--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/05/30 19:07:45	540
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/07/14 15:04:55	596
@@ -9,24 +9,30 @@ 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 double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
+const int maxIteration = 300;
+const double tol = 1.0e-6;
+
 class Integrator : public BaseIntegrator {
 
 public:
-  Symplectic( SimInfo &theInfo, ForceFields* the_ff );
-  virtual ~Symplectic();
+  Integrator( SimInfo *theInfo, ForceFields* the_ff );
+  virtual ~Integrator();
   void integrate( void );
 
 
 protected:
-
   
   virtual void integrateStep( int calcPot, int calcStress );
+  virtual void preMove( void );
   virtual void moveA( void );
   virtual void moveB( void );
   virtual void constrainA( void );
   virtual void constrainB( void );
+  virtual int  readyCheck( void ) { return 1; }
   
-  
   void checkConstraints( void );
   void rotate( int axes1, int axes2, double angle, double j[3], 
 	       double A[3][3] );
@@ -36,20 +42,32 @@ class Integrator : public BaseIntegrator { (protected)
 
   SimInfo *info; // all the info we'll ever need
   int nAtoms;  /* the number of atoms */
+  int oldAtoms;
   Atom **atoms; /* array of atom pointers */
   Molecule* molecules;
   int nMols;
 
-  int isConstrained; /*boolean to know whether the systems contains
-		       constraints. */
-  int nConstrained; /*counter for number of constraints */
-  int *constrainedI; /* the i of a constraint pair */
-  int *constrainedJ; /* the j of a constraint pair */
-  double *constrainedDsqr; /* the square of the constraint distance */
+  int isConstrained; // boolean to know whether the systems contains
+		     // constraints.
+  int nConstrained;  // counter for number of constraints 
+  int *constrainedA; // the i of a constraint pair 
+  int *constrainedB; // the j of a constraint pair 
+  double *constrainedDsqr; // the square of the constraint distance 
+  
+  int* moving; // tells whether we are moving atom i
+  int* moved;  // tells whether we have moved atom i
+  double* oldPos; // pre constrained positions 
+
   short isFirst; /*boolean for the first time integrate is called */
   
   double dt;
+  double dt2;
 
+  double* pos;
+  double* vel;
+  double* frc;
+  double* trq;
+  double* Amat;
 
   Thermo *tStats;
   StatWriter*  statOut;
@@ -57,19 +75,218 @@ class Integrator : public BaseIntegrator { (protected)
   
 };
 
+class NVE : public Integrator{
 
+public:
+  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
+    Integrator( theInfo, the_ff ){}
+  virtual ~NVE(){}
+
+  
+
+};
+
 class NVT : public Integrator{
 
-  NVT ( void );
-  virtual ~NVT();
+public:
 
+  NVT ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NVT() {}
+
+  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 );
 
+  virtual int readyCheck();
+
+  // chi is a propagated degree of freedom.
+
+  double chi;
+
+  // targetTemp must be set.  tauThermostat must also be set;
+
+  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;
+
+  // 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{
+
+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();
+
+  // 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:
+
+  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTf() {};
+
+  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[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;
+
+};
+
+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();
+
+  // 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;
+
+};
+
 #endif