--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/07/15 03:27:24	605
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/08/13 19:21:53	693
@@ -1,6 +1,8 @@
 #ifndef _INTEGRATOR_H_
 #define _INTEGRATOR_H_
 
+#include <string>
+#include <vector>
 #include "Atom.hpp"
 #include "Molecule.hpp"
 #include "SRI.hpp"
@@ -9,15 +11,18 @@
 #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();
@@ -33,12 +38,14 @@ class Integrator : public BaseIntegrator { (protected)
   virtual void constrainA( void );
   virtual void constrainB( void );
   virtual int  readyCheck( void ) { return 1; }
+
+  virtual void calcForce( int calcPot, int calcStress );  
+  virtual void thermalize();
   
   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
@@ -70,19 +77,19 @@ class NVE : public Integrator{
   
 };
 
-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:
 
   NVT ( SimInfo *theInfo, ForceFields* the_ff);
@@ -112,8 +119,9 @@ class NPTi : public Integrator{
 };
 
 
-class NPTi : public Integrator{
 
+template<typename T> class NPTi : public T{
+
 public:
 
   NPTi ( SimInfo *theInfo, ForceFields* the_ff);
@@ -121,7 +129,7 @@ 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;}
@@ -155,7 +163,7 @@ class NPTim : public Integrator{
 
 };
 
-class NPTim : public Integrator{
+template<typename T> class NPTim : public T{
 
 public:
 
@@ -164,7 +172,7 @@ 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;}
@@ -201,7 +209,7 @@ class NPTf : public Integrator{
 
 };
 
-class NPTf : public Integrator{
+template<typename T> class NPTf : public T{
 
 public:
 
@@ -210,7 +218,7 @@ 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;}
@@ -244,7 +252,7 @@ class NPTfm : public Integrator{
 
 };
 
-class NPTfm : public Integrator{
+template<typename T> class NPTfm : public T{
 
 public:
 
@@ -253,7 +261,7 @@ 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;}
@@ -290,4 +298,85 @@ class NPTfm : public Integrator{ (public)
 
 };
 
+template<typename T> class ZConstraint : public T {
+
+public:
+
+  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
+  ~ZConstraint();
+    
+  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;}
+  
+  virtual void integrate();
+  
+
+#ifdef IS_MPI
+  virtual void update(); //which is called to indicate the molecules' migration
 #endif
+
+protected:
+
+  enum ZConsState {zcsMoving, zcsFixed};
+
+
+ 
+  virtual void calcForce( int calcPot, int calcStress ); 
+  virtual void thermalize(void);
+  
+  void zeroOutVel();
+  void doZconstraintForce();
+  void doHarmonic();
+  bool checkZConsState();
+
+  bool haveFixedZMols();
+  bool haveMovingZMols();
+
+  double calcZSys();
+
+  int isZConstraintMol(Molecule* mol);
+
+
+  double zconsTime;
+  double zconsTol;
+  double zForceConst;
+  
+  vector<Molecule*> zconsMols;
+  vector<double> massOfZConsMols;
+  vector<double> kz;
+  vector<ZConsState> states; 
+  vector<double> zPos;
+  
+  
+  vector<Molecule*> unconsMols;
+  vector<double> massOfUnconsMols;
+  double totalMassOfUncons;
+
+  vector<ZConsParaItem>* parameters;
+  
+  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
+
+  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
+  double* fz;
+  
+  int totNumOfUnconsAtoms;
+
+  int whichDirection;                           //constraint direction 
+  
+private:
+  
+  string zconsOutput;
+  ZConsWriter* fzOut;
+
+  double calcCOMVel();
+  double calcCOMVel2();
+
+};
+
+#endif