--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/09/09 20:35:25	755
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/09/15 16:52:02	763
@@ -27,8 +27,8 @@ template<typename T = BaseIntegrator> class Integrator
   Integrator( SimInfo *theInfo, ForceFields* the_ff );
   virtual ~Integrator();
   void integrate( void );
+  virtual double  getConservedQuantity(void);
 
-
 protected:
   
   virtual void integrateStep( int calcPot, int calcStress );
@@ -40,7 +40,7 @@ template<typename T = BaseIntegrator> class Integrator
   virtual int  readyCheck( void ) { return 1; }
 
   virtual void resetIntegrator( void ) { }
-
+ 
   virtual void calcForce( int calcPot, int calcStress );  
   virtual void thermalize();
   
@@ -95,10 +95,12 @@ template<typename T> class NVT : public T { (public)
 public:
 
   NVT ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NVT() {}
+  virtual ~NVT();
 
   void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
   void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
+  void setChiTolerance(double tol) {chiTolerance = tol;}
+  virtual double  getConservedQuantity(void);
 
 protected:
 
@@ -113,6 +115,9 @@ template<typename T> class NVT : public T { (public)
 
   double chi;
 
+  //integral of chi(t)dt
+  double integralOfChidt;
+
   // targetTemp must be set.  tauThermostat must also be set;
 
   double targetTemp;
@@ -120,6 +125,12 @@ template<typename T> class NVT : public T { (public)
   
   short int have_tau_thermostat, have_target_temp;
 
+  double *oldVel;
+  double *oldJi;
+
+  double chiTolerance;
+  short int have_chi_tolerance;
+
 };
 
 
@@ -129,17 +140,23 @@ template<typename T> class NPTi : public T{ (public)
 public:
 
   NPTi ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTi() {};
-
+  virtual ~NPTi();
+  
   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; have_chi_tolerance = 1;}
+  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
+  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
 
 protected:
 
@@ -150,12 +167,19 @@ template<typename T> class NPTi : public T{ (public)
 
   virtual void resetIntegrator( void );
 
+  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
+
   // chi and eta are the propagated degrees of freedom
 
   double chi;
   double eta;
   double NkBT;
+  double fkBT;
 
+  int Nparticles;
+
+  double integralOfChidt;
+
   // targetTemp, targetPressure, and tauBarostat must be set.  
   // One of qmass or tauThermostat must be set;
 
@@ -166,6 +190,19 @@ template<typename T> class NPTi : public T{ (public)
 
   short int have_tau_thermostat, have_tau_barostat, have_target_temp;
   short int have_target_pressure;
+
+  double *oldPos;
+  double *oldVel;
+  double *oldJi;
+
+  double chiTolerance;
+  short int have_chi_tolerance;
+  double posIterTolerance;
+  short int have_pos_iter_tolerance;
+  double etaTolerance;
+  short int have_eta_tolerance;
+
+  double volume;
 
 };
 
@@ -174,17 +211,22 @@ template<typename T> class NPTim : public T{ (public)
 public:
 
   NPTim ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTim() {};
+  virtual ~NPTim() {}
 
   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:
 
@@ -195,6 +237,8 @@ template<typename T> class NPTim : public T{ (public)
 
   virtual void resetIntegrator( void );
 
+  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
+  
   Molecule* myMolecules;
   Atom** myAtoms;
 
@@ -203,6 +247,7 @@ template<typename T> class NPTim : public T{ (public)
   double chi;
   double eta;
   double NkBT;
+  double integralOfChidt;
 
   // targetTemp, targetPressure, and tauBarostat must be set.  
   // One of qmass or tauThermostat must be set;
@@ -214,6 +259,10 @@ template<typename T> class NPTim : public T{ (public)
 
   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;
 
 };
 
@@ -276,12 +325,17 @@ template<typename T> class NPTf : public T{ (public)
   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:
 
@@ -292,12 +346,16 @@ template<typename T> class NPTf : public T{ (public)
 
   virtual int readyCheck();
 
+  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
+
   // 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;
 
@@ -308,6 +366,10 @@ template<typename T> class NPTf : public T{ (public)
 
   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;
 
 };
 
@@ -372,12 +434,17 @@ template<typename T> class NPTfm : public T{ (public)
   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:
 
@@ -388,6 +455,8 @@ template<typename T> class NPTfm : public T{ (public)
 
   virtual int readyCheck();
 
+  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
+
   Molecule* myMolecules;
   Atom** myAtoms;
 
@@ -396,6 +465,7 @@ template<typename T> class NPTfm : public T{ (public)
   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;
@@ -407,6 +477,10 @@ template<typename T> class NPTfm : public T{ (public)
 
   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;
 
 };
 
@@ -427,6 +501,8 @@ template<typename T> class NPTpr : public T{ (public)
   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:
 
@@ -453,6 +529,10 @@ template<typename T> class NPTpr : public T{ (public)
 
   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;
 
 };
 
@@ -485,7 +565,7 @@ template<typename T> class ZConstraint : public T {
       virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
     
     private:
-    int totNumOfMovingAtoms;
+      int totNumOfMovingAtoms;
   };
 
   class PolicyByMass : public ForceSubtractionPolicy{