Make DifBuffer look more like other moose classes and fix ticks

Reintroduced implementation of Difbuffer used moose objects that have
been since rewritten and renamed.  Change used moose objects to
current version.

moose-core/biophysics/DifBuffer.h

@@ -54,58 +54,75 @@ class DifBuffer
   
   //Field access functions
 
-  double getActivation() const;
-  void setActivation(double value);
+  double getActivation(const Eref& e) const;
+  void setActivation(const Eref& e,double value);
 
-  double getBFree() const;
-  double getBBound() const;
+  double getBFree(const Eref& e) const;
+  double getBBound(const Eref& e) const;
 
-  double getPrevFree() const;   // Bfree at previous time step
-  double getPrevBound() const;  // Bbound at previous time step
+  //double getPrevFree(const Eref& e) const;   // Bfree at previous time step
+  //double getPrevBound(const Eref& e) const;  // Bbound at previous time step
 
-  double getBTot() const;           //  total buffer concentration in mM (free + bound)
-  void setBTot(double value);
+  double getBTot(const Eref& e) const;           //  total buffer concentration in mM (free + bound)
+  void setBTot(const Eref& e,double value);
 
-  double getKf() const;         // forward rate constant in 1/(mM*sec)
-  void setKf(double value);
+  double getKf(const Eref& e) const;         // forward rate constant in 1/(mM*sec)
+  void setKf(const Eref& e,double value);
 
-  double getKb() const;         // backward rate constant in 1/sec
-  void setKb(double value);
+  double getKb(const Eref& e) const;         // backward rate constant in 1/sec
+  void setKb(const Eref& e,double value);
   
-  double getD() const;          // diffusion constant of buffer molecules, m^2/sec
-  void setD(double value);
+  double getD(const Eref& e) const;          // diffusion constant of buffer molecules, m^2/sec
+  void setD(const Eref& e,double value);
 
-  int getShapeMode() const; //    Set to one of the predefined global
-  void setShapeMode(int value); // variables SHELL=0, SLICE=SLAB=1, USERDEF=3.
+  int getShapeMode(const Eref& e) const; //    Set to one of the predefined global
+  void setShapeMode(const Eref& e,int value); // variables SHELL=0, SLICE=SLAB=1, USERDEF=3.
 
-  double getLength() const; //             shell length
-  void setLength(double value);
+  double getLength(const Eref& e) const; //             shell length
+  void setLength(const Eref& e,double value);
 
-  double getDiameter() const; //            shell diameter
-  void setDiameter(double value);
+  double getDiameter(const Eref& e) const; //            shell diameter
+  void setDiameter(const Eref& e,double value);
   
-  double getThickness() const; //           shell thickness
-  void setThickness(double value);
-
-  double getVolume() const; //             shell volume
-  void setVolume(double volume) const; //            
+  double getThickness(const Eref& e) const; //           shell thickness
+  void setThickness(const Eref& e,double value);
+  
+  void setOuterArea( const Eref& e,double outerArea );
+  double getOuterArea(const Eref& e) const; //         area of upper (outer) shell surface
+  
+  void setInnerArea( const Eref& e,double innerArea );
+  double getInnerArea(const Eref& e) const; //       area of lower (inner) shell surface
 
-  double getOuterArea() const; //         area of upper (outer) shell surface
-  double getInnerArea() const; //       area of lower (inner) shell surface
+  double getVolume(const Eref& e) const; //             shell volume
+  void setVolume(const Eref& e,double volume); //
+  
+  //void concentration();
+  void  buffer(const Eref& e,double C);
 
-  void concentration();
+  void reinit( const Eref & e, ProcPtr p );
 
-  void reinit(const Eref & e, ProcPtr p);
-  void init(const Eref & e, ProcPtr p);
+  void process(const Eref & e, ProcPtr p );
   
+  void fluxFromOut(const Eref& e,double outerC, double outerThickness );
+
+  void fluxFromIn( const Eref& e,double innerC, double innerThickness );
+  static SrcFinfo4< double, double, double, double >* reactionOut();
+  static SrcFinfo2< double, double >* innerDifSourceOut();
+  static SrcFinfo2< double, double >* outerDifSourceOut();
   static const Cinfo * initCinfo();
 
  private:
+  
+  void localReinit_0(  const Eref & e, ProcPtr p );
+  void localProcess_0( const Eref & e, ProcPtr p );
+  
   double activation_; //ion concentration from incoming CONCEN message
+  double Af_;
+  double Bf_;
   double bFree_; //free buffer concentration
   double bBound_; //bound buffer concentration
-  double prevFree_; //bFree at previous time
-  double prevBound_; //bBound at previous time
+  //double prevFree_; //bFree at previous time
+  //double prevBound_; //bBound at previous time
   double bTot_; //bFree+bBound
   double kf_; //forward rate constant
   double kb_; //backward rate constant
@@ -116,7 +133,7 @@ class DifBuffer
   double thickness_; //shell thickness
   double outerArea_; //area of upper (outer) shell surface
   double innerArea_; //area of lower (inner) shell surface
-  
+  double volume_;
 };
 
 #endif // _DifBuffer_h