--- trunk/OOPSE/libmdtools/Integrator.hpp	2003/06/20 20:29:36	561
+++ trunk/OOPSE/libmdtools/Integrator.hpp	2004/08/23 15:11:36	1452
@@ -1,100 +1,125 @@
 #ifndef _INTEGRATOR_H_
 #define _INTEGRATOR_H_
 
+#include <string>
+#include <vector>
 #include "Atom.hpp"
+#include "StuntDouble.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"
+#include "Restraints.hpp"
+#include "Quaternion.hpp"
+#include "Mat4x4d.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 {
+class VelVerletConsFramework;
+template<typename T = BaseIntegrator> class Integrator : public T {
 
 public:
   Integrator( SimInfo *theInfo, ForceFields* the_ff );
   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; }
-  
-  void checkConstraints( void );
-  void rotate( int axes1, int axes2, double angle, double j[3], 
-	       double A[9] );
 
+  virtual void resetIntegrator( void ) { }
 
+  virtual void calcForce( int calcPot, int calcStress );
+  virtual void thermalize();
+
+  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] );
+
+  void printQuaternion(StuntDouble* sd);
+  Mat4x4d getS(const Quaternion& q);
+
   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 
+  VelVerletConsFramework* consFramework;
 
+  //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;
 
-  double* pos;
-  double* vel;
-  double* frc;
-  double* trq;
-  double* Amat;
-
   Thermo *tStats;
   StatWriter*  statOut;
   DumpWriter*  dumpOut;
-  
+
 };
 
-class NVE : public Integrator{
+typedef Integrator<BaseIntegrator> RealIntegrator;
 
+// ansi instantiation
+// template class Integrator<BaseIntegrator>;
+
+
+template<typename T> class NVE : public T {
+
 public:
   NVE ( SimInfo *theInfo, ForceFields* the_ff ):
-    Integrator( theInfo, the_ff ){}
+    T( theInfo, the_ff ){}
   virtual ~NVE(){}
-
-  
-
 };
 
-class NVT : public Integrator{
 
+template<typename T> class NVT : public T {
+
 public:
 
   NVT ( SimInfo *theInfo, ForceFields* the_ff);
-  virtual ~NVT() {}
+  virtual ~NVT();
 
-  void setQmass(double q) {qmass = q; have_qmass = 1;}
   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);
+  virtual string getAdditionalParameters(void);
 
 protected:
 
@@ -103,35 +128,57 @@ class NVT : public Integrator{ (protected)
 
   virtual int readyCheck();
 
-  // zeta is a propagated degree of freedom.
+  virtual void resetIntegrator( void );
 
-  double zeta;
+  // chi is a propagated degree of freedom.
 
-  // targetTemp must be set.  One of qmass or tauThermostat must be set;
+  double chi;
 
-  double qmass;
+  //integral of chi(t)dt
+  double integralOfChidt;
+
+  // targetTemp must be set.  tauThermostat must also be set;
+
   double targetTemp;
   double tauThermostat;
 
-  double NkBT;
-  
-  short int have_tau_thermostat, have_target_temp, have_qmass;
+  short int have_tau_thermostat, have_target_temp;
 
+  double *oldVel;
+  double *oldJi;
+
+  double chiTolerance;
+  short int have_chi_tolerance;
+
 };
 
 
-class NPT : public Integrator{
 
+template<typename T> class NPT : public T{
+
 public:
 
   NPT ( SimInfo *theInfo, ForceFields* the_ff);
   virtual ~NPT();
 
-  void setQmass(double q) {qmass = q; have_qmass = 1;}
+  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;}
   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:
 
@@ -140,25 +187,339 @@ class NPT : public Integrator{ (protected)
 
   virtual int readyCheck();
 
-  Atom** atoms;
+  virtual void resetIntegrator( void );
 
-  // zeta and epsilonDot are the propagated degrees of freedom.
+  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],
+			   int index, double sc[3]) = 0;
 
-  double zeta;
-  double epsilonDot;
+  virtual void calcVelScale( void ) = 0;
 
-  // targetTemp, targetPressure, and tauBarostat must be set.  
+  virtual bool chiConverged( void );
+  virtual bool etaConverged( void ) = 0;
+
+  virtual void evolveChiA( void );
+  virtual void evolveEtaA( void ) = 0;
+  virtual void evolveChiB( void );
+  virtual void evolveEtaB( void ) = 0;
+
+  virtual void scaleSimBox( void ) = 0;
+
+  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
+
+  // chi and eta are the propagated degrees of freedom
+
+  double oldChi;
+  double prevChi;
+  double chi;
+  double NkBT;
+  double fkBT;
+
+  double tt2, tb2;
+  double instaTemp, instaPress, instaVol;
+  double press[3][3];
+
+  int Nparticles;
+
+  double integralOfChidt;
+
+  // targetTemp, targetPressure, and tauBarostat must be set.
   // One of qmass or tauThermostat must be set;
 
-  double qmass;
   double targetTemp;
   double targetPressure;
   double tauThermostat;
   double tauBarostat;
 
   short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-  short int have_target_pressure, have_qmass;
+  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;
+
 };
 
+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);
+
+  virtual bool etaConverged( void );
+
+  virtual void scaleSimBox( void );
+
+  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]);
+
+  virtual void calcVelScale( void );
+
+  double eta, oldEta, prevEta;
+  double vScale;
+};
+
+template<typename T> class NPTf : public T{
+
+public:
+
+  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTf();
+
+  virtual double getConservedQuantity(void);
+  virtual string getAdditionalParameters(void);
+  virtual void resetIntegrator(void);
+
+protected:
+
+  virtual void evolveEtaA(void);
+  virtual void evolveEtaB(void);
+
+  virtual bool etaConverged( void );
+
+  virtual void scaleSimBox( void );
+
+  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]);
+
+  virtual void calcVelScale( void );
+
+  double eta[3][3];
+  double oldEta[3][3];
+  double prevEta[3][3];
+  double vScale[3][3];
+};
+
+template<typename T> class NPTxyz : public T{
+
+public:
+
+  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
+  virtual ~NPTxyz();
+
+  virtual double getConservedQuantity(void);
+  virtual string getAdditionalParameters(void);
+  virtual void resetIntegrator(void);
+
+protected:
+
+  virtual void evolveEtaA(void);
+  virtual void evolveEtaB(void);
+
+  virtual bool etaConverged( void );
+
+  virtual void scaleSimBox( void );
+
+  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]);
+
+  virtual void calcVelScale( void );
+
+  double eta[3][3];
+  double oldEta[3][3];
+  double prevEta[3][3];
+  double vScale[3][3];
+};
+
+
+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
+
+  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:
+
+
+
+  virtual void calcForce( int calcPot, int calcStress );
+  virtual void thermalize(void);
+
+  void zeroOutVel();
+  void doZconstraintForce();
+  void doHarmonic(vector<double>& resPos);
+  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<double> massOfZConsMols;       //mass of z-constraint molecule
+  vector<double> kz;                              //force constant array
+
+  vector<double> zPos;                          //
+
+
+  vector<Molecule*> unconsMols;           //unconstraint molecules array
+  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
+
+
+  vector<ZConsParaItem>* parameters; //
+
+  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
+
+  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:
+
+  string zconsOutput;                         //filename of zconstraint output
+  ZConsWriter* fzOut;                         //z-constraint writer
+
+  double curZconsTime;
+
+  double calcMovingMolsCOMVel();
+  double calcSysCOMVel();
+  double calcTotalForce();
+  void updateZPos();
+  void updateCantPos();
+  
+  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
+  friend class ForceSubtractionPolicy;
+
+};
+
+
+//Sympletic quaternion Scheme Integrator
+//Reference:
+// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
+//Symplectic quaternion Scheme for biophysical molecular dynamics
+//116(20), 8649, J. Chem. Phys. (2002)
+template<typename T> class SQSIntegrator : public T{
+  public:
+    SQSIntegrator( SimInfo *theInfo, ForceFields* the_ff );
+    virtual void moveA();
+    virtual void moveB();
+  protected:
+    void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I);
+    void rotate(int k, double dt,  Quaternion& q,  Vector4d& qdot, double Ik);
+  private:
+    Quaternion getPk(int i, const Vector4d& q);
+    Mat4x4d getS(const Quaternion& q);
+    vector<Quaternion> q;
+    vector<Vector4d> p_qua;
+    vector<double> I0;
+
+		Vector4d p2j(const Vector4d& p, Mat4x4d& m);    
+		Vector4d j2p(const Vector4d& j, Mat4x4d& m);
+};
+#endif