--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/07/14 15:04:55	596
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/07/31 15:35:07	658
@@ -1,22 +1,28 @@
 #ifndef _INTEGRATOR_H_
 #define _INTEGRATOR_H_
 
+#include <string>
+#include <vector>
 #include "Atom.hpp"
+#include "Molecule.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
 #include "SimInfo.hpp"
 #include "ForceFields.hpp"
 #include "Thermo.hpp"
 #include "ReadWrite.hpp"
+#include "ZConsWriter.hpp"
 
+using namespace std;
 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 double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
 const int maxIteration = 300;
 const double tol = 1.0e-6;
 
-class Integrator : public BaseIntegrator {
 
+template<typename T = BaseIntegrator> class Integrator : public T {
+
 public:
   Integrator( SimInfo *theInfo, ForceFields* the_ff );
   virtual ~Integrator();
@@ -63,30 +69,24 @@ class Integrator : public BaseIntegrator { (protected)
   double dt;
   double dt2;
 
-  double* pos;
-  double* vel;
-  double* frc;
-  double* trq;
-  double* Amat;
-
   Thermo *tStats;
   StatWriter*  statOut;
   DumpWriter*  dumpOut;
   
 };
 
-class NVE : public Integrator{
+typedef Integrator<BaseIntegrator> RealIntegrator;
 
+template<typename T> class NVE : public T {
+
 public:
   NVE ( SimInfo *theInfo, ForceFields* the_ff ):
-    Integrator( theInfo, the_ff ){}
-  virtual ~NVE(){}
-
-  
-
+    T( theInfo, the_ff ){}
+  virtual ~NVE(){}  
 };
 
-class NVT : public Integrator{
+
+template<typename T> class NVT : public T {
 
 public:
 
@@ -117,8 +117,9 @@ class NPTi : public Integrator{
 };
 
 
-class NPTi : public Integrator{
 
+template<typename T> class NPTi : public T{
+
 public:
 
   NPTi ( SimInfo *theInfo, ForceFields* the_ff);
@@ -126,7 +127,7 @@ class NPTi : public Integrator{ (public)
 
   virtual void integrateStep( int calcPot, int calcStress ){
     calcStress = 1;
-    Integrator::integrateStep( calcPot, calcStress );
+    T::integrateStep( calcPot, calcStress );
   }
 
   void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
@@ -160,7 +161,7 @@ class NPTim : public Integrator{
 
 };
 
-class NPTim : public Integrator{
+template<typename T> class NPTim : public T{
 
 public:
 
@@ -169,7 +170,7 @@ class NPTim : public Integrator{ (public)
 
   virtual void integrateStep( int calcPot, int calcStress ){
     calcStress = 1;
-    Integrator::integrateStep( calcPot, calcStress );
+    T::integrateStep( calcPot, calcStress );
   }
 
   void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
@@ -179,11 +180,14 @@ class NPTim : public Integrator{ (public)
 
 protected:
 
-  virtual void  moveA( void );
+  virtual void moveA( void );
   virtual void moveB( void );
 
   virtual int readyCheck();
 
+  Molecule* myMolecules;
+  Atom** myAtoms;
+
   // chi and eta are the propagated degrees of freedom
 
   double chi;
@@ -203,7 +207,7 @@ class NPTf : public Integrator{
 
 };
 
-class NPTf : public Integrator{
+template<typename T> class NPTf : public T{
 
 public:
 
@@ -212,7 +216,7 @@ class NPTf : public Integrator{ (public)
 
   virtual void integrateStep( int calcPot, int calcStress ){
     calcStress = 1;
-    Integrator::integrateStep( calcPot, calcStress );
+    T::integrateStep( calcPot, calcStress );
   }
 
   void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
@@ -246,7 +250,7 @@ class NPTfm : public Integrator{
 
 };
 
-class NPTfm : public Integrator{
+template<typename T> class NPTfm : public T{
 
 public:
 
@@ -255,7 +259,7 @@ class NPTfm : public Integrator{ (public)
 
   virtual void integrateStep( int calcPot, int calcStress ){
     calcStress = 1;
-    Integrator::integrateStep( calcPot, calcStress );
+    T::integrateStep( calcPot, calcStress );
   }
 
   void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
@@ -269,6 +273,9 @@ class NPTfm : public Integrator{ (public)
   virtual void moveB( void );
 
   virtual int readyCheck();
+
+  Molecule* myMolecules;
+  Atom** myAtoms;
 
   // chi and eta are the propagated degrees of freedom
 
@@ -289,4 +296,55 @@ class NPTfm : public Integrator{ (public)
 
 };
 
+template<typename T> class ZConstraint : public T {
+
+public:
+
+  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
+  ~ZConstraint();
+
+  virtual void integrateStep( int calcPot, int calcStress );
+  
+  
+  void setZConsTime(double time)                  {this->zconsTime = time;}
+  void getZConsTime()                             {return zconsTime;}
+  
+  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
+  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
+  
+  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
+  string getZConsOutput()                         {return zconsOutput;}
+
+#ifdef IS_MPI
+  virtual void update(); //which is called to indicate the molecules' migration
 #endif
+
+protected:
+
+  double zconsTime;
+  
+  void resetZ(void);
+  
+  vector<Molecule*> zconsMols;
+  vector<double> massOfZConsMols;
+  
+  vector<Molecule*> unconsMols;
+  vector<double> massOfUnconsMols;
+  double totalMassOfUncons;
+
+  vector<double> allRefZ;    
+  vector<double> refZ;
+  
+  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
+  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
+    
+  double* fz;
+  
+private:
+
+  int isZConstraintMol(Molecule* mol);
+  string zconsOutput;
+  ZConsWriter* fzOut;
+};
+
+#endif