--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/10/29 20:41:39	843
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2004/05/11 21:44:05	1161
@@ -4,6 +4,7 @@
 #include <string>
 #include <vector>
 #include "Atom.hpp"
+#include "StuntDouble.hpp"
 #include "Molecule.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
@@ -20,7 +21,6 @@ const double tol = 1.0e-6;
 const int maxIteration = 300;
 const double tol = 1.0e-6;
 
-
 template<typename T = BaseIntegrator> class Integrator : public T {
 
 public:
@@ -45,8 +45,10 @@ template<typename T = BaseIntegrator> class Integrator
   virtual void calcForce( int calcPot, int calcStress );
   virtual void thermalize();
 
-  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
+  virtual bool stopIntegrator() {return false;}
 
+  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
+
   void checkConstraints( void );
   void rotate( int axes1, int axes2, double angle, double j[3],
          double A[3][3] );
@@ -54,6 +56,7 @@ template<typename T = BaseIntegrator> class Integrator
   ForceFields* myFF;
 
   SimInfo *info; // all the info we'll ever need
+  vector<StuntDouble*> integrableObjects;
   int nAtoms;  /* the number of atoms */
   int oldAtoms;
   Atom **atoms; /* array of atom pointers */
@@ -84,6 +87,9 @@ template<typename T> class NVE : public T {
 
 typedef Integrator<BaseIntegrator> RealIntegrator;
 
+// ansi instantiation
+template class Integrator<BaseIntegrator>;
+
 template<typename T> class NVE : public T {
 
 public:
@@ -179,6 +185,8 @@ template<typename T> class NPT : public T{ (protected)
   virtual void getPosScale(double pos[3], double COM[3],
 			   int index, double sc[3]) = 0;
 
+  virtual void calcVelScale( void ) = 0;
+
   virtual bool chiConverged( void );
   virtual bool etaConverged( void ) = 0;
 
@@ -255,8 +263,11 @@ template<typename T> class NPTi : public T{ (protected
   virtual void getVelScaleB( double sc[3], int index );
   virtual void getPosScale(double pos[3], double COM[3],
 			   int index, double sc[3]);
+
+  virtual void calcVelScale( void );
 
   double eta, oldEta, prevEta;
+  double vScale;
 };
 
 template<typename T> class NPTf : public T{
@@ -284,9 +295,12 @@ template<typename T> class NPTf : public T{ (protected
   virtual void getPosScale(double pos[3], double COM[3],
 			   int index, double sc[3]);
 
+  virtual void calcVelScale( void );
+
   double eta[3][3];
   double oldEta[3][3];
   double prevEta[3][3];
+  double vScale[3][3];
 };
 
 template<typename T> class NPTxyz : public T{
@@ -314,9 +328,12 @@ template<typename T> class NPTxyz : public T{ (protect
   virtual void getPosScale(double pos[3], double COM[3],
 			   int index, double sc[3]);
 
+  virtual void calcVelScale( void );
+
   double eta[3][3];
   double oldEta[3][3];
   double prevEta[3][3];
+  double vScale[3][3];
 };
 
 
@@ -407,7 +424,7 @@ template<typename T> class ZConstraint : public T { (p
 
   void zeroOutVel();
   void doZconstraintForce();
-  void doHarmonic();
+  void doHarmonic(vector<double>& resPos);
   bool checkZConsState();
 
   bool haveFixedZMols();
@@ -438,12 +455,20 @@ template<typename T> class ZConstraint : public T { (p
 
   vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
 
-  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
-  double* fz;
-  double* curZPos;
+  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
+  vector<double> fz;
+  vector<double> curZPos;
 
+  bool usingSMD;
+  vector<double> prevCantPos;
+  vector<double> cantPos;
+  vector<double> cantVel;
 
-
+  double zconsFixTime;  
+  double zconsGap;
+  bool hasZConsGap;
+  vector<double> endFixTime;
+  
   int whichDirection;                           //constraint direction
 
 private:
@@ -456,10 +481,69 @@ template<typename T> class ZConstraint : public T { (p
   double calcMovingMolsCOMVel();
   double calcSysCOMVel();
   double calcTotalForce();
-
+  void updateZPos();
+  void updateCantPos();
+  
   ForceSubtractionPolicy* forcePolicy; //force subtraction policy
   friend class ForceSubtractionPolicy;
+
+};
+
+/*
+template<typename T> class SingleZConstrain : public T{
+
+
+};
+*/
 
+template<typename T> class NonEquMD : public T {
+  public:
+    
+
+
 };
 
+
+//
+template<typename T> class SingleZConstraint : public T{
+  public:
+    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
+    ~SingleZConstraint();
+    
+    bool stopIntegrator();
+    
+  protected:
+    
+};
+
+//Steered Molecular Dynamics, curret implement only support one steered molecule
+ template<typename T> class SMD : public T{
+  public:
+    SMD( SimInfo *theInfo, ForceFields* the_ff);
+    ~SMD();
+  
+    virtual void integrate();
+    virtual void calcForce( int calcPot, int calcStress );  
+    bool stopIntegrator();
+  private:
+    
+};
+
+//By using state pattern, Coordinate Drive is responsible for switching back and forth between
+//Driven Molecular Dynamics and ZConstraint Method. 
+template<typename T> class CoordinateDriver : public T {
+  public:
+    typedef T ParentIntegrator;
+
+    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
+    ~CoordinateDriver();
+    
+    virtual void integrate();
+
+  private:    
+    BaseIntegrator* zconsIntegrator;
+    BaseIntegrator* drivenIntegrator;
+    
+};
+
 #endif