Field definitions
+    //////////////////////////////////////////////////////////////////
+    
+   
+    &Vmax,
+    &Kd,
+    //////////////////////////////////////////////////////////////////
+    // SharedFinfo definitions
+    /////////////////////////////////////////////////////////////////
+   
+    &proc,
+    PumpOut(),
+    //////////////////////////////////////////////////////////////////
+    // DestFinfo definitions
+    //////////////////////////////////////////////////////////////////
+
+  };
+
+  static string doc[] = {
+    "Name", "MMPump",
+    "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 MMPumpCinfo(
+			      "MMPump",
+			      Neutral::initCinfo(),
+			      difBufferFinfos,
+			      sizeof(difBufferFinfos)/sizeof(Finfo*),
+			      &dinfo,
+			      doc,
+			      sizeof(doc)/sizeof(string));
+
+  return &MMPumpCinfo;
+}
+
+static const Cinfo * MMpumpCinfo = MMPump::initCinfo();
+
+
+////////////////////////////////////////////////////////////////////////////////
+// Class functions
+////////////////////////////////////////////////////////////////////////////////
+
+MMPump::MMPump()
+{ ; }
+
+
+
+
+double MMPump::getVmax(const Eref& e) const
+{
+
+  return Vmax_;
+}
+void MMPump::setVmax(const Eref& e,double value)
+{
+if ( value  < 0.0 ) {
+    cerr << "Error: MMPump: Vmax cannot be negative!\n";
+    return;
+  }
+  Vmax_ = value;
+}
+
+
+double MMPump::getKd(const Eref& e) const
+{
+  return Kd_;
+}
+void MMPump::setKd(const Eref& e,double value)
+{
+if ( value  < 0.0 ) {
+    cerr << "Error: MMPump: Kd cannot be negative!\n";
+    return;
+  }
+  Kd_ = value;
+}
+
+
+void MMPump::process(const Eref& e, ProcPtr p)
+{
+  PumpOut()->send(e,Vmax_,Kd_); 
+}
+
+void MMPump::reinit(const Eref& e, ProcPtr p)
+{
+  return;
+}

moose-core/biophysics/MMPump.h

+/**********************************************************************
+ ** This program is part of 'MOOSE', the
+ ** Multiscale Object Oriented Simulation Environment.
+ **           copyright (C) 2003-2008
+ **           Upinder S. Bhalla, Niraj Dudani 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.
+ **********************************************************************/
+
+#ifndef _MMPUMP_H
+#define _MMPUMP_H
+/*This is base class for MMPump*/
+class MMPump
+{
+public:
+  MMPump();
+  void process( const Eref & e, ProcPtr p);
+  void reinit(const Eref &e, ProcPtr p);
+
+  double getVmax(const Eref& e) const; //Vmax of the pump
+  void setVmax(const Eref& e,double value);
+  
+  int getVal(const Eref& e) const; //Valence
+  void setVal(const Eref& e,int value);
+ 
+  double getKd(const Eref& e) const;           //  Pump's Kd
+  void setKd(const Eref& e,double value);
+  
+ 
+
+  static SrcFinfo2< double,double >* PumpOut(); //Pump parameters;
+
+  static const Cinfo * initCinfo();
+
+private:
+      
+  double Vmax_;
+  double Kd_; 
+};
+
+
+
+
+#endif //_MMPUMP_BASE_H