--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/06/17 21:56:15	555
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2003/09/16 20:02:11	767
@@ -1,24 +1,35 @@
 #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"
 
-class Integrator : public BaseIntegrator {
+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;
 
+
+template<typename T = BaseIntegrator> class Integrator : public T {
+
 public:
-  Integrator( SimInfo &theInfo, ForceFields* the_ff );
+  Integrator( SimInfo *theInfo, ForceFields* the_ff );
   virtual ~Integrator();
   void integrate( void );
+  virtual double  getConservedQuantity(void);
 
-
 protected:
-
   
   virtual void integrateStep( int calcPot, int calcStress );
   virtual void preMove( void );
@@ -26,13 +37,17 @@ class Integrator : public BaseIntegrator { (protected)
   virtual void moveB( 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 thermalize();
   
-  
   void checkConstraints( void );
   void rotate( int axes1, int axes2, double angle, double j[3], 
-	       double A[3][3] );
-
-
+         double A[3][3] );
+         
   ForceFields* myFF;
 
   SimInfo *info; // all the info we'll ever need
@@ -43,7 +58,7 @@ class Integrator : public BaseIntegrator { (protected)
   int nMols;
 
   int isConstrained; // boolean to know whether the systems contains
-		     // constraints.
+         // constraints.
   int nConstrained;  // counter for number of constraints 
   int *constrainedA; // the i of a constraint pair 
   int *constrainedB; // the j of a constraint pair 
@@ -51,55 +66,610 @@ class Integrator : public BaseIntegrator { (protected)
   
   int* moving; // tells whether we are moving atom i
   int* moved;  // tells whether we have moved atom i
-  double* prePos; // pre constrained positions 
+  double* oldPos; // pre constrained positions 
 
   short isFirst; /*boolean for the first time integrate is called */
   
   double dt;
   double dt2;
-  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
 
-  const int maxIteration = 300;
-  const double tol = 1.0e-6;
+  Thermo *tStats;
+  StatWriter*  statOut;
+  DumpWriter*  dumpOut;
+  
+};
 
+typedef Integrator<BaseIntegrator> RealIntegrator;
+
+template<typename T> class NVE : public T {
+
+public:
+  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
+    T( theInfo, the_ff ){}
+  virtual ~NVE(){}  
+};
+
+
+template<typename T> class NVT : public T {
+
+public:
+
+  NVT ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NVT();
+
+  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
+  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
+  void setChiTolerance(double tol) {chiTolerance = tol;}
+  virtual double  getConservedQuantity(void);
+
+protected:
+
+  virtual void moveA( void );
+  virtual void moveB( void );
+
+  virtual int readyCheck();
+
+  virtual void resetIntegrator( void );
+
+  // chi is a propagated degree of freedom.
+
+  double chi;
+
+  //integral of chi(t)dt
+  double integralOfChidt;
+
+  // targetTemp must be set.  tauThermostat must also be set;
+
+  double targetTemp;
+  double tauThermostat;
   
-  double* pos;
-  double* vel;
-  double* frc;
-  double* trq;
-  double* Amat;
-  
+  short int have_tau_thermostat, have_target_temp;
 
+  double *oldVel;
+  double *oldJi;
 
-  Thermo *tStats;
-  StatWriter*  statOut;
-  DumpWriter*  dumpOut;
+  double chiTolerance;
+  short int have_chi_tolerance;
+
+};
+
+
+
+template<typename T> class NPTi : public T{
+
+public:
+
+  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTi();
   
+  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; have_chi_tolerance = 1;}
+  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
+  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
+
+protected:
+
+  virtual void  moveA( void );
+  virtual void moveB( void );
+
+  virtual int readyCheck();
+
+  virtual void resetIntegrator( void );
+
+  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
+
+  // chi and eta are the propagated degrees of freedom
+
+  double chi;
+  double eta;
+  double NkBT;
+  double fkBT;
+
+  int Nparticles;
+
+  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 *oldPos;
+  double *oldVel;
+  double *oldJi;
+
+  double chiTolerance;
+  short int have_chi_tolerance;
+  double posIterTolerance;
+  short int have_pos_iter_tolerance;
+  double etaTolerance;
+  short int have_eta_tolerance;
+
 };
 
-class NVE : public Integrator{
+template<typename T> class NPTim : public T{
 
-  NVE ( void ):
-    Integrator( theInfo, the_ff ){}
-  virtual ~NVE(){}
+public:
 
+  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTim() {}
+
+  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 int readyCheck();
+
+  virtual void resetIntegrator( void );
+
+  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
   
+  Molecule* myMolecules;
+  Atom** myAtoms;
 
+  // chi and eta are the propagated degrees of freedom
+
+  double chi;
+  double eta;
+  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;
+
 };
 
-class NVT : public Integrator{
+template<typename T> class NPTzm : public T{
 
-  NVT ( SimInfo &theInfo, ForceFields* the_ff ) :
-    Integrator( theInfo, the_ff );
-  virtual ~NVT();
+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 moveA( void );
-  virtual moveB( void );
+
+  virtual void moveA( void );
+  virtual void moveB( void );
+
+  virtual int readyCheck();
+
+  virtual void resetIntegrator( 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;
+
+};
+
+template<typename T> class NPTf : public T{
+
+public:
+
+  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTf();
+
+  virtual void integrateStep( int calcPot, int calcStress ){
+    calcStress = 1;
+    T::integrateStep( calcPot, calcStress );
+  }
+  
+  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();
+
+
+  // chi and eta are the propagated degrees of freedom
+
+  double chi;
+  double eta[3][3];
+  double NkBT;
+  double fkBT;
 
+  int Nparticles;
+
+  double *oldPos;
+  double *oldVel;
+  double *oldJi;
+
+  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 etaTolerance;
+  short int have_eta_tolerance;
 };
 
+template<typename T> class NPTxym : public T{
+
+public:
+
+  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTxym() {};
+
+  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 );
+
+  Molecule* myMolecules;
+  Atom** myAtoms;
+
+  // chi and eta are the propagated degrees of freedom
+
+  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;
+
+};
+
+
+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: 
+  class ForceSubtractionPolicy{
+    public:
+      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
+
+      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;;
+  };
+
+  class PolicyByNumber : public ForceSubtractionPolicy{
+
+    public:
+      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;
+  };
+
+  class PolicyByMass : public ForceSubtractionPolicy{
+
+    public:
+      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);
+      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
+
+   private:
+     double totMassOfMovingAtoms;
+  };
+
+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;                              //sample time
+  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> 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
+
+  int whichDirection;                           //constraint direction 
+  
+private:
+  
+  string zconsOutput;                         //filename of zconstraint output
+  ZConsWriter* fzOut;                         //z-constraint writer
+
+  double curZconsTime;                      
+
+  double calcMovingMolsCOMVel();
+  double calcSysCOMVel();
+  double calcTotalForce();
+  
+  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
+  friend class ForceSubtractionPolicy;
+
+};
+
+#endif