--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/06/20 16:49:33	560
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/07/08 21:10:16	576
@@ -9,10 +9,15 @@ class Integrator : public BaseIntegrator {
 #include "Thermo.hpp"
 #include "ReadWrite.hpp"
 
+const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
+const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
+const int maxIteration = 300;
+const double tol = 1.0e-6;
+
 class Integrator : public BaseIntegrator {
 
 public:
-  Integrator( SimInfo &theInfo, ForceFields* the_ff );
+  Integrator( SimInfo *theInfo, ForceFields* the_ff );
   virtual ~Integrator();
   void integrate( void );
 
@@ -29,7 +34,7 @@ class Integrator : public BaseIntegrator { (protected)
   
   void checkConstraints( void );
   void rotate( int axes1, int axes2, double angle, double j[3], 
-	       double A[3][3] );
+	       double A[9] );
 
 
   ForceFields* myFF;
@@ -50,18 +55,13 @@ class Integrator : public BaseIntegrator { (protected)
   
   int* moving; // tells whether we are moving atom i
   int* moved;  // tells whether we have moved atom i
-  double* prePos; // pre constrained positions 
+  double* oldPos; // pre constrained positions 
 
   short isFirst; /*boolean for the first time integrate is called */
   
   double dt;
   double dt2;
 
-  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
-  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
-  const int maxIteration = 300;
-  const double tol = 1.0e-6;
-  
   double* pos;
   double* vel;
   double* frc;
@@ -76,7 +76,8 @@ class NVE : public Integrator{
 
 class NVE : public Integrator{
 
-  NVE ( void ):
+public:
+  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
     Integrator( theInfo, the_ff ){}
   virtual ~NVE(){}
 
@@ -88,47 +89,40 @@ class NVT : public Integrator{ (public)
 
 public:
 
-  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
-    Integrator( theInfo, the_ff );
-  virtual ~NVT();
+  NVT ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NVT() {}
 
-  void setQmass(double q) {qmass = q; have_qmass = 1;}
   void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
   void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
 
 protected:
 
-  virtual moveA( void );
-  virtual moveB( void );
+  virtual void moveA( void );
+  virtual void moveB( void );
 
-  int readyCheck();
+  virtual int readyCheck();
 
-  Atom** atoms;
+  // chi is a propagated degree of freedom.
 
-  // zeta is a propagated degree of freedom.
+  double chi;
 
-  double zeta;
+  // targetTemp must be set.  tauThermostat must also be set;
 
-  // targetTemp must be set.  One of qmass or tauThermostat must be set;
-
-  double qmass;
   double targetTemp;
   double tauThermostat;
+  
+  short int have_tau_thermostat, have_target_temp;
 
-  short int have_tau_thermostat, have_target_temp, have_qmass;
-
 };
 
 
-class NPT : public Integrator{
+class NPTi : public Integrator{
 
 public:
 
-  NPT ( SimInfo &theInfo, ForceFields* the_ff) :
-    Integrator( theInfo, the_ff );
-  virtual ~NPT();
+  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTi() {};
 
-  void setQmass(double q) {qmass = q; have_qmass = 1;}
   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;}
@@ -136,29 +130,65 @@ class NPT : public Integrator{ (protected)
 
 protected:
 
-  virtual moveA( void );
-  virtual moveB( void );
+  virtual void  moveA( void );
+  virtual void moveB( void );
 
-  int readyCheck();
+  virtual int readyCheck();
 
-  Atom** atoms;
+  // chi and eta are the propagated degrees of freedom
 
-  // zeta and epsilonDot are the propagated degrees of freedom.
+  double chi;
+  double eta;
+  double NkBT;
 
-  double zeta;
-  double epsilonDot;
+  // 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;
+
+};
+
+class NPTf : public Integrator{
+
+public:
+
+  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTf() {};
+
+  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();
+
+  // chi and eta are the propagated degrees of freedom
+
+  double chi;
+  double eta[9];
+  double NkBT;
+
   // targetTemp, targetPressure, and tauBarostat must be set.  
   // One of qmass or tauThermostat must be set;
 
-  double qmass;
   double targetTemp;
   double targetPressure;
   double tauThermostat;
   double tauBarostat;
 
   short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-  short int have_target_pressure, have_qmass;
+  short int have_target_pressure;
 
 };