--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/04/07 14:30:36	466
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/06/20 20:29:36	561
@@ -6,77 +6,159 @@
 #include "AbstractClasses.hpp"
 #include "SimInfo.hpp"
 #include "ForceFields.hpp"
-#include "ExtendedSystem.hpp"
+#include "Thermo.hpp"
+#include "ReadWrite.hpp"
 
-class Verlet : public Integrator {
+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:
-  Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es );
-  ~Verlet();
+  Integrator( SimInfo *theInfo, ForceFields* the_ff );
+  virtual ~Integrator();
   void integrate( void );
 
-private:
+
+protected:
   
-  void move_a( double dt );
-  void move_b( double dt );
+  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[9] );
 
+
   ForceFields* myFF;
-  ExtendedSystem* myES;
 
-  SimInfo *entry_plug; // all the info we'll ever need
-  int c_natoms;  /* the number of atoms */
-  Atom **c_atoms; /* array of atom pointers */
+  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 c_is_constrained; /*boolean to know whether the systems contains
-			  constraints. */
-  int c_n_constrained; /*counter for number of constraints */
-  int *c_constrained_i; /* the i of a constraint pair */
-  int *c_constrained_j; /* the j of a constraint pair */
-  double *c_constrained_dsqr; /* the square of the constraint distance */
-  double *c_mass; /* the array of masses */
-  short is_first; /*boolean for the first time integrate is called */
-  double c_box_x;
-  double c_box_y;
-  double c_box_z;
-};
+  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 
 
-class Symplectic : public Integrator {
+  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;
+  DumpWriter*  dumpOut;
+  
+};
+
+class NVE : public Integrator{
+
 public:
-  Symplectic( SimInfo* the_entry_plug,  
-              ForceFields* the_ff, 
-              ExtendedSystem* the_es);
-  ~Symplectic();
+  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
+    Integrator( theInfo, the_ff ){}
+  virtual ~NVE(){}
+
   
-  void integrate( void );
 
-private:
+};
 
-  void rotate( int axes1, int axes2, double angle, double j[3], 
-	       double A[3][3] );
+class NVT : public Integrator{
 
-  SimInfo* entry_plug;
-  ForceFields* myFF;
-  ExtendedSystem* myES;
+public:
 
-  Molecule* molecules;
-  int nMols;
+  NVT ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NVT() {}
 
-  int is_constrained; /*boolean to know whether the systems contains
-			  constraints. */
-  int n_constrained; /*counter for number of constraints */
-  int *constrained_i; /* the i of a constraint pair */
-  int *constrained_j; /* the j of a constraint pair */
-  double *constrained_dsqr; /* the square of the constraint distance */
-  double *mass; /* the array of masses */
+  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;}
 
-  short int isFirst;
+protected:
 
-  SRI **srInteractions; /* array of SRI pointers */
-  int nSRI; /* the number of short range interactions */
+  virtual void moveA( void );
+  virtual void moveB( void );
+
+  virtual int readyCheck();
+
+  // zeta is a propagated degree of freedom.
+
+  double zeta;
+
+  // targetTemp must be set.  One of qmass or tauThermostat must be set;
+
+  double qmass;
+  double targetTemp;
+  double tauThermostat;
+
+  double NkBT;
   
+  short int have_tau_thermostat, have_target_temp, have_qmass;
+
 };
 
+
+class NPT : public Integrator{
+
+public:
+
+  NPT ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPT();
+
+  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;}
+  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
+
+protected:
+
+  virtual void  moveA( void );
+  virtual void moveB( void );
+
+  virtual int readyCheck();
+
+  Atom** atoms;
+
+  // zeta and epsilonDot are the propagated degrees of freedom.
+
+  double zeta;
+  double epsilonDot;
+
+  // 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;
+
+};
+
 #endif