--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/08/15 19:24:13	699
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/08/20 14:34:04	701
@@ -44,8 +44,8 @@ template<typename T = BaseIntegrator> class Integrator
   
   void checkConstraints( void );
   void rotate( int axes1, int axes2, double angle, double j[3], 
-	       double A[3][3] );
-	       
+         double A[3][3] );
+         
   ForceFields* myFF;
 
   SimInfo *info; // all the info we'll ever need
@@ -56,7 +56,7 @@ template<typename T = BaseIntegrator> class Integrator
   int nMols;
 
   int isConstrained; // boolean to know whether the systems contains
-		     // constraints.
+         // constraints.
   int nConstrained;  // counter for number of constraints 
   int *constrainedA; // the i of a constraint pair 
   int *constrainedB; // the j of a constraint pair 
@@ -299,47 +299,47 @@ template<typename T> class ZConstraint : public T {
 };
 
 template<typename T> class ZConstraint : public T {
-	
-  public:	
+  
+  public: 
   class ForceSubstractionPolicy{
     public:
       ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
 
-		virtual void update() = 0;		
+      virtual void update() = 0;    
       virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
       virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
-	   virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
-		virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
-		
-	 protected:
-	   ZConstraint<T>* zconsIntegrator;;
+      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
+      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
+    
+   protected:
+     ZConstraint<T>* zconsIntegrator;;
   };
 
   class PolicyByNumber : ForceSubstractionPolicy{
     public:
-		PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}		
-		virtual void update();		
+      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}    
+      virtual void update();    
       virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
       virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
-	   virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
-		virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
-		
+      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
+      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
+    
     private:
-		int totNumOfMovingAtoms;
+    int totNumOfMovingAtoms;
   };
 
   class PolicyByMass :ForceSubstractionPolicy{
     public:
-      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}	
-			
-		virtual void update();		
+      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}  
+      
+      virtual void update();    
       virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
       virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
-	   virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
-		virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
+      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
+      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
 
-	 private:
-	   double totMassOfMovingAtoms;
+   private:
+     double totMassOfMovingAtoms;
   };
 
 public:
@@ -350,24 +350,22 @@ template<typename T> class ZConstraint : public T {
   void setZConsTime(double time)                  {this->zconsTime = time;}
   void getZConsTime()                             {return zconsTime;}
   
-  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
-  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
+  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
+  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
   
-  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
+  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
   string getZConsOutput()                         {return zconsOutput;}
   
   virtual void integrate();
   
 
 #ifdef IS_MPI
-  virtual void update(); //which is called to indicate the molecules' migration
+  virtual void update();                      //which is called to indicate the molecules' migration
 #endif
 
 protected:
 
-  enum ZConsState {zcsMoving, zcsFixed};
-
-
+  enum ZConsState {zcsMoving, zcsFixed};  
  
   virtual void calcForce( int calcPot, int calcStress ); 
   virtual void thermalize(void);
@@ -385,22 +383,23 @@ template<typename T> class ZConstraint : public T {
   int isZConstraintMol(Molecule* mol);
 
 
-  double zconsTime; 
-  double zconsTol;
-  double zForceConst;
+  double zconsTime;                              //sample time
+  double zconsTol;                                 //tolerance of z-contratint
+  double zForceConst;                           //base force constant term
+                                                          //which is estimate by OOPSE
   
-  vector<Molecule*> zconsMols;
-  vector<double> massOfZConsMols;
-  vector<double> kz;
-  vector<ZConsState> states; 
-  vector<double> zPos;
+  vector<Molecule*> zconsMols;              //z-constraint molecules array
+  vector<double> massOfZConsMols;       //mass of z-constraint molecule 
+  vector<double> kz;                              //force constant array
+  vector<ZConsState> states;                 //state of z-constraint molecules
+  vector<double> zPos;                          //
   
   
-  vector<Molecule*> unconsMols;
-  vector<double> massOfUnconsMols;
-  double totalMassOfUncons;
+  vector<Molecule*> unconsMols;           //unconstraint molecules array
+  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
+  double totalMassOfUncons;                //total mas of unconstraint molecules
 
-  vector<ZConsParaItem>* parameters;
+  vector<ZConsParaItem>* parameters; //
   
   vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
 
@@ -408,22 +407,22 @@ template<typename T> class ZConstraint : public T {
   double* fz;
   double* curZPos;
   
-  int totNumOfUnconsAtoms;
+  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
 
   int whichDirection;                           //constraint direction 
   
 private:
   
-  string zconsOutput;
-  ZConsWriter* fzOut;
+  string zconsOutput;                         //filename of zconstraint output
+  ZConsWriter* fzOut;                         //z-constraint writer
 
-  double curZconsTime;
+  double curZconsTime;                      
 
   double calcMovingMolsCOMVel();
   double calcSysCOMVel();
   double calcTotalForce();
-	
-  ForceSubstractionPolicy* forcePolicy;
+  
+  ForceSubstractionPolicy* forcePolicy; //force substration policy
   friend class ForceSubstractionPolicy;
 
 };