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;

  double volume;

};

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 );
    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;}

  // 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 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:	763
Committed:	Mon Sep 15 16:52:02 2003 UTC (20 years, 9 months ago) by tim
File size:	18215 byte(s)
Log Message:	add conserved quantity to statWriter fix bug of vector wrapping at NPTi
#	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	double volume;
206
207	};
208
209	template<typename T> class NPTim : public T{
210
211	public:
212
213	NPTim ( SimInfo theInfo, ForceFields the_ff);
214	virtual ~NPTim() {}
215
216	virtual void integrateStep( int calcPot, int calcStress ){
217	calcStress = 1;
218	T::integrateStep( calcPot, calcStress );
219	accIntegralOfChidt();
220	}
221
222	virtual double getConservedQuantity(void);
223
224	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
225	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
226	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
227	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
228	void setChiTolerance(double tol) {chiTolerance = tol;}
229	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
230
231	protected:
232
233	virtual void moveA( void );
234	virtual void moveB( void );
235
236	virtual int readyCheck();
237
238	virtual void resetIntegrator( void );
239
240	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
241
242	Molecule* myMolecules;
243	Atom** myAtoms;
244
245	// chi and eta are the propagated degrees of freedom
246
247	double chi;
248	double eta;
249	double NkBT;
250	double integralOfChidt;
251
252	// targetTemp, targetPressure, and tauBarostat must be set.
253	// One of qmass or tauThermostat must be set;
254
255	double targetTemp;
256	double targetPressure;
257	double tauThermostat;
258	double tauBarostat;
259
260	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
261	short int have_target_pressure;
262	double chiTolerance;
263	short int have_chi_tolerance;
264	double posIterTolerance;
265	short int have_pos_iter_tolerance;
266
267	};
268
269	template<typename T> class NPTzm : public T{
270
271	public:
272
273	NPTzm ( SimInfo theInfo, ForceFields the_ff);
274	virtual ~NPTzm() {};
275
276	virtual void integrateStep( int calcPot, int calcStress ){
277	calcStress = 1;
278	T::integrateStep( calcPot, calcStress );
279	}
280
281	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
282	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
283	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
284	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
285
286	protected:
287
288	virtual void moveA( void );
289	virtual void moveB( void );
290
291	virtual int readyCheck();
292
293	virtual void resetIntegrator( void );
294
295	Molecule* myMolecules;
296	Atom** myAtoms;
297
298	// chi and eta are the propagated degrees of freedom
299
300	double chi;
301	double eta;
302	double etaZ;
303	double NkBT;
304
305	// targetTemp, targetPressure, and tauBarostat must be set.
306	// One of qmass or tauThermostat must be set;
307
308	double targetTemp;
309	double targetPressure;
310	double tauThermostat;
311	double tauBarostat;
312
313	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
314	short int have_target_pressure;
315
316	};
317
318	template<typename T> class NPTf : public T{
319
320	public:
321
322	NPTf ( SimInfo theInfo, ForceFields the_ff);
323	virtual ~NPTf() {};
324
325	virtual void integrateStep( int calcPot, int calcStress ){
326	calcStress = 1;
327	T::integrateStep( calcPot, calcStress );
328	accIntegralOfChidt();
329	}
330
331	virtual double getConservedQuantity(void);
332
333	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
334	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
335	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
336	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
337	void setChiTolerance(double tol) {chiTolerance = tol;}
338	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
339
340	protected:
341
342	virtual void moveA( void );
343	virtual void moveB( void );
344
345	virtual void resetIntegrator( void );
346
347	virtual int readyCheck();
348
349	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
350
351	// chi and eta are the propagated degrees of freedom
352
353	double chi;
354	double eta[3][3];
355	double NkBT;
356
357	double integralOfChidt;
358
359	// targetTemp, targetPressure, and tauBarostat must be set.
360	// One of qmass or tauThermostat must be set;
361
362	double targetTemp;
363	double targetPressure;
364	double tauThermostat;
365	double tauBarostat;
366
367	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
368	short int have_target_pressure;
369	double chiTolerance;
370	short int have_chi_tolerance;
371	double posIterTolerance;
372	short int have_pos_iter_tolerance;
373
374	};
375
376	template<typename T> class NPTxym : public T{
377
378	public:
379
380	NPTxym ( SimInfo theInfo, ForceFields the_ff);
381	virtual ~NPTxym() {};
382
383	virtual void integrateStep( int calcPot, int calcStress ){
384	calcStress = 1;
385	T::integrateStep( calcPot, calcStress );
386	}
387
388	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
389	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
390	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
391	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
392
393	protected:
394
395	virtual void moveA( void );
396	virtual void moveB( void );
397
398	virtual int readyCheck();
399
400	virtual void resetIntegrator( void );
401
402	Molecule* myMolecules;
403	Atom** myAtoms;
404
405	// chi and eta are the propagated degrees of freedom
406
407	double chi;
408	double eta;
409	double etaX;
410	double etaY;
411	double NkBT;
412
413	// targetTemp, targetPressure, and tauBarostat must be set.
414	// One of qmass or tauThermostat must be set;
415
416	double targetTemp;
417	double targetPressure;
418	double tauThermostat;
419	double tauBarostat;
420
421	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
422	short int have_target_pressure;
423
424	};
425
426
427	template<typename T> class NPTfm : public T{
428
429	public:
430
431	NPTfm ( SimInfo theInfo, ForceFields the_ff);
432	virtual ~NPTfm() {};
433
434	virtual void integrateStep( int calcPot, int calcStress ){
435	calcStress = 1;
436	T::integrateStep( calcPot, calcStress );
437	accIntegralOfChidt();
438	}
439
440	virtual double getConservedQuantity(void);
441
442	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
443	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
444	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
445	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
446	void setChiTolerance(double tol) {chiTolerance = tol;}
447	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
448
449	protected:
450
451	virtual void moveA( void );
452	virtual void moveB( void );
453
454	virtual void resetIntegrator( void );
455
456	virtual int readyCheck();
457
458	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
459
460	Molecule* myMolecules;
461	Atom** myAtoms;
462
463	// chi and eta are the propagated degrees of freedom
464
465	double chi;
466	double eta[3][3];
467	double NkBT;
468	double integralOfChidt;
469
470	// targetTemp, targetPressure, and tauBarostat must be set.
471	// One of qmass or tauThermostat must be set;
472
473	double targetTemp;
474	double targetPressure;
475	double tauThermostat;
476	double tauBarostat;
477
478	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
479	short int have_target_pressure;
480	double chiTolerance;
481	short int have_chi_tolerance;
482	double posIterTolerance;
483	short int have_pos_iter_tolerance;
484
485	};
486
487
488	template<typename T> class NPTpr : public T{
489
490	public:
491
492	NPTpr ( SimInfo theInfo, ForceFields the_ff);
493	virtual ~NPTpr() {};
494
495	virtual void integrateStep( int calcPot, int calcStress ){
496	calcStress = 1;
497	T::integrateStep( calcPot, calcStress );
498	}
499
500	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
501	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
502	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
503	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
504	void setChiTolerance(double tol) {chiTolerance = tol;}
505	void setPosIterTolerance(double tol) {posIterTolerance = tol;}
506
507	protected:
508
509	virtual void moveA( void );
510	virtual void moveB( void );
511
512	virtual int readyCheck();
513
514	virtual void resetIntegrator( void );
515
516	// chi and eta are the propagated degrees of freedom
517
518	double chi;
519	double eta[3][3];
520	double NkBT;
521
522	// targetTemp, targetPressure, and tauBarostat must be set.
523	// One of qmass or tauThermostat must be set;
524
525	double targetTemp;
526	double targetPressure;
527	double tauThermostat;
528	double tauBarostat;
529
530	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
531	short int have_target_pressure;
532	double chiTolerance;
533	short int have_chi_tolerance;
534	double posIterTolerance;
535	short int have_pos_iter_tolerance;
536
537	};
538
539
540	template<typename T> class ZConstraint : public T {
541
542	public:
543	class ForceSubtractionPolicy{
544	public:
545	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
546
547	virtual void update() = 0;
548	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
549	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
550	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
551	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
552
553	protected:
554	ZConstraint<T>* zconsIntegrator;;
555	};
556
557	class PolicyByNumber : public ForceSubtractionPolicy{
558
559	public:
560	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
561	virtual void update();
562	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
563	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
564	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
565	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
566
567	private:
568	int totNumOfMovingAtoms;
569	};
570
571	class PolicyByMass : public ForceSubtractionPolicy{
572
573	public:
574	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
575
576	virtual void update();
577	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
578	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
579	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
580	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
581
582	private:
583	double totMassOfMovingAtoms;
584	};
585
586	public:
587
588	ZConstraint( SimInfo theInfo, ForceFields the_ff);
589	~ZConstraint();
590
591	void setZConsTime(double time) {this->zconsTime = time;}
592	void getZConsTime() {return zconsTime;}
593
594	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
595	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
596
597	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
598	string getZConsOutput() {return zconsOutput;}
599
600	virtual void integrate();
601
602
603	#ifdef IS_MPI
604	virtual void update(); //which is called to indicate the molecules' migration
605	#endif
606
607	protected:
608
609	enum ZConsState {zcsMoving, zcsFixed};
610
611	virtual void calcForce( int calcPot, int calcStress );
612	virtual void thermalize(void);
613
614	void zeroOutVel();
615	void doZconstraintForce();
616	void doHarmonic();
617	bool checkZConsState();
618
619	bool haveFixedZMols();
620	bool haveMovingZMols();
621
622	double calcZSys();
623
624	int isZConstraintMol(Molecule* mol);
625
626
627	double zconsTime; //sample time
628	double zconsTol; //tolerance of z-contratint
629	double zForceConst; //base force constant term
630	//which is estimate by OOPSE
631
632	vector<Molecule*> zconsMols; //z-constraint molecules array
633	vector<double> massOfZConsMols; //mass of z-constraint molecule
634	vector<double> kz; //force constant array
635	vector<ZConsState> states; //state of z-constraint molecules
636	vector<double> zPos; //
637
638
639	vector<Molecule*> unconsMols; //unconstraint molecules array
640	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
641	double totalMassOfUncons; //total mas of unconstraint molecules
642
643	vector<ZConsParaItem>* parameters; //
644
645	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
646
647	int* indexOfZConsMols; //index of local Z-Constraint Molecules
648	double* fz;
649	double* curZPos;
650
651	int totNumOfUnconsAtoms; //total number of uncontraint atoms
652
653	int whichDirection; //constraint direction
654
655	private:
656
657	string zconsOutput; //filename of zconstraint output
658	ZConsWriter* fzOut; //z-constraint writer
659
660	double curZconsTime;
661
662	double calcMovingMolsCOMVel();
663	double calcSysCOMVel();
664	double calcTotalForce();
665
666	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
667	friend class ForceSubtractionPolicy;
668
669	};
670
671	#endif