--- trunk/OOPSE/libmdtools/Integrator.hpp	2004/05/27 00:48:12	1198
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2004/08/23 15:11:36	1452
@@ -14,6 +14,8 @@
 #include "ReadWrite.hpp"
 #include "ZConsWriter.hpp"
 #include "Restraints.hpp"
+#include "Quaternion.hpp"
+#include "Mat4x4d.hpp"
 
 using namespace std;
 const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
@@ -22,6 +24,7 @@ template<typename T = BaseIntegrator> class Integrator
 const int maxIteration = 300;
 const double tol = 1.0e-6;
 
+class VelVerletConsFramework;
 template<typename T = BaseIntegrator> class Integrator : public T {
 
 public:
@@ -34,11 +37,11 @@ template<typename T = BaseIntegrator> class Integrator
 protected:
 
   virtual void integrateStep( int calcPot, int calcStress );
-  virtual void preMove( void );
+  //virtual void preMove( void );
   virtual void moveA( void );
   virtual void moveB( void );
-  virtual void constrainA( void );
-  virtual void constrainB( void );
+  //virtual void constrainA( void );
+  //virtual void constrainB( void );
   virtual int  readyCheck( void ) { return 1; }
 
   virtual void resetIntegrator( void ) { }
@@ -50,10 +53,13 @@ template<typename T = BaseIntegrator> class Integrator
 
   virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
 
-  void checkConstraints( void );
+  //void checkConstraints( void );
   void rotate( int axes1, int axes2, double angle, double j[3],
          double A[3][3] );
 
+  void printQuaternion(StuntDouble* sd);
+  Mat4x4d getS(const Quaternion& q);
+
   ForceFields* myFF;
 
   SimInfo *info; // all the info we'll ever need
@@ -64,16 +70,17 @@ template<typename T = BaseIntegrator> class Integrator
   Molecule* molecules;
   int nMols;
 
-  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
+  VelVerletConsFramework* consFramework;
 
-  int* moving; // tells whether we are moving atom i
-  int* moved;  // tells whether we have moved atom i
-  double* oldPos; // pre constrained positions
+  //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 */
 
@@ -89,8 +96,9 @@ template class Integrator<BaseIntegrator>;
 typedef Integrator<BaseIntegrator> RealIntegrator;
 
 // ansi instantiation
-template class Integrator<BaseIntegrator>;
+// template class Integrator<BaseIntegrator>;
 
+
 template<typename T> class NVE : public T {
 
 public:
@@ -490,4 +498,28 @@ template<typename T> class ZConstraint : public T { (p
 
 };
 
+
+//Sympletic quaternion Scheme Integrator
+//Reference:
+// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
+//Symplectic quaternion Scheme for biophysical molecular dynamics
+//116(20), 8649, J. Chem. Phys. (2002)
+template<typename T> class SQSIntegrator : public T{
+  public:
+    SQSIntegrator( SimInfo *theInfo, ForceFields* the_ff );
+    virtual void moveA();
+    virtual void moveB();
+  protected:
+    void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I);
+    void rotate(int k, double dt,  Quaternion& q,  Vector4d& qdot, double Ik);
+  private:
+    Quaternion getPk(int i, const Vector4d& q);
+    Mat4x4d getS(const Quaternion& q);
+    vector<Quaternion> q;
+    vector<Vector4d> p_qua;
+    vector<double> I0;
+
+		Vector4d p2j(const Vector4d& p, Mat4x4d& m);    
+		Vector4d j2p(const Vector4d& j, Mat4x4d& m);
+};
 #endif