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;
  double press[3][3];

  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 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 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[3][3];
  double oldEta[3][3];
  double prevEta[3][3];
};

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:	780
Committed:	Mon Sep 22 21:23:25 2003 UTC (20 years, 9 months ago) by mmeineke
File size:	16946 byte(s)
Log Message:	Converted NPTf to work with the NPT base class. Removed NPTfm and NPTim from cvs
#	User	Rev	Content
1	mmeineke	377	#ifndef _INTEGRATOR_H_
2			#define _INTEGRATOR_H_
3
4	tim	658	#include <string>
5			#include <vector>
6	mmeineke	377	#include "Atom.hpp"
7	gezelter	604	#include "Molecule.hpp"
8	mmeineke	377	#include "SRI.hpp"
9			#include "AbstractClasses.hpp"
10			#include "SimInfo.hpp"
11			#include "ForceFields.hpp"
12	mmeineke	540	#include "Thermo.hpp"
13			#include "ReadWrite.hpp"
14	tim	658	#include "ZConsWriter.hpp"
15	mmeineke	377
16	tim	658	using namespace std;
17	mmeineke	561	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	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
20	mmeineke	561	const int maxIteration = 300;
21			const double tol = 1.0e-6;
22
23	mmeineke	377
24	tim	645	template<typename T = BaseIntegrator> class Integrator : public T {
25
26	mmeineke	377	public:
27	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
28	mmeineke	548	virtual ~Integrator();
29	mmeineke	377	void integrate( void );
30	tim	763	virtual double getConservedQuantity(void);
31	mmeineke	377
32	mmeineke	540	protected:
33	mmeineke	778
34	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
35	mmeineke	548	virtual void preMove( void );
36	mmeineke	540	virtual void moveA( void );
37			virtual void moveB( void );
38			virtual void constrainA( void );
39			virtual void constrainB( void );
40	mmeineke	559	virtual int readyCheck( void ) { return 1; }
41	tim	677
42	mmeineke	746	virtual void resetIntegrator( void ) { }
43	tim	763
44	tim	677	virtual void calcForce( int calcPot, int calcStress );
45			virtual void thermalize();
46	mmeineke	377
47	mmeineke	778	virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48
49	mmeineke	540	void checkConstraints( void );
50	mmeineke	377	void rotate( int axes1, int axes2, double angle, double j[3],
51	tim	701	double A[3][3] );
52
53	mmeineke	377	ForceFields* myFF;
54
55	mmeineke	540	SimInfo *info; // all the info we'll ever need
56			int nAtoms; /* the number of atoms */
57	mmeineke	548	int oldAtoms;
58	mmeineke	540	Atom *atoms; / array of atom pointers */
59	mmeineke	423	Molecule* molecules;
60			int nMols;
61
62	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
63	tim	701	// constraints.
64	mmeineke	548	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	mmeineke	561	double* oldPos; // pre constrained positions
72	mmeineke	548
73	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
74
75			double dt;
76	mmeineke	541	double dt2;
77	gezelter	560
78	mmeineke	540	Thermo *tStats;
79			StatWriter* statOut;
80			DumpWriter* dumpOut;
81	mmeineke	377
82			};
83
84	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
85	mmeineke	540
86	tim	645	template<typename T> class NVE : public T {
87
88	mmeineke	561	public:
89			NVE ( SimInfo theInfo, ForceFields the_ff ):
90	tim	645	T( theInfo, the_ff ){}
91			virtual ~NVE(){}
92			};
93	mmeineke	555
94
95	tim	645	template<typename T> class NVT : public T {
96	mmeineke	555
97	gezelter	560	public:
98
99	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
100	tim	763	virtual ~NVT();
101	mmeineke	540
102	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
103			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
104	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
105			virtual double getConservedQuantity(void);
106	gezelter	560
107	mmeineke	540	protected:
108	gezelter	560
109	mmeineke	561	virtual void moveA( void );
110			virtual void moveB( void );
111	mmeineke	540
112	mmeineke	561	virtual int readyCheck();
113	gezelter	560
114	mmeineke	746	virtual void resetIntegrator( void );
115
116	gezelter	565	// chi is a propagated degree of freedom.
117	gezelter	560
118	gezelter	565	double chi;
119	gezelter	560
120	tim	763	//integral of chi(t)dt
121			double integralOfChidt;
122
123	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
124	gezelter	560
125			double targetTemp;
126			double tauThermostat;
127	mmeineke	561
128	gezelter	565	short int have_tau_thermostat, have_target_temp;
129	gezelter	560
130	tim	763	double *oldVel;
131			double *oldJi;
132
133			double chiTolerance;
134			short int have_chi_tolerance;
135
136	mmeineke	540	};
137
138
139
140	mmeineke	778	template<typename T> class NPT : public T{
141	tim	645
142	gezelter	560	public:
143
144	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
145			virtual ~NPT();
146	tim	763
147	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
148			calcStress = 1;
149	tim	645	T::integrateStep( calcPot, calcStress );
150	mmeineke	594	}
151
152	mmeineke	778	virtual double getConservedQuantity(void) = 0;
153	tim	763
154	gezelter	560	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	tim	763	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	gezelter	560
162			protected:
163
164	mmeineke	561	virtual void moveA( void );
165			virtual void moveB( void );
166	gezelter	560
167	mmeineke	561	virtual int readyCheck();
168	gezelter	560
169	mmeineke	746	virtual void resetIntegrator( void );
170
171	mmeineke	778	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	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
187
188	gezelter	565	// chi and eta are the propagated degrees of freedom
189	gezelter	560
190	mmeineke	778	double oldChi;
191			double prevChi;
192	gezelter	565	double chi;
193	gezelter	574	double NkBT;
194	tim	763	double fkBT;
195	gezelter	560
196	mmeineke	778	double tt2, tb2;
197			double instaTemp, instaPress, instaVol;
198	mmeineke	780	double press[3][3];
199	mmeineke	778
200	tim	763	int Nparticles;
201
202			double integralOfChidt;
203
204	gezelter	560	// targetTemp, targetPressure, and tauBarostat must be set.
205			// One of qmass or tauThermostat must be set;
206
207			double targetTemp;
208			double targetPressure;
209			double tauThermostat;
210			double tauBarostat;
211
212			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
213	gezelter	565	short int have_target_pressure;
214	gezelter	560
215	tim	763	double *oldPos;
216			double *oldVel;
217			double *oldJi;
218
219			double chiTolerance;
220			short int have_chi_tolerance;
221			double posIterTolerance;
222			short int have_pos_iter_tolerance;
223			double etaTolerance;
224			short int have_eta_tolerance;
225
226	gezelter	560	};
227
228	mmeineke	778	template<typename T> class NPTi : public T{
229
230			public:
231			NPTi( SimInfo theInfo, ForceFields the_ff);
232			~NPTi();
233
234			virtual double getConservedQuantity(void);
235			virtual void resetIntegrator(void);
236
237			protected:
238
239
240
241			virtual void evolveEtaA(void);
242			virtual void evolveEtaB(void);
243
244			virtual bool etaConverged( void );
245
246			virtual void scaleSimBox( void );
247
248			virtual void getVelScaleA( double sc[3], double vel[3] );
249			virtual void getVelScaleB( double sc[3], int index );
250			virtual void getPosScale(double pos[3], double COM[3],
251			int index, double sc[3]);
252
253			double eta, oldEta, prevEta;
254			};
255
256	mmeineke	755	template<typename T> class NPTzm : public T{
257
258			public:
259
260			NPTzm ( SimInfo theInfo, ForceFields the_ff);
261			virtual ~NPTzm() {};
262
263			virtual void integrateStep( int calcPot, int calcStress ){
264			calcStress = 1;
265			T::integrateStep( calcPot, calcStress );
266			}
267
268			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
269			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
270			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
271			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
272
273			protected:
274
275			virtual void moveA( void );
276			virtual void moveB( void );
277
278			virtual int readyCheck();
279
280			virtual void resetIntegrator( void );
281
282			Molecule* myMolecules;
283			Atom** myAtoms;
284
285			// chi and eta are the propagated degrees of freedom
286
287			double chi;
288			double eta;
289			double etaZ;
290			double NkBT;
291
292			// targetTemp, targetPressure, and tauBarostat must be set.
293			// One of qmass or tauThermostat must be set;
294
295			double targetTemp;
296			double targetPressure;
297			double tauThermostat;
298			double tauBarostat;
299
300			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
301			short int have_target_pressure;
302
303			};
304
305	tim	645	template<typename T> class NPTf : public T{
306	gezelter	576
307			public:
308
309			NPTf ( SimInfo theInfo, ForceFields the_ff);
310	tim	767	virtual ~NPTf();
311	gezelter	576
312	tim	763	virtual double getConservedQuantity(void);
313	mmeineke	780	virtual void resetIntegrator(void);
314	mmeineke	594
315	gezelter	576	protected:
316
317	mmeineke	780	virtual void evolveEtaA(void);
318			virtual void evolveEtaB(void);
319	gezelter	576
320	mmeineke	780	virtual bool etaConverged( void );
321	mmeineke	746
322	mmeineke	780	virtual void scaleSimBox( void );
323	gezelter	576
324	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
325			virtual void getVelScaleB( double sc[3], int index );
326			virtual void getPosScale(double pos[3], double COM[3],
327			int index, double sc[3]);
328	tim	763
329	gezelter	588	double eta[3][3];
330	mmeineke	780	double oldEta[3][3];
331			double prevEta[3][3];
332	gezelter	576	};
333
334	mmeineke	755	template<typename T> class NPTxym : public T{
335
336			public:
337
338			NPTxym ( SimInfo theInfo, ForceFields the_ff);
339			virtual ~NPTxym() {};
340
341			virtual void integrateStep( int calcPot, int calcStress ){
342			calcStress = 1;
343			T::integrateStep( calcPot, calcStress );
344			}
345
346			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
347			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
348			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
349			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
350
351			protected:
352
353			virtual void moveA( void );
354			virtual void moveB( void );
355
356			virtual int readyCheck();
357
358			virtual void resetIntegrator( void );
359
360			Molecule* myMolecules;
361			Atom** myAtoms;
362
363			// chi and eta are the propagated degrees of freedom
364
365			double chi;
366			double eta;
367			double etaX;
368			double etaY;
369			double NkBT;
370
371			// targetTemp, targetPressure, and tauBarostat must be set.
372			// One of qmass or tauThermostat must be set;
373
374			double targetTemp;
375			double targetPressure;
376			double tauThermostat;
377			double tauBarostat;
378
379			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
380			short int have_target_pressure;
381
382			};
383
384
385	tim	645	template<typename T> class NPTfm : public T{
386	gezelter	596
387			public:
388
389			NPTfm ( SimInfo theInfo, ForceFields the_ff);
390			virtual ~NPTfm() {};
391
392			virtual void integrateStep( int calcPot, int calcStress ){
393			calcStress = 1;
394	tim	645	T::integrateStep( calcPot, calcStress );
395	tim	763	accIntegralOfChidt();
396	gezelter	596	}
397
398	tim	763	virtual double getConservedQuantity(void);
399
400	gezelter	596	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
401			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
402			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
403			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
404	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
405			void setPosIterTolerance(double tol) {posIterTolerance = tol;}
406	gezelter	596
407			protected:
408
409			virtual void moveA( void );
410			virtual void moveB( void );
411
412	mmeineke	746	virtual void resetIntegrator( void );
413
414	gezelter	596	virtual int readyCheck();
415
416	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
417
418	gezelter	605	Molecule* myMolecules;
419			Atom** myAtoms;
420
421	gezelter	596	// chi and eta are the propagated degrees of freedom
422
423			double chi;
424			double eta[3][3];
425			double NkBT;
426	tim	763	double integralOfChidt;
427	gezelter	596
428			// targetTemp, targetPressure, and tauBarostat must be set.
429			// One of qmass or tauThermostat must be set;
430
431			double targetTemp;
432			double targetPressure;
433			double tauThermostat;
434			double tauBarostat;
435
436			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
437			short int have_target_pressure;
438	tim	763	double chiTolerance;
439			short int have_chi_tolerance;
440			double posIterTolerance;
441			short int have_pos_iter_tolerance;
442	gezelter	596
443			};
444
445	gezelter	718
446			template<typename T> class NPTpr : public T{
447
448			public:
449
450			NPTpr ( SimInfo theInfo, ForceFields the_ff);
451			virtual ~NPTpr() {};
452
453			virtual void integrateStep( int calcPot, int calcStress ){
454			calcStress = 1;
455			T::integrateStep( calcPot, calcStress );
456			}
457
458			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
459			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
460			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
461			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
462	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
463			void setPosIterTolerance(double tol) {posIterTolerance = tol;}
464	gezelter	718
465			protected:
466
467			virtual void moveA( void );
468			virtual void moveB( void );
469
470			virtual int readyCheck();
471
472	mmeineke	746	virtual void resetIntegrator( void );
473
474	gezelter	718	// chi and eta are the propagated degrees of freedom
475
476			double chi;
477			double eta[3][3];
478			double NkBT;
479
480			// targetTemp, targetPressure, and tauBarostat must be set.
481			// One of qmass or tauThermostat must be set;
482
483			double targetTemp;
484			double targetPressure;
485			double tauThermostat;
486			double tauBarostat;
487
488			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
489			short int have_target_pressure;
490	tim	763	double chiTolerance;
491			short int have_chi_tolerance;
492			double posIterTolerance;
493			short int have_pos_iter_tolerance;
494	gezelter	718
495			};
496
497
498	tim	658	template<typename T> class ZConstraint : public T {
499	tim	701
500			public:
501	tim	738	class ForceSubtractionPolicy{
502	tim	699	public:
503	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
504	tim	658
505	tim	701	virtual void update() = 0;
506	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
507			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
508	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
509			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
510
511			protected:
512			ZConstraint<T>* zconsIntegrator;;
513	tim	699	};
514
515	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
516	gezelter	747
517	tim	699	public:
518	tim	738	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
519	tim	701	virtual void update();
520	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
521			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
522	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
523			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
524
525	tim	699	private:
526	tim	763	int totNumOfMovingAtoms;
527	tim	699	};
528
529	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
530	gezelter	747
531	tim	699	public:
532	tim	738	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
533	tim	701
534			virtual void update();
535	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
536			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
537	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
538			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
539	tim	699
540	tim	701	private:
541			double totMassOfMovingAtoms;
542	tim	699	};
543
544	tim	658	public:
545
546			ZConstraint( SimInfo theInfo, ForceFields the_ff);
547			~ZConstraint();
548	tim	677
549	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
550			void getZConsTime() {return zconsTime;}
551
552	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
553			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
554	tim	658
555	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
556	tim	658	string getZConsOutput() {return zconsOutput;}
557	tim	677
558			virtual void integrate();
559
560	tim	658
561			#ifdef IS_MPI
562	tim	701	virtual void update(); //which is called to indicate the molecules' migration
563	mmeineke	377	#endif
564	tim	658
565			protected:
566
567	tim	701	enum ZConsState {zcsMoving, zcsFixed};
568	tim	677
569			virtual void calcForce( int calcPot, int calcStress );
570			virtual void thermalize(void);
571
572			void zeroOutVel();
573			void doZconstraintForce();
574	tim	682	void doHarmonic();
575	tim	677	bool checkZConsState();
576
577			bool haveFixedZMols();
578			bool haveMovingZMols();
579
580			double calcZSys();
581
582			int isZConstraintMol(Molecule* mol);
583
584
585	tim	701	double zconsTime; //sample time
586			double zconsTol; //tolerance of z-contratint
587			double zForceConst; //base force constant term
588			//which is estimate by OOPSE
589	tim	658
590	tim	701	vector<Molecule*> zconsMols; //z-constraint molecules array
591			vector<double> massOfZConsMols; //mass of z-constraint molecule
592			vector<double> kz; //force constant array
593			vector<ZConsState> states; //state of z-constraint molecules
594			vector<double> zPos; //
595	tim	658
596	tim	677
597	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
598			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
599			double totalMassOfUncons; //total mas of unconstraint molecules
600	tim	682
601	tim	701	vector<ZConsParaItem>* parameters; //
602	tim	658
603			vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
604	tim	677
605			int* indexOfZConsMols; //index of local Z-Constraint Molecules
606	tim	658	double* fz;
607	tim	699	double* curZPos;
608	tim	658
609	tim	701	int totNumOfUnconsAtoms; //total number of uncontraint atoms
610	tim	677
611			int whichDirection; //constraint direction
612
613	tim	658	private:
614	tim	677
615	tim	701	string zconsOutput; //filename of zconstraint output
616			ZConsWriter* fzOut; //z-constraint writer
617	tim	677
618	tim	701	double curZconsTime;
619	tim	699
620	tim	696	double calcMovingMolsCOMVel();
621			double calcSysCOMVel();
622			double calcTotalForce();
623	tim	701
624	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
625	tim	738	friend class ForceSubtractionPolicy;
626	tim	677
627	tim	658	};
628
629			#endif