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();
  
  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 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;

};

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:	767
Committed:	Tue Sep 16 20:02:11 2003 UTC (20 years, 9 months ago) by tim
File size:	18246 byte(s)
Log Message:	fixed ecr grow in SimInfo fixed conserved quantity in NPT (Still some small bug) NPTi appears very stable.
#	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	void checkConstraints( void );
48	void rotate( int axes1, int axes2, double angle, double j[3],
49	double A[3][3] );
50
51	ForceFields* myFF;
52
53	SimInfo *info; // all the info we'll ever need
54	int nAtoms; /* the number of atoms */
55	int oldAtoms;
56	Atom *atoms; / array of atom pointers */
57	Molecule* molecules;
58	int nMols;
59
60	int isConstrained; // boolean to know whether the systems contains
61	// constraints.
62	int nConstrained; // counter for number of constraints
63	int *constrainedA; // the i of a constraint pair
64	int *constrainedB; // the j of a constraint pair
65	double *constrainedDsqr; // the square of the constraint distance
66
67	int* moving; // tells whether we are moving atom i
68	int* moved; // tells whether we have moved atom i
69	double* oldPos; // pre constrained positions
70
71	short isFirst; /boolean for the first time integrate is called /
72
73	double dt;
74	double dt2;
75
76	Thermo *tStats;
77	StatWriter* statOut;
78	DumpWriter* dumpOut;
79
80	};
81
82	typedef Integrator<BaseIntegrator> RealIntegrator;
83
84	template<typename T> class NVE : public T {
85
86	public:
87	NVE ( SimInfo theInfo, ForceFields the_ff ):
88	T( theInfo, the_ff ){}
89	virtual ~NVE(){}
90	};
91
92
93	template<typename T> class NVT : public T {
94
95	public:
96
97	NVT ( SimInfo theInfo, ForceFields the_ff);
98	virtual ~NVT();
99
100	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
101	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
102	void setChiTolerance(double tol) {chiTolerance = tol;}
103	virtual double getConservedQuantity(void);
104
105	protected:
106
107	virtual void moveA( void );
108	virtual void moveB( void );
109
110	virtual int readyCheck();
111
112	virtual void resetIntegrator( void );
113
114	// chi is a propagated degree of freedom.
115
116	double chi;
117
118	//integral of chi(t)dt
119	double integralOfChidt;
120
121	// targetTemp must be set. tauThermostat must also be set;
122
123	double targetTemp;
124	double tauThermostat;
125
126	short int have_tau_thermostat, have_target_temp;
127
128	double *oldVel;
129	double *oldJi;
130
131	double chiTolerance;
132	short int have_chi_tolerance;
133
134	};
135
136
137
138	template<typename T> class NPTi : public T{
139
140	public:
141
142	NPTi ( SimInfo theInfo, ForceFields the_ff);
143	virtual ~NPTi();
144
145	virtual void integrateStep( int calcPot, int calcStress ){
146	calcStress = 1;
147	T::integrateStep( calcPot, calcStress );
148	/* accIntegralOfChidt(); */
149	}
150
151	virtual double getConservedQuantity(void);
152
153	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
154	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
155	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
156	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
157	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
158	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
159	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
160
161	protected:
162
163	virtual void moveA( void );
164	virtual void moveB( void );
165
166	virtual int readyCheck();
167
168	virtual void resetIntegrator( void );
169
170	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
171
172	// chi and eta are the propagated degrees of freedom
173
174	double chi;
175	double eta;
176	double NkBT;
177	double fkBT;
178
179	int Nparticles;
180
181	double integralOfChidt;
182
183	// targetTemp, targetPressure, and tauBarostat must be set.
184	// One of qmass or tauThermostat must be set;
185
186	double targetTemp;
187	double targetPressure;
188	double tauThermostat;
189	double tauBarostat;
190
191	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
192	short int have_target_pressure;
193
194	double *oldPos;
195	double *oldVel;
196	double *oldJi;
197
198	double chiTolerance;
199	short int have_chi_tolerance;
200	double posIterTolerance;
201	short int have_pos_iter_tolerance;
202	double etaTolerance;
203	short int have_eta_tolerance;
204
205	};
206
207	template<typename T> class NPTim : public T{
208
209	public:
210
211	NPTim ( SimInfo theInfo, ForceFields the_ff);
212	virtual ~NPTim() {}
213
214	virtual void integrateStep( int calcPot, int calcStress ){
215	calcStress = 1;
216	T::integrateStep( calcPot, calcStress );
217	accIntegralOfChidt();
218	}
219
220	virtual double getConservedQuantity(void);
221
222	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
223	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
224	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
225	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
226	void setChiTolerance(double tol) {chiTolerance = tol;}
227	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
228
229	protected:
230
231	virtual void moveA( void );
232	virtual void moveB( void );
233
234	virtual int readyCheck();
235
236	virtual void resetIntegrator( void );
237
238	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
239
240	Molecule* myMolecules;
241	Atom** myAtoms;
242
243	// chi and eta are the propagated degrees of freedom
244
245	double chi;
246	double eta;
247	double NkBT;
248	double integralOfChidt;
249
250	// targetTemp, targetPressure, and tauBarostat must be set.
251	// One of qmass or tauThermostat must be set;
252
253	double targetTemp;
254	double targetPressure;
255	double tauThermostat;
256	double tauBarostat;
257
258	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
259	short int have_target_pressure;
260	double chiTolerance;
261	short int have_chi_tolerance;
262	double posIterTolerance;
263	short int have_pos_iter_tolerance;
264
265	};
266
267	template<typename T> class NPTzm : public T{
268
269	public:
270
271	NPTzm ( SimInfo theInfo, ForceFields the_ff);
272	virtual ~NPTzm() {};
273
274	virtual void integrateStep( int calcPot, int calcStress ){
275	calcStress = 1;
276	T::integrateStep( calcPot, calcStress );
277	}
278
279	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
280	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
281	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
282	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
283
284	protected:
285
286	virtual void moveA( void );
287	virtual void moveB( void );
288
289	virtual int readyCheck();
290
291	virtual void resetIntegrator( void );
292
293	Molecule* myMolecules;
294	Atom** myAtoms;
295
296	// chi and eta are the propagated degrees of freedom
297
298	double chi;
299	double eta;
300	double etaZ;
301	double NkBT;
302
303	// targetTemp, targetPressure, and tauBarostat must be set.
304	// One of qmass or tauThermostat must be set;
305
306	double targetTemp;
307	double targetPressure;
308	double tauThermostat;
309	double tauBarostat;
310
311	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
312	short int have_target_pressure;
313
314	};
315
316	template<typename T> class NPTf : public T{
317
318	public:
319
320	NPTf ( SimInfo theInfo, ForceFields the_ff);
321	virtual ~NPTf();
322
323	virtual void integrateStep( int calcPot, int calcStress ){
324	calcStress = 1;
325	T::integrateStep( calcPot, calcStress );
326	}
327
328	virtual double getConservedQuantity(void);
329
330	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
331	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
332	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
333	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
334	void setChiTolerance(double tol) {chiTolerance = tol;}
335	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
336
337	protected:
338
339	virtual void moveA( void );
340	virtual void moveB( void );
341
342	virtual void resetIntegrator( void );
343
344	virtual int readyCheck();
345
346
347	// chi and eta are the propagated degrees of freedom
348
349	double chi;
350	double eta[3][3];
351	double NkBT;
352	double fkBT;
353
354	int Nparticles;
355
356	double *oldPos;
357	double *oldVel;
358	double *oldJi;
359
360	double integralOfChidt;
361
362	// targetTemp, targetPressure, and tauBarostat must be set.
363	// One of qmass or tauThermostat must be set;
364
365	double targetTemp;
366	double targetPressure;
367	double tauThermostat;
368	double tauBarostat;
369
370	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
371	short int have_target_pressure;
372	double chiTolerance;
373	short int have_chi_tolerance;
374	double posIterTolerance;
375	short int have_pos_iter_tolerance;
376	double etaTolerance;
377	short int have_eta_tolerance;
378	};
379
380	template<typename T> class NPTxym : public T{
381
382	public:
383
384	NPTxym ( SimInfo theInfo, ForceFields the_ff);
385	virtual ~NPTxym() {};
386
387	virtual void integrateStep( int calcPot, int calcStress ){
388	calcStress = 1;
389	T::integrateStep( calcPot, calcStress );
390	}
391
392	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
393	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
394	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
395	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
396
397	protected:
398
399	virtual void moveA( void );
400	virtual void moveB( void );
401
402	virtual int readyCheck();
403
404	virtual void resetIntegrator( void );
405
406	Molecule* myMolecules;
407	Atom** myAtoms;
408
409	// chi and eta are the propagated degrees of freedom
410
411	double chi;
412	double eta;
413	double etaX;
414	double etaY;
415	double NkBT;
416
417	// targetTemp, targetPressure, and tauBarostat must be set.
418	// One of qmass or tauThermostat must be set;
419
420	double targetTemp;
421	double targetPressure;
422	double tauThermostat;
423	double tauBarostat;
424
425	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
426	short int have_target_pressure;
427
428	};
429
430
431	template<typename T> class NPTfm : public T{
432
433	public:
434
435	NPTfm ( SimInfo theInfo, ForceFields the_ff);
436	virtual ~NPTfm() {};
437
438	virtual void integrateStep( int calcPot, int calcStress ){
439	calcStress = 1;
440	T::integrateStep( calcPot, calcStress );
441	accIntegralOfChidt();
442	}
443
444	virtual double getConservedQuantity(void);
445
446	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
447	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
448	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
449	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
450	void setChiTolerance(double tol) {chiTolerance = tol;}
451	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
452
453	protected:
454
455	virtual void moveA( void );
456	virtual void moveB( void );
457
458	virtual void resetIntegrator( void );
459
460	virtual int readyCheck();
461
462	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
463
464	Molecule* myMolecules;
465	Atom** myAtoms;
466
467	// chi and eta are the propagated degrees of freedom
468
469	double chi;
470	double eta[3][3];
471	double NkBT;
472	double integralOfChidt;
473
474	// targetTemp, targetPressure, and tauBarostat must be set.
475	// One of qmass or tauThermostat must be set;
476
477	double targetTemp;
478	double targetPressure;
479	double tauThermostat;
480	double tauBarostat;
481
482	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
483	short int have_target_pressure;
484	double chiTolerance;
485	short int have_chi_tolerance;
486	double posIterTolerance;
487	short int have_pos_iter_tolerance;
488
489	};
490
491
492	template<typename T> class NPTpr : public T{
493
494	public:
495
496	NPTpr ( SimInfo theInfo, ForceFields the_ff);
497	virtual ~NPTpr() {};
498
499	virtual void integrateStep( int calcPot, int calcStress ){
500	calcStress = 1;
501	T::integrateStep( calcPot, calcStress );
502	}
503
504	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
505	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
506	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
507	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
508	void setChiTolerance(double tol) {chiTolerance = tol;}
509	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
510
511	protected:
512
513	virtual void moveA( void );
514	virtual void moveB( void );
515
516	virtual int readyCheck();
517
518	virtual void resetIntegrator( void );
519
520	// chi and eta are the propagated degrees of freedom
521
522	double chi;
523	double eta[3][3];
524	double NkBT;
525
526	// targetTemp, targetPressure, and tauBarostat must be set.
527	// One of qmass or tauThermostat must be set;
528
529	double targetTemp;
530	double targetPressure;
531	double tauThermostat;
532	double tauBarostat;
533
534	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
535	short int have_target_pressure;
536	double chiTolerance;
537	short int have_chi_tolerance;
538	double posIterTolerance;
539	short int have_pos_iter_tolerance;
540
541	};
542
543
544	template<typename T> class ZConstraint : public T {
545
546	public:
547	class ForceSubtractionPolicy{
548	public:
549	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
550
551	virtual void update() = 0;
552	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
553	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
554	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
555	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
556
557	protected:
558	ZConstraint<T>* zconsIntegrator;;
559	};
560
561	class PolicyByNumber : public ForceSubtractionPolicy{
562
563	public:
564	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
565	virtual void update();
566	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
567	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
568	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
569	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
570
571	private:
572	int totNumOfMovingAtoms;
573	};
574
575	class PolicyByMass : public ForceSubtractionPolicy{
576
577	public:
578	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
579
580	virtual void update();
581	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
582	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
583	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
584	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
585
586	private:
587	double totMassOfMovingAtoms;
588	};
589
590	public:
591
592	ZConstraint( SimInfo theInfo, ForceFields the_ff);
593	~ZConstraint();
594
595	void setZConsTime(double time) {this->zconsTime = time;}
596	void getZConsTime() {return zconsTime;}
597
598	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
599	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
600
601	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
602	string getZConsOutput() {return zconsOutput;}
603
604	virtual void integrate();
605
606
607	#ifdef IS_MPI
608	virtual void update(); //which is called to indicate the molecules' migration
609	#endif
610
611	protected:
612
613	enum ZConsState {zcsMoving, zcsFixed};
614
615	virtual void calcForce( int calcPot, int calcStress );
616	virtual void thermalize(void);
617
618	void zeroOutVel();
619	void doZconstraintForce();
620	void doHarmonic();
621	bool checkZConsState();
622
623	bool haveFixedZMols();
624	bool haveMovingZMols();
625
626	double calcZSys();
627
628	int isZConstraintMol(Molecule* mol);
629
630
631	double zconsTime; //sample time
632	double zconsTol; //tolerance of z-contratint
633	double zForceConst; //base force constant term
634	//which is estimate by OOPSE
635
636	vector<Molecule*> zconsMols; //z-constraint molecules array
637	vector<double> massOfZConsMols; //mass of z-constraint molecule
638	vector<double> kz; //force constant array
639	vector<ZConsState> states; //state of z-constraint molecules
640	vector<double> zPos; //
641
642
643	vector<Molecule*> unconsMols; //unconstraint molecules array
644	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
645	double totalMassOfUncons; //total mas of unconstraint molecules
646
647	vector<ZConsParaItem>* parameters; //
648
649	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
650
651	int* indexOfZConsMols; //index of local Z-Constraint Molecules
652	double* fz;
653	double* curZPos;
654
655	int totNumOfUnconsAtoms; //total number of uncontraint atoms
656
657	int whichDirection; //constraint direction
658
659	private:
660
661	string zconsOutput; //filename of zconstraint output
662	ZConsWriter* fzOut; //z-constraint writer
663
664	double curZconsTime;
665
666	double calcMovingMolsCOMVel();
667	double calcSysCOMVel();
668	double calcTotalForce();
669
670	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
671	friend class ForceSubtractionPolicy;
672
673	};
674
675	#endif