--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/09/22 21:23:25	780
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2004/06/04 03:15:31	1234
@@ -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:
@@ -28,67 +30,75 @@ template<typename T = BaseIntegrator> class Integrator
   virtual ~Integrator();
   void integrate( void );
   virtual double  getConservedQuantity(void);
+  virtual string getAdditionalParameters(void);
 
 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 ) { }
- 
-  virtual void calcForce( int calcPot, int calcStress );  
+
+  virtual void calcForce( int calcPot, int calcStress );
   virtual void thermalize();
-  
-  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
 
-  void checkConstraints( void );
-  void rotate( int axes1, int axes2, double angle, double j[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] );
-         
+
   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 
-  
-  int* moving; // tells whether we are moving atom i
-  int* moved;  // tells whether we have moved atom i
-  double* oldPos; // pre constrained positions 
+  RattleFramework* rattle;
 
+  //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 */
-  
+
   double dt;
   double dt2;
 
   Thermo *tStats;
   StatWriter*  statOut;
   DumpWriter*  dumpOut;
-  
+
 };
 
 typedef Integrator<BaseIntegrator> RealIntegrator;
+
+// ansi instantiation
+template class Integrator<BaseIntegrator>;
 
 template<typename T> class NVE : public T {
 
 public:
   NVE ( SimInfo *theInfo, ForceFields* the_ff ):
     T( theInfo, the_ff ){}
-  virtual ~NVE(){}  
+  virtual ~NVE(){}
 };
 
 
@@ -103,6 +113,7 @@ template<typename T> class NVT : public T { (public)
   void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
   void setChiTolerance(double tol) {chiTolerance = tol;}
   virtual double  getConservedQuantity(void);
+  virtual string getAdditionalParameters(void);
 
 protected:
 
@@ -124,7 +135,7 @@ template<typename T> class NVT : public T { (public)
 
   double targetTemp;
   double tauThermostat;
-  
+
   short int have_tau_thermostat, have_target_temp;
 
   double *oldVel;
@@ -143,13 +154,17 @@ template<typename T> class NPT : public T{ (public)
 
   NPT ( SimInfo *theInfo, ForceFields* the_ff);
   virtual ~NPT();
-  
+
   virtual void integrateStep( int calcPot, int calcStress ){
     calcStress = 1;
     T::integrateStep( calcPot, calcStress );
   }
 
   virtual double getConservedQuantity(void) = 0;
+  virtual string getAdditionalParameters(void) = 0;
+  
+  double myTauThermo( void ) { return tauThermostat; }
+  double myTauBaro( void ) { return tauBarostat; }
 
   void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
   void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
@@ -170,12 +185,14 @@ template<typename T> class NPT : public T{ (public)
 
   virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
   virtual void getVelScaleB( double sc[3], int index ) = 0;
-  virtual void getPosScale(double pos[3], double COM[3], 
+  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;
-  
+
   virtual void evolveChiA( void );
   virtual void evolveEtaA( void ) = 0;
   virtual void evolveChiB( void );
@@ -201,7 +218,7 @@ template<typename T> class NPT : public T{ (public)
 
   double integralOfChidt;
 
-  // targetTemp, targetPressure, and tauBarostat must be set.  
+  // targetTemp, targetPressure, and tauBarostat must be set.
   // One of qmass or tauThermostat must be set;
 
   double targetTemp;
@@ -226,18 +243,18 @@ template<typename T> class NPTi : public T{
 };
 
 template<typename T> class NPTi : public T{
-  
+
 public:
   NPTi( SimInfo *theInfo, ForceFields* the_ff);
   ~NPTi();
 
   virtual double getConservedQuantity(void);
   virtual void resetIntegrator(void);
-
+  virtual string getAdditionalParameters(void);
 protected:
 
- 
 
+
   virtual void evolveEtaA(void);
   virtual void evolveEtaB(void);
 
@@ -247,59 +264,13 @@ template<typename T> class NPTi : public T{
 
   virtual void getVelScaleA( double sc[3], double vel[3] );
   virtual void getVelScaleB( double sc[3], int index );
-  virtual void getPosScale(double pos[3], double COM[3], 
+  virtual void getPosScale(double pos[3], double COM[3],
 			   int index, double sc[3]);
 
-  double eta, oldEta, prevEta;
-};
-
-template<typename T> class NPTzm : public T{
-
-public:
-
-  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTzm() {};
-
-  virtual void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-  }
-
-  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
-  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
-  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
-  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
-
-protected:
-
-  virtual void moveA( void );
-  virtual void moveB( void );
-
-  virtual int readyCheck();
-
-  virtual void resetIntegrator( void );
+  virtual void calcVelScale( void );
 
-  Molecule* myMolecules;
-  Atom** myAtoms;
-
-  // chi and eta are the propagated degrees of freedom
-
-  double chi;
-  double eta;
-  double etaZ;
-  double NkBT;
-
-  // targetTemp, targetPressure, and tauBarostat must be set.  
-  // One of qmass or tauThermostat must be set;
-
-  double targetTemp;
-  double targetPressure;
-  double tauThermostat;
-  double tauBarostat;
-
-  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-  short int have_target_pressure;
-
+  double eta, oldEta, prevEta;
+  double vScale;
 };
 
 template<typename T> class NPTf : public T{
@@ -310,6 +281,7 @@ template<typename T> class NPTf : public T{ (public)
   virtual ~NPTf();
 
   virtual double getConservedQuantity(void);
+  virtual string getAdditionalParameters(void);
   virtual void resetIntegrator(void);
 
 protected:
@@ -323,205 +295,78 @@ template<typename T> class NPTf : public T{ (public)
 
   virtual void getVelScaleA( double sc[3], double vel[3] );
   virtual void getVelScaleB( double sc[3], int index );
-  virtual void getPosScale(double pos[3], double COM[3], 
+  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 NPTxym : public T{
+template<typename T> class NPTxyz : public T{
 
 public:
 
-  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTxym() {};
+  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTxyz();
 
-  virtual void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-  }
+  virtual double getConservedQuantity(void);
+  virtual string getAdditionalParameters(void);
+  virtual void resetIntegrator(void);
 
-  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
-  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
-  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
-  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
-
 protected:
 
-  virtual void moveA( void );
-  virtual void moveB( void );
+  virtual void evolveEtaA(void);
+  virtual void evolveEtaB(void);
 
-  virtual int readyCheck();
+  virtual bool etaConverged( void );
 
-  virtual void resetIntegrator( void );
+  virtual void scaleSimBox( void );
 
-  Molecule* myMolecules;
-  Atom** myAtoms;
+  virtual void getVelScaleA( double sc[3], double vel[3] );
+  virtual void getVelScaleB( double sc[3], int index );
+  virtual void getPosScale(double pos[3], double COM[3],
+			   int index, double sc[3]);
 
-  // chi and eta are the propagated degrees of freedom
+  virtual void calcVelScale( void );
 
-  double chi;
-  double eta;
-  double etaX;
-  double etaY;
-  double NkBT;
-
-  // targetTemp, targetPressure, and tauBarostat must be set.  
-  // One of qmass or tauThermostat must be set;
-
-  double targetTemp;
-  double targetPressure;
-  double tauThermostat;
-  double tauBarostat;
-
-  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-  short int have_target_pressure;
-
-};
-
-
-template<typename T> class NPTfm : public T{
-
-public:
-
-  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTfm() {};
-
-  virtual void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-    accIntegralOfChidt();
-  }
-
-  virtual double getConservedQuantity(void);
-  
-  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
-  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
-  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
-  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
-  void setChiTolerance(double tol) {chiTolerance = tol;}
-  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
-
-protected:
-
-  virtual void  moveA( void );
-  virtual void moveB( void );
-
-  virtual void resetIntegrator( void );
-
-  virtual int readyCheck();
-
-  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
-
-  Molecule* myMolecules;
-  Atom** myAtoms;
-
-  // chi and eta are the propagated degrees of freedom
-
-  double chi;
-  double eta[3][3];
-  double NkBT;
-  double integralOfChidt;
-
-  // targetTemp, targetPressure, and tauBarostat must be set.  
-  // One of qmass or tauThermostat must be set;
-
-  double targetTemp;
-  double targetPressure;
-  double tauThermostat;
-  double tauBarostat;
-
-  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-  short int have_target_pressure;
-  double chiTolerance;
-  short int have_chi_tolerance;
-  double posIterTolerance;
-  short int have_pos_iter_tolerance;
-
+  double eta[3][3];
+  double oldEta[3][3];
+  double prevEta[3][3];
+  double vScale[3][3];
 };
 
 
-template<typename T> class NPTpr : public T{
-
-public:
-
-  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NPTpr() {};
-
-  virtual void integrateStep( int calcPot, int calcStress ){
-    calcStress = 1;
-    T::integrateStep( calcPot, calcStress );
-  }
-
-  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
-  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
-  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
-  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
-  void setChiTolerance(double tol) {chiTolerance = tol;}
-  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
-
-protected:
-
-  virtual void  moveA( void );
-  virtual void moveB( void );
-
-  virtual int readyCheck();
-
-  virtual void resetIntegrator( void );
-
-  // chi and eta are the propagated degrees of freedom
-
-  double chi;
-  double eta[3][3];
-  double NkBT;
-
-  // targetTemp, targetPressure, and tauBarostat must be set.  
-  // One of qmass or tauThermostat must be set;
-
-  double targetTemp;
-  double targetPressure;
-  double tauThermostat;
-  double tauBarostat;
-
-  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-  short int have_target_pressure;
-  double chiTolerance;
-  short int have_chi_tolerance;
-  double posIterTolerance;
-  short int have_pos_iter_tolerance;
-
-};
-
-
 template<typename T> class ZConstraint : public T {
-  
-  public: 
+
+  public:
   class ForceSubtractionPolicy{
     public:
       ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
 
-      virtual void update() = 0;    
+      virtual void update() = 0;
       virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
       virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
       virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
       virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
-    
+
    protected:
-     ZConstraint<T>* zconsIntegrator;;
+     ZConstraint<T>* zconsIntegrator;
   };
 
   class PolicyByNumber : public ForceSubtractionPolicy{
 
     public:
-      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
-      virtual void update();    
+      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
+      virtual void update();
       virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
       virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
       virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
       virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
-    
+
     private:
       int totNumOfMovingAtoms;
   };
@@ -529,9 +374,9 @@ template<typename T> class ZConstraint : public T {
   class PolicyByMass : public ForceSubtractionPolicy{
 
     public:
-      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
-      
-      virtual void update();    
+      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
+
+      virtual void update();
       virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
       virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
       virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
@@ -545,33 +390,44 @@ template<typename T> class ZConstraint : public T {
 
   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
 
+  enum ZConsState {zcsMoving, zcsFixed};
+
+  vector<Molecule*> zconsMols;              //z-constraint molecules array
+  vector<ZConsState> states;                 //state of z-constraint molecules
+
+
+
+  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
+  double totalMassOfUncons;                //total mas of unconstraint molecules
+
+
 protected:
 
-  enum ZConsState {zcsMoving, zcsFixed};  
- 
-  virtual void calcForce( int calcPot, int calcStress ); 
+
+
+  virtual void calcForce( int calcPot, int calcStress );
   virtual void thermalize(void);
-  
+
   void zeroOutVel();
   void doZconstraintForce();
-  void doHarmonic();
+  void doHarmonic(vector<double>& resPos);
   bool checkZConsState();
 
   bool haveFixedZMols();
@@ -586,40 +442,50 @@ template<typename T> class ZConstraint : public T {
   double zconsTol;                                 //tolerance of z-contratint
   double zForceConst;                           //base force constant term
                                                           //which is estimate by OOPSE
-  
-  vector<Molecule*> zconsMols;              //z-constraint molecules array
-  vector<double> massOfZConsMols;       //mass of z-constraint molecule 
+
+
+  vector<double> massOfZConsMols;       //mass of z-constraint molecule
   vector<double> kz;                              //force constant array
-  vector<ZConsState> states;                 //state of z-constraint molecules
+
   vector<double> zPos;                          //
-  
-  
+
+
   vector<Molecule*> unconsMols;           //unconstraint molecules array
   vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
-  double totalMassOfUncons;                //total mas of unconstraint molecules
 
+
   vector<ZConsParaItem>* parameters; //
-  
+
   vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
 
-  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
-  double* fz;
-  double* curZPos;
-  
-  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
+  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
+  vector<double> fz;
+  vector<double> curZPos;
 
-  int whichDirection;                           //constraint direction 
+  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:
-  
+
   string zconsOutput;                         //filename of zconstraint output
   ZConsWriter* fzOut;                         //z-constraint writer
 
-  double curZconsTime;                      
+  double curZconsTime;
 
   double calcMovingMolsCOMVel();
   double calcSysCOMVel();
   double calcTotalForce();
+  void updateZPos();
+  void updateCantPos();
   
   ForceSubtractionPolicy* forcePolicy; //force subtraction policy
   friend class ForceSubtractionPolicy;