--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/09/19 20:00:27	778
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/10/22 21:17:32	812
@@ -195,6 +195,7 @@ template<typename T> class NPT : public T{ (protected)
 
   double tt2, tb2;
   double instaTemp, instaPress, instaVol;
+  double press[3][3];
 
   int Nparticles;
 
@@ -252,344 +253,65 @@ template<typename T> class NPTi : public T{ (protected
   double eta, oldEta, prevEta;
 };
 
-
-template<typename T> class NPTim : public T{
+template<typename T> class NPTf : public T{
 
 public:
-
-  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTim() {}
 
-  virtual void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-    accIntegralOfChidt();   
-  }
+  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTf();
 
   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;}
-  void setChiTolerance(double tol) {chiTolerance = tol;}
-  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
-
 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 );
 
-  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
-  
-  Molecule* myMolecules;
-  Atom** myAtoms;
-
-  // chi and eta are the propagated degrees of freedom
-
-  double chi;
-  double eta;
-  double NkBT;
-  double integralOfChidt;
-
-  // targetTemp, targetPressure, and tauBarostat must be set.  
-  // One of qmass or tauThermostat must be set;
-
-  double targetTemp;
-  double targetPressure;
-  double tauThermostat;
-  double tauBarostat;
+  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]);
 
-  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;
-
+  double eta[3][3];
+  double oldEta[3][3];
+  double prevEta[3][3];
 };
 
-template<typename T> class NPTzm : public T{
+template<typename T> class NPTxyz : public T{
 
 public:
 
-  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTzm() {};
+  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 );
-
-  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 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 void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-  }
-  
-  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();
-
-
-  // chi and eta are the propagated degrees of freedom
-
-  double chi;
   double eta[3][3];
-  double NkBT;
-  double fkBT;
-
-  int Nparticles;
-
-  double *oldPos;
-  double *oldVel;
-  double *oldJi;
-
-  double integralOfChidt;
-  
-  // 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;
-  double etaTolerance;
-  short int have_eta_tolerance;
-};
-
-template<typename T> class NPTxym : public T{
-
-public:
-
-  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTxym() {};
-
-  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 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;
-
+  double oldEta[3][3];
+  double prevEta[3][3];
 };
 
 
-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;
-
-  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 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: 
@@ -604,7 +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{
@@ -657,9 +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);
@@ -682,17 +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
@@ -701,8 +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: