--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/06/20 20:29:36	561
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/07/15 03:27:24	605
@@ -2,6 +2,7 @@
 #define _INTEGRATOR_H_
 
 #include "Atom.hpp"
+#include "Molecule.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
 #include "SimInfo.hpp"
@@ -11,6 +12,7 @@ const int maxIteration = 300;
 
 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 double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
 const int maxIteration = 300;
 const double tol = 1.0e-6;
 
@@ -34,7 +36,7 @@ class Integrator : public BaseIntegrator { (protected)
   
   void checkConstraints( void );
   void rotate( int axes1, int axes2, double angle, double j[3], 
-	       double A[9] );
+	       double A[3][3] );
 
 
   ForceFields* myFF;
@@ -62,12 +64,6 @@ class Integrator : public BaseIntegrator { (protected)
   double dt;
   double dt2;
 
-  double* pos;
-  double* vel;
-  double* frc;
-  double* trq;
-  double* Amat;
-
   Thermo *tStats;
   StatWriter*  statOut;
   DumpWriter*  dumpOut;
@@ -92,7 +88,6 @@ class NVT : public Integrator{ (public)
   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;}
 
@@ -103,31 +98,121 @@ class NVT : public Integrator{ (public)
 
   virtual int readyCheck();
 
-  // zeta is a propagated degree of freedom.
+  // chi is a propagated degree of freedom.
 
-  double zeta;
+  double chi;
 
-  // targetTemp must be set.  One of qmass or tauThermostat must be set;
+  // targetTemp must be set.  tauThermostat must also be set;
 
-  double qmass;
   double targetTemp;
   double tauThermostat;
+  
+  short int have_tau_thermostat, have_target_temp;
 
+};
+
+
+class NPTi : public Integrator{
+
+public:
+
+  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTi() {};
+
+  virtual void integrateStep( int calcPot, int calcStress ){
+    calcStress = 1;
+    Integrator::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();
+
+  // chi and eta are the propagated degrees of freedom
+
+  double chi;
+  double eta;
   double NkBT;
-  
-  short int have_tau_thermostat, have_target_temp, have_qmass;
 
+  // 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 NPTim : public Integrator{
 
-class NPT : public Integrator{
+public:
 
+  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTim() {};
+
+  virtual void integrateStep( int calcPot, int calcStress ){
+    calcStress = 1;
+    Integrator::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();
+
+  Molecule* myMolecules;
+  Atom** myAtoms;
+
+  // chi and eta are the propagated degrees of freedom
+
+  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;
+
+};
+
+class NPTf : public Integrator{
+
 public:
 
-  NPT ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPT();
+  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTf() {};
 
-  void setQmass(double q) {qmass = q; have_qmass = 1;}
+  virtual void integrateStep( int calcPot, int calcStress ){
+    calcStress = 1;
+    Integrator::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;}
@@ -140,24 +225,68 @@ class NPT : public Integrator{ (protected)
 
   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[3][3];
+  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 NPTfm : public Integrator{
+
+public:
+
+  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTfm() {};
+
+  virtual void integrateStep( int calcPot, int calcStress ){
+    calcStress = 1;
+    Integrator::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();
+
+  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 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;
 
 };