--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/09/22 21:23:25	780
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/09/29 21:16:11	790
@@ -366,64 +366,7 @@ template<typename T> class NPTxym : public T{ (protect
   double eta;
   double etaX;
   double etaY;
-  double NkBT;
-
-  // targetTemp, targetPressure, and tauBarostat must be set.  
-  // One of qmass or tauThermostat must be set;
-
-  double targetTemp;
-  double targetPressure;
-  double tauThermostat;
-  double tauBarostat;
-
-  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-  short int have_target_pressure;
-
-};
-
-
-template<typename T> class NPTfm : public T{
-
-public:
-
-  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTfm() {};
-
-  virtual void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-    accIntegralOfChidt();
-  }
-
-  virtual double getConservedQuantity(void);
-  
-  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
-  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
-  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
-  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
-  void setChiTolerance(double tol) {chiTolerance = tol;}
-  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
-
-protected:
-
-  virtual void  moveA( void );
-  virtual void moveB( void );
-
-  virtual void resetIntegrator( void );
-
-  virtual int readyCheck();
-
-  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
-
-  Molecule* myMolecules;
-  Atom** myAtoms;
-
-  // chi and eta are the propagated degrees of freedom
-
-  double chi;
-  double eta[3][3];
   double NkBT;
-  double integralOfChidt;
 
   // targetTemp, targetPressure, and tauBarostat must be set.  
   // One of qmass or tauThermostat must be set;
@@ -435,66 +378,9 @@ template<typename T> class NPTfm : public T{ (protecte
 
   short int have_tau_thermostat, have_tau_barostat, have_target_temp;
   short int have_target_pressure;
-  double chiTolerance;
-  short int have_chi_tolerance;
-  double posIterTolerance;
-  short int have_pos_iter_tolerance;
 
 };
 
-
-template<typename T> class NPTpr : public T{
-
-public:
-
-  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTpr() {};
-
-  virtual void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-  }
-
-  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
-  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
-  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
-  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
-  void setChiTolerance(double tol) {chiTolerance = tol;}
-  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
-
-protected:
-
-  virtual void  moveA( void );
-  virtual void moveB( void );
-
-  virtual int readyCheck();
-
-  virtual void resetIntegrator( void );
-
-  // chi and eta are the propagated degrees of freedom
-
-  double chi;
-  double eta[3][3];
-  double NkBT;
-
-  // targetTemp, targetPressure, and tauBarostat must be set.  
-  // One of qmass or tauThermostat must be set;
-
-  double targetTemp;
-  double targetPressure;
-  double tauThermostat;
-  double tauBarostat;
-
-  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-  short int have_target_pressure;
-  double chiTolerance;
-  short int have_chi_tolerance;
-  double posIterTolerance;
-  short int have_pos_iter_tolerance;
-
-};
-
-
 template<typename T> class ZConstraint : public T {
   
   public: 
@@ -509,7 +395,7 @@ template<typename T> class ZConstraint : public T {
       virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
     
    protected:
-     ZConstraint<T>* zconsIntegrator;;
+     ZConstraint<T>* zconsIntegrator;
   };
 
   class PolicyByNumber : public ForceSubtractionPolicy{
@@ -562,9 +448,20 @@ template<typename T> class ZConstraint : public T {
   virtual void update();                      //which is called to indicate the molecules' migration
 #endif
 
+  enum ZConsState {zcsMoving, zcsFixed};  
+
+  vector<Molecule*> zconsMols;              //z-constraint molecules array
+  vector<ZConsState> states;                 //state of z-constraint molecules
+
+ 
+
+  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
+  double totalMassOfUncons;                //total mas of unconstraint molecules
+
+
 protected:
 
-  enum ZConsState {zcsMoving, zcsFixed};  
+
  
   virtual void calcForce( int calcPot, int calcStress ); 
   virtual void thermalize(void);
@@ -587,17 +484,17 @@ template<typename T> class ZConstraint : public T {
   double zForceConst;                           //base force constant term
                                                           //which is estimate by OOPSE
   
-  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;           //unconstraint molecules array
   vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
-  double totalMassOfUncons;                //total mas of unconstraint molecules
 
+
   vector<ZConsParaItem>* parameters; //
   
   vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
@@ -606,8 +503,8 @@ template<typename T> class ZConstraint : public T {
   double* fz;
   double* curZPos;
   
-  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
 
+
   int whichDirection;                           //constraint direction 
   
 private: