--- trunk/OOPSE/libmdtools/Integrator.hpp	2004/02/24 15:44:45	1064
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2004/06/04 20:29:36	1249
@@ -4,6 +4,7 @@
 #include <string>
 #include <vector>
 #include "Atom.hpp"
+#include "StuntDouble.hpp"
 #include "Molecule.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
@@ -12,6 +13,7 @@
 #include "Thermo.hpp"
 #include "ReadWrite.hpp"
 #include "ZConsWriter.hpp"
+#include "Restraints.hpp"
 
 using namespace std;
 const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
@@ -20,7 +22,7 @@ const double tol = 1.0e-6;
 const int maxIteration = 300;
 const double tol = 1.0e-6;
 
-
+class RattleFramework;
 template<typename T = BaseIntegrator> class Integrator : public T {
 
 public:
@@ -33,11 +35,11 @@ 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 ) { }
@@ -45,31 +47,35 @@ 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;}
 
-  void checkConstraints( void );
+  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] );
 
   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 */
   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
+  RattleFramework* rattle;
 
-  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 */
 
@@ -84,6 +90,9 @@ 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:
@@ -418,7 +427,7 @@ template<typename T> class ZConstraint : public T { (p
 
   void zeroOutVel();
   void doZconstraintForce();
-  void doHarmonic();
+  void doHarmonic(vector<double>& resPos);
   bool checkZConsState();
 
   bool haveFixedZMols();
@@ -449,12 +458,20 @@ 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:
@@ -467,36 +484,12 @@ 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;
 
 };
 
-/*
-class OOPSEMinimizerBase : public RealIntegrator {
-  public:
-
-    OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff );
-    virtual ~OOPSEMinimizerBase();
-    
-    double calcGradient(vector<double>& x, vector<double>& grad);
-    void setCoor(vector<double>& x);
-    vector<double> getCoor();
-    void output(vector<double>& x, int iteration);
-    int getDim() {return dim;}
-    void constraintMove();
-    void shakeF();
-    void shakeR();
-  protected:
-    
-    int dim;
-    void calcDim();
-};
-
-//template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
-//  public:
-//    void writeOutput();
-//};
-*/  
 #endif