--- branches/mmeineke/OOPSE/libmdtools/Integrator.hpp	2003/03/21 17:42:12	377
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/06/19 22:02:44	559
@@ -6,69 +6,100 @@
 #include "AbstractClasses.hpp"
 #include "SimInfo.hpp"
 #include "ForceFields.hpp"
+#include "Thermo.hpp"
+#include "ReadWrite.hpp"
 
-class Verlet : public Integrator {
+class Integrator : public BaseIntegrator {
 
 public:
-  Verlet( SimInfo &info, ForceFields* the_ff );
-  ~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[3][3] );
 
+
   ForceFields* myFF;
 
-  SimInfo *entry_plug; // all the info we'll ever need
-  int c_natoms;  /* the number of atoms */
-  Atom **c_atoms; /* array of atom pointers */
-  SRI **c_sr_interactions; /* array of SRI pointers */
-  int c_n_SRI; /* the number of short range interactions */
+  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* prePos; // pre constrained positions 
 
-class Symplectic : public Integrator {
+  short isFirst; /*boolean for the first time integrate is called */
   
-public:
-  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
-  ~Symplectic();
-  
-  void integrate( void );
+  double dt;
+  double dt2;
+  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
 
-private:
+  const int maxIteration = 300;
+  const double tol = 1.0e-6;
 
-  void rotate( int axes1, int axes2, double angle, double j[3], 
-	       double A[3][3] );
+  
+  double* pos;
+  double* vel;
+  double* frc;
+  double* trq;
+  double* Amat;
+  
 
-  SimInfo* entry_plug;
-  ForceFields* myFF;
 
-  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 */
+  Thermo *tStats;
+  StatWriter*  statOut;
+  DumpWriter*  dumpOut;
+  
+};
 
-  short int isFirst;
+class NVE : public Integrator{
 
-  SRI **srInteractions; /* array of SRI pointers */
-  int nSRI; /* the number of short range interactions */
+  NVE ( void ):
+    Integrator( theInfo, the_ff ){}
+  virtual ~NVE(){}
+
   
+
 };
 
+class NVT : public Integrator{
+
+  NVT ( SimInfo &theInfo, ForceFields* the_ff ) :
+    Integrator( theInfo, the_ff );
+  virtual ~NVT();
+
+protected:
+  virtual moveA( void );
+  virtual moveB( void );
+
+};
+
+  
+
+
 #endif