OOPSE/libmdtools/Integrator.hpp

#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;


template<typename T = BaseIntegrator> class Integrator : public T {

public:
  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 );
  virtual void moveA( void );
  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();
  
  virtual void rotationPropagation( DirectionalAtom* dAtom, 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
  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 

  short isFirst; /*boolean for the first time integrate is called */
  
  double dt;
  double dt2;

  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;
  
  short int have_tau_thermostat, have_target_temp;

  double *oldVel;
  double *oldJi;

  double chiTolerance;
  short int have_chi_tolerance;

};


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;

  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 );

  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;

  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;

  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;

};

template<typename T> class NPTi : public T{
  
public:
  NPTi( SimInfo *theInfo, ForceFields* the_ff);
  ~NPTi();

  virtual double getConservedQuantity(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]);

  double eta, oldEta, prevEta;
};


template<typename T> class NPTim : public T{

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;

};

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 );

  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
Revision:	778
Committed:	Fri Sep 19 20:00:27 2003 UTC (20 years, 9 months ago) by mmeineke
File size:	19462 byte(s)
Log Message:	added NPT base class. NPTi is up to date. NPTf is not.
#	Content
1	#ifndef _INTEGRATOR_H_
2	#define _INTEGRATOR_H_
3
4	#include <string>
5	#include <vector>
6	#include "Atom.hpp"
7	#include "Molecule.hpp"
8	#include "SRI.hpp"
9	#include "AbstractClasses.hpp"
10	#include "SimInfo.hpp"
11	#include "ForceFields.hpp"
12	#include "Thermo.hpp"
13	#include "ReadWrite.hpp"
14	#include "ZConsWriter.hpp"
15
16	using namespace std;
17	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
18	const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
20	const int maxIteration = 300;
21	const double tol = 1.0e-6;
22
23
24	template<typename T = BaseIntegrator> class Integrator : public T {
25
26	public:
27	Integrator( SimInfo theInfo, ForceFields the_ff );
28	virtual ~Integrator();
29	void integrate( void );
30	virtual double getConservedQuantity(void);
31
32	protected:
33
34	virtual void integrateStep( int calcPot, int calcStress );
35	virtual void preMove( void );
36	virtual void moveA( void );
37	virtual void moveB( void );
38	virtual void constrainA( void );
39	virtual void constrainB( void );
40	virtual int readyCheck( void ) { return 1; }
41
42	virtual void resetIntegrator( void ) { }
43
44	virtual void calcForce( int calcPot, int calcStress );
45	virtual void thermalize();
46
47	virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48
49	void checkConstraints( void );
50	void rotate( int axes1, int axes2, double angle, double j[3],
51	double A[3][3] );
52
53	ForceFields* myFF;
54
55	SimInfo *info; // all the info we'll ever need
56	int nAtoms; /* the number of atoms */
57	int oldAtoms;
58	Atom *atoms; / array of atom pointers */
59	Molecule* molecules;
60	int nMols;
61
62	int isConstrained; // boolean to know whether the systems contains
63	// constraints.
64	int nConstrained; // counter for number of constraints
65	int *constrainedA; // the i of a constraint pair
66	int *constrainedB; // the j of a constraint pair
67	double *constrainedDsqr; // the square of the constraint distance
68
69	int* moving; // tells whether we are moving atom i
70	int* moved; // tells whether we have moved atom i
71	double* oldPos; // pre constrained positions
72
73	short isFirst; /boolean for the first time integrate is called /
74
75	double dt;
76	double dt2;
77
78	Thermo *tStats;
79	StatWriter* statOut;
80	DumpWriter* dumpOut;
81
82	};
83
84	typedef Integrator<BaseIntegrator> RealIntegrator;
85
86	template<typename T> class NVE : public T {
87
88	public:
89	NVE ( SimInfo theInfo, ForceFields the_ff ):
90	T( theInfo, the_ff ){}
91	virtual ~NVE(){}
92	};
93
94
95	template<typename T> class NVT : public T {
96
97	public:
98
99	NVT ( SimInfo theInfo, ForceFields the_ff);
100	virtual ~NVT();
101
102	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
103	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
104	void setChiTolerance(double tol) {chiTolerance = tol;}
105	virtual double getConservedQuantity(void);
106
107	protected:
108
109	virtual void moveA( void );
110	virtual void moveB( void );
111
112	virtual int readyCheck();
113
114	virtual void resetIntegrator( void );
115
116	// chi is a propagated degree of freedom.
117
118	double chi;
119
120	//integral of chi(t)dt
121	double integralOfChidt;
122
123	// targetTemp must be set. tauThermostat must also be set;
124
125	double targetTemp;
126	double tauThermostat;
127
128	short int have_tau_thermostat, have_target_temp;
129
130	double *oldVel;
131	double *oldJi;
132
133	double chiTolerance;
134	short int have_chi_tolerance;
135
136	};
137
138
139
140	template<typename T> class NPT : public T{
141
142	public:
143
144	NPT ( SimInfo theInfo, ForceFields the_ff);
145	virtual ~NPT();
146
147	virtual void integrateStep( int calcPot, int calcStress ){
148	calcStress = 1;
149	T::integrateStep( calcPot, calcStress );
150	}
151
152	virtual double getConservedQuantity(void) = 0;
153
154	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
155	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
156	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
157	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
158	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
159	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
160	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
161
162	protected:
163
164	virtual void moveA( void );
165	virtual void moveB( void );
166
167	virtual int readyCheck();
168
169	virtual void resetIntegrator( void );
170
171	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
172	virtual void getVelScaleB( double sc[3], int index ) = 0;
173	virtual void getPosScale(double pos[3], double COM[3],
174	int index, double sc[3]) = 0;
175
176	virtual bool chiConverged( void );
177	virtual bool etaConverged( void ) = 0;
178
179	virtual void evolveChiA( void );
180	virtual void evolveEtaA( void ) = 0;
181	virtual void evolveChiB( void );
182	virtual void evolveEtaB( void ) = 0;
183
184	virtual void scaleSimBox( void ) = 0;
185
186	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
187
188	// chi and eta are the propagated degrees of freedom
189
190	double oldChi;
191	double prevChi;
192	double chi;
193	double NkBT;
194	double fkBT;
195
196	double tt2, tb2;
197	double instaTemp, instaPress, instaVol;
198
199	int Nparticles;
200
201	double integralOfChidt;
202
203	// targetTemp, targetPressure, and tauBarostat must be set.
204	// One of qmass or tauThermostat must be set;
205
206	double targetTemp;
207	double targetPressure;
208	double tauThermostat;
209	double tauBarostat;
210
211	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
212	short int have_target_pressure;
213
214	double *oldPos;
215	double *oldVel;
216	double *oldJi;
217
218	double chiTolerance;
219	short int have_chi_tolerance;
220	double posIterTolerance;
221	short int have_pos_iter_tolerance;
222	double etaTolerance;
223	short int have_eta_tolerance;
224
225	};
226
227	template<typename T> class NPTi : public T{
228
229	public:
230	NPTi( SimInfo theInfo, ForceFields the_ff);
231	~NPTi();
232
233	virtual double getConservedQuantity(void);
234	virtual void resetIntegrator(void);
235
236	protected:
237
238
239
240	virtual void evolveEtaA(void);
241	virtual void evolveEtaB(void);
242
243	virtual bool etaConverged( void );
244
245	virtual void scaleSimBox( void );
246
247	virtual void getVelScaleA( double sc[3], double vel[3] );
248	virtual void getVelScaleB( double sc[3], int index );
249	virtual void getPosScale(double pos[3], double COM[3],
250	int index, double sc[3]);
251
252	double eta, oldEta, prevEta;
253	};
254
255
256	template<typename T> class NPTim : public T{
257
258	public:
259
260	NPTim ( SimInfo theInfo, ForceFields the_ff);
261	virtual ~NPTim() {}
262
263	virtual void integrateStep( int calcPot, int calcStress ){
264	calcStress = 1;
265	T::integrateStep( calcPot, calcStress );
266	accIntegralOfChidt();
267	}
268
269	virtual double getConservedQuantity(void);
270
271	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
272	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
273	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
274	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
275	void setChiTolerance(double tol) {chiTolerance = tol;}
276	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
277
278	protected:
279
280	virtual void moveA( void );
281	virtual void moveB( void );
282
283	virtual int readyCheck();
284
285	virtual void resetIntegrator( void );
286
287	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
288
289	Molecule* myMolecules;
290	Atom** myAtoms;
291
292	// chi and eta are the propagated degrees of freedom
293
294	double chi;
295	double eta;
296	double NkBT;
297	double integralOfChidt;
298
299	// targetTemp, targetPressure, and tauBarostat must be set.
300	// One of qmass or tauThermostat must be set;
301
302	double targetTemp;
303	double targetPressure;
304	double tauThermostat;
305	double tauBarostat;
306
307	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
308	short int have_target_pressure;
309	double chiTolerance;
310	short int have_chi_tolerance;
311	double posIterTolerance;
312	short int have_pos_iter_tolerance;
313
314	};
315
316	template<typename T> class NPTzm : public T{
317
318	public:
319
320	NPTzm ( SimInfo theInfo, ForceFields the_ff);
321	virtual ~NPTzm() {};
322
323	virtual void integrateStep( int calcPot, int calcStress ){
324	calcStress = 1;
325	T::integrateStep( calcPot, calcStress );
326	}
327
328	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
329	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
330	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
331	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
332
333	protected:
334
335	virtual void moveA( void );
336	virtual void moveB( void );
337
338	virtual int readyCheck();
339
340	virtual void resetIntegrator( void );
341
342	Molecule* myMolecules;
343	Atom** myAtoms;
344
345	// chi and eta are the propagated degrees of freedom
346
347	double chi;
348	double eta;
349	double etaZ;
350	double NkBT;
351
352	// targetTemp, targetPressure, and tauBarostat must be set.
353	// One of qmass or tauThermostat must be set;
354
355	double targetTemp;
356	double targetPressure;
357	double tauThermostat;
358	double tauBarostat;
359
360	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
361	short int have_target_pressure;
362
363	};
364
365	template<typename T> class NPTf : public T{
366
367	public:
368
369	NPTf ( SimInfo theInfo, ForceFields the_ff);
370	virtual ~NPTf();
371
372	virtual void integrateStep( int calcPot, int calcStress ){
373	calcStress = 1;
374	T::integrateStep( calcPot, calcStress );
375	}
376
377	virtual double getConservedQuantity(void);
378
379	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
380	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
381	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
382	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
383	void setChiTolerance(double tol) {chiTolerance = tol;}
384	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
385
386	protected:
387
388	virtual void moveA( void );
389	virtual void moveB( void );
390
391	virtual void resetIntegrator( void );
392
393	virtual int readyCheck();
394
395
396	// chi and eta are the propagated degrees of freedom
397
398	double chi;
399	double eta[3][3];
400	double NkBT;
401	double fkBT;
402
403	int Nparticles;
404
405	double *oldPos;
406	double *oldVel;
407	double *oldJi;
408
409	double integralOfChidt;
410
411	// targetTemp, targetPressure, and tauBarostat must be set.
412	// One of qmass or tauThermostat must be set;
413
414	double targetTemp;
415	double targetPressure;
416	double tauThermostat;
417	double tauBarostat;
418
419	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
420	short int have_target_pressure;
421	double chiTolerance;
422	short int have_chi_tolerance;
423	double posIterTolerance;
424	short int have_pos_iter_tolerance;
425	double etaTolerance;
426	short int have_eta_tolerance;
427	};
428
429	template<typename T> class NPTxym : public T{
430
431	public:
432
433	NPTxym ( SimInfo theInfo, ForceFields the_ff);
434	virtual ~NPTxym() {};
435
436	virtual void integrateStep( int calcPot, int calcStress ){
437	calcStress = 1;
438	T::integrateStep( calcPot, calcStress );
439	}
440
441	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
442	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
443	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
444	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
445
446	protected:
447
448	virtual void moveA( void );
449	virtual void moveB( void );
450
451	virtual int readyCheck();
452
453	virtual void resetIntegrator( void );
454
455	Molecule* myMolecules;
456	Atom** myAtoms;
457
458	// chi and eta are the propagated degrees of freedom
459
460	double chi;
461	double eta;
462	double etaX;
463	double etaY;
464	double NkBT;
465
466	// targetTemp, targetPressure, and tauBarostat must be set.
467	// One of qmass or tauThermostat must be set;
468
469	double targetTemp;
470	double targetPressure;
471	double tauThermostat;
472	double tauBarostat;
473
474	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
475	short int have_target_pressure;
476
477	};
478
479
480	template<typename T> class NPTfm : public T{
481
482	public:
483
484	NPTfm ( SimInfo theInfo, ForceFields the_ff);
485	virtual ~NPTfm() {};
486
487	virtual void integrateStep( int calcPot, int calcStress ){
488	calcStress = 1;
489	T::integrateStep( calcPot, calcStress );
490	accIntegralOfChidt();
491	}
492
493	virtual double getConservedQuantity(void);
494
495	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
496	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
497	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
498	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
499	void setChiTolerance(double tol) {chiTolerance = tol;}
500	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
501
502	protected:
503
504	virtual void moveA( void );
505	virtual void moveB( void );
506
507	virtual void resetIntegrator( void );
508
509	virtual int readyCheck();
510
511	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
512
513	Molecule* myMolecules;
514	Atom** myAtoms;
515
516	// chi and eta are the propagated degrees of freedom
517
518	double chi;
519	double eta[3][3];
520	double NkBT;
521	double integralOfChidt;
522
523	// targetTemp, targetPressure, and tauBarostat must be set.
524	// One of qmass or tauThermostat must be set;
525
526	double targetTemp;
527	double targetPressure;
528	double tauThermostat;
529	double tauBarostat;
530
531	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
532	short int have_target_pressure;
533	double chiTolerance;
534	short int have_chi_tolerance;
535	double posIterTolerance;
536	short int have_pos_iter_tolerance;
537
538	};
539
540
541	template<typename T> class NPTpr : public T{
542
543	public:
544
545	NPTpr ( SimInfo theInfo, ForceFields the_ff);
546	virtual ~NPTpr() {};
547
548	virtual void integrateStep( int calcPot, int calcStress ){
549	calcStress = 1;
550	T::integrateStep( calcPot, calcStress );
551	}
552
553	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
554	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
555	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
556	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
557	void setChiTolerance(double tol) {chiTolerance = tol;}
558	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
559
560	protected:
561
562	virtual void moveA( void );
563	virtual void moveB( void );
564
565	virtual int readyCheck();
566
567	virtual void resetIntegrator( void );
568
569	// chi and eta are the propagated degrees of freedom
570
571	double chi;
572	double eta[3][3];
573	double NkBT;
574
575	// targetTemp, targetPressure, and tauBarostat must be set.
576	// One of qmass or tauThermostat must be set;
577
578	double targetTemp;
579	double targetPressure;
580	double tauThermostat;
581	double tauBarostat;
582
583	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
584	short int have_target_pressure;
585	double chiTolerance;
586	short int have_chi_tolerance;
587	double posIterTolerance;
588	short int have_pos_iter_tolerance;
589
590	};
591
592
593	template<typename T> class ZConstraint : public T {
594
595	public:
596	class ForceSubtractionPolicy{
597	public:
598	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
599
600	virtual void update() = 0;
601	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
602	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
603	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
604	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
605
606	protected:
607	ZConstraint<T>* zconsIntegrator;;
608	};
609
610	class PolicyByNumber : public ForceSubtractionPolicy{
611
612	public:
613	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
614	virtual void update();
615	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
616	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
617	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
618	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
619
620	private:
621	int totNumOfMovingAtoms;
622	};
623
624	class PolicyByMass : public ForceSubtractionPolicy{
625
626	public:
627	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
628
629	virtual void update();
630	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
631	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
632	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
633	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
634
635	private:
636	double totMassOfMovingAtoms;
637	};
638
639	public:
640
641	ZConstraint( SimInfo theInfo, ForceFields the_ff);
642	~ZConstraint();
643
644	void setZConsTime(double time) {this->zconsTime = time;}
645	void getZConsTime() {return zconsTime;}
646
647	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
648	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
649
650	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
651	string getZConsOutput() {return zconsOutput;}
652
653	virtual void integrate();
654
655
656	#ifdef IS_MPI
657	virtual void update(); //which is called to indicate the molecules' migration
658	#endif
659
660	protected:
661
662	enum ZConsState {zcsMoving, zcsFixed};
663
664	virtual void calcForce( int calcPot, int calcStress );
665	virtual void thermalize(void);
666
667	void zeroOutVel();
668	void doZconstraintForce();
669	void doHarmonic();
670	bool checkZConsState();
671
672	bool haveFixedZMols();
673	bool haveMovingZMols();
674
675	double calcZSys();
676
677	int isZConstraintMol(Molecule* mol);
678
679
680	double zconsTime; //sample time
681	double zconsTol; //tolerance of z-contratint
682	double zForceConst; //base force constant term
683	//which is estimate by OOPSE
684
685	vector<Molecule*> zconsMols; //z-constraint molecules array
686	vector<double> massOfZConsMols; //mass of z-constraint molecule
687	vector<double> kz; //force constant array
688	vector<ZConsState> states; //state of z-constraint molecules
689	vector<double> zPos; //
690
691
692	vector<Molecule*> unconsMols; //unconstraint molecules array
693	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
694	double totalMassOfUncons; //total mas of unconstraint molecules
695
696	vector<ZConsParaItem>* parameters; //
697
698	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
699
700	int* indexOfZConsMols; //index of local Z-Constraint Molecules
701	double* fz;
702	double* curZPos;
703
704	int totNumOfUnconsAtoms; //total number of uncontraint atoms
705
706	int whichDirection; //constraint direction
707
708	private:
709
710	string zconsOutput; //filename of zconstraint output
711	ZConsWriter* fzOut; //z-constraint writer
712
713	double curZconsTime;
714
715	double calcMovingMolsCOMVel();
716	double calcSysCOMVel();
717	double calcTotalForce();
718
719	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
720	friend class ForceSubtractionPolicy;
721
722	};
723
724	#endif