--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/09/09 20:35:25	755
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/10/22 21:17:32	812
@@ -27,10 +27,10 @@ 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 );
   virtual void preMove( void );
   virtual void moveA( void );
@@ -40,10 +40,12 @@ 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();
   
+  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
+
   void checkConstraints( void );
   void rotate( int axes1, int axes2, double angle, double j[3], 
          double A[3][3] );
@@ -95,10 +97,12 @@ 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 +117,9 @@ 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;
@@ -120,26 +127,37 @@ 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;
+
 };
 
 
 
-template<typename T> class NPTi : public T{
+template<typename T> class NPT : public T{
 
 public:
 
-  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTi() {};
-
+  NPT ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPT();
+  
   virtual void integrateStep( int calcPot, int calcStress ){
     calcStress = 1;
     T::integrateStep( calcPot, calcStress );
   }
 
+  virtual double getConservedQuantity(void) = 0;
+
   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 +168,39 @@ template<typename T> class NPTi : public T{ (protected
 
   virtual void resetIntegrator( void );
 
+  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
+  virtual void getVelScaleB( double sc[3], int index ) = 0;
+  virtual void getPosScale(double pos[3], double COM[3], 
+			   int index, double sc[3]) = 0;
+
+  virtual bool chiConverged( void );
+  virtual bool etaConverged( void ) = 0;
+  
+  virtual void evolveChiA( void );
+  virtual void evolveEtaA( void ) = 0;
+  virtual void evolveChiB( void );
+  virtual void evolveEtaB( void ) = 0;
+
+  virtual void scaleSimBox( void ) = 0;
+
+  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
+
   // chi and eta are the propagated degrees of freedom
 
+  double oldChi;
+  double prevChi;
   double chi;
-  double eta;
   double NkBT;
+  double fkBT;
 
+  double tt2, tb2;
+  double instaTemp, instaPress, instaVol;
+  double press[3][3];
+
+  int Nparticles;
+
+  double integralOfChidt;
+
   // targetTemp, targetPressure, and tauBarostat must be set.  
   // One of qmass or tauThermostat must be set;
 
@@ -167,296 +212,106 @@ template<typename T> class NPTi : public T{ (protected
   short int have_tau_thermostat, have_tau_barostat, have_target_temp;
   short int have_target_pressure;
 
-};
+  double *oldPos;
+  double *oldVel;
+  double *oldJi;
 
-template<typename T> class NPTim : public T{
+  double chiTolerance;
+  short int have_chi_tolerance;
+  double posIterTolerance;
+  short int have_pos_iter_tolerance;
+  double etaTolerance;
+  short int have_eta_tolerance;
 
+};
+
+template<typename T> class NPTi : public T{
+  
 public:
+  NPTi( SimInfo *theInfo, ForceFields* the_ff);
+  ~NPTi();
 
-  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTim() {};
+  virtual double getConservedQuantity(void);
+  virtual void resetIntegrator(void);
 
-  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;}
-
 protected:
 
-  virtual void moveA( void );
-  virtual void moveB( void );
+ 
 
-  virtual int readyCheck();
+  virtual void evolveEtaA(void);
+  virtual void evolveEtaB(void);
 
-  virtual void resetIntegrator( void );
+  virtual bool etaConverged( void );
 
-  Molecule* myMolecules;
-  Atom** myAtoms;
+  virtual void scaleSimBox( void );
 
-  // chi and eta are the propagated degrees of freedom
+  virtual void getVelScaleA( double sc[3], double vel[3] );
+  virtual void getVelScaleB( double sc[3], int index );
+  virtual void getPosScale(double pos[3], double COM[3], 
+			   int index, double sc[3]);
 
-  double chi;
-  double eta;
-  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 eta, oldEta, prevEta;
 };
 
-template<typename T> class NPTzm : public T{
-
-public:
-
-  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTzm() {};
-
-  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;}
-
-protected:
-
-  virtual void moveA( void );
-  virtual void moveB( void );
-
-  virtual int readyCheck();
-
-  virtual void resetIntegrator( void );
-
-  Molecule* myMolecules;
-  Atom** myAtoms;
-
-  // chi and eta are the propagated degrees of freedom
-
-  double chi;
-  double eta;
-  double etaZ;
-  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 NPTf : public T{
 
 public:
 
   NPTf ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTf() {};
+  virtual ~NPTf();
 
-  virtual void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-  }
+  virtual double getConservedQuantity(void);
+  virtual void resetIntegrator(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;}
-
 protected:
 
-  virtual void  moveA( void );
-  virtual void moveB( void );
+  virtual void evolveEtaA(void);
+  virtual void evolveEtaB(void);
 
-  virtual void resetIntegrator( void );
+  virtual bool etaConverged( void );
 
-  virtual int readyCheck();
+  virtual void scaleSimBox( void );
 
-  // chi and eta are the propagated degrees of freedom
+  virtual void getVelScaleA( double sc[3], double vel[3] );
+  virtual void getVelScaleB( double sc[3], int index );
+  virtual void getPosScale(double pos[3], double COM[3], 
+			   int index, double sc[3]);
 
-  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 oldEta[3][3];
+  double prevEta[3][3];
 };
 
-template<typename T> class NPTxym : public T{
+template<typename T> class NPTxyz : public T{
 
 public:
 
-  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTxym() {};
+  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTxyz();
 
-  virtual void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-  }
+  virtual double getConservedQuantity(void);
+  virtual void resetIntegrator(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;}
-
 protected:
 
-  virtual void moveA( void );
-  virtual void moveB( void );
+  virtual void evolveEtaA(void);
+  virtual void evolveEtaB(void);
 
-  virtual int readyCheck();
+  virtual bool etaConverged( void );
 
-  virtual void resetIntegrator( void );
+  virtual void scaleSimBox( void );
 
-  Molecule* myMolecules;
-  Atom** myAtoms;
+  virtual void getVelScaleA( double sc[3], double vel[3] );
+  virtual void getVelScaleB( double sc[3], int index );
+  virtual void getPosScale(double pos[3], double COM[3], 
+			   int index, double sc[3]);
 
-  // chi and eta are the propagated degrees of freedom
-
-  double chi;
-  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 );
-  }
-
-  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;}
-
-protected:
-
-  virtual void  moveA( void );
-  virtual void moveB( void );
-
-  virtual void resetIntegrator( void );
-
-  virtual int readyCheck();
-
-  Molecule* myMolecules;
-  Atom** myAtoms;
-
-  // 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 oldEta[3][3];
+  double prevEta[3][3];
 };
 
 
-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;}
-
-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;
-
-};
-
-
 template<typename T> class ZConstraint : public T {
   
   public: 
@@ -471,7 +326,7 @@ 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{
@@ -485,7 +340,7 @@ template<typename T> class ZConstraint : public T {
       virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
     
     private:
-    int totNumOfMovingAtoms;
+      int totNumOfMovingAtoms;
   };
 
   class PolicyByMass : public ForceSubtractionPolicy{
@@ -524,9 +379,20 @@ 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);
@@ -549,17 +415,17 @@ 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
@@ -568,8 +434,8 @@ template<typename T> class ZConstraint : public T {
   double* fz;
   double* curZPos;
   
-  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
 
+
   int whichDirection;                           //constraint direction 
   
 private: