OOPSE/libmdtools/Integrator.hpp

#ifndef _INTEGRATOR_H_
#define _INTEGRATOR_H_

#include <string>
#include <vector>
#include "Atom.hpp"
#include "StuntDouble.hpp"
#include "Molecule.hpp"
#include "SRI.hpp"
#include "AbstractClasses.hpp"
#include "SimInfo.hpp"
#include "ForceFields.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"
#include "ZConsWriter.hpp"

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);
  virtual string getAdditionalParameters(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 bool stopIntegrator() {return false;}

  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );

  void checkConstraints( void );
  void rotate( int axes1, int axes2, double angle, double j[3],
         double A[3][3] );

  ForceFields* myFF;

  SimInfo *info; // all the info we'll ever need
  vector<StuntDouble*> integrableObjects;
  int nAtoms;  /* the number of atoms */
  int oldAtoms;
  Atom **atoms; /* array of atom pointers */
  Molecule* molecules;
  int nMols;

  int isConstrained; // boolean to know whether the systems contains
         // constraints.
  int nConstrained;  // counter for number of constraints
  int *constrainedA; // the i of a constraint pair
  int *constrainedB; // the j of a constraint pair
  double *constrainedDsqr; // the square of the constraint distance

  int* moving; // tells whether we are moving atom i
  int* moved;  // tells whether we have moved atom i
  double* oldPos; // pre constrained positions

  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);
  virtual string getAdditionalParameters(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;
  virtual string getAdditionalParameters(void) = 0;
  
  double myTauThermo( void ) { return tauThermostat; }
  double myTauBaro( void ) { return tauBarostat; }

  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}

protected:

  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 void calcVelScale( void ) = 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);
  virtual string getAdditionalParameters(void);
protected:


  virtual void evolveEtaA(void);
  virtual void evolveEtaB(void);

  virtual bool etaConverged( void );

  virtual void scaleSimBox( void );

  virtual void getVelScaleA( double sc[3], double vel[3] );
  virtual void getVelScaleB( double sc[3], int index );
  virtual void getPosScale(double pos[3], double COM[3],
                           int index, double sc[3]);

  virtual void calcVelScale( void );

  double eta, oldEta, prevEta;
  double vScale;
};

template<typename T> class NPTf : public T{

public:

  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTf();

  virtual double getConservedQuantity(void);
  virtual string getAdditionalParameters(void);
  virtual void resetIntegrator(void);

protected:

  virtual void evolveEtaA(void);
  virtual void evolveEtaB(void);

  virtual bool etaConverged( void );

  virtual void scaleSimBox( void );

  virtual void getVelScaleA( double sc[3], double vel[3] );
  virtual void getVelScaleB( double sc[3], int index );
  virtual void getPosScale(double pos[3], double COM[3],
                           int index, double sc[3]);

  virtual void calcVelScale( void );

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

template<typename T> class NPTxyz : public T{

public:

  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTxyz();

  virtual double getConservedQuantity(void);
  virtual string getAdditionalParameters(void);
  virtual void resetIntegrator(void);

protected:

  virtual void evolveEtaA(void);
  virtual void evolveEtaB(void);

  virtual bool etaConverged( void );

  virtual void scaleSimBox( void );

  virtual void getVelScaleA( double sc[3], double vel[3] );
  virtual void getVelScaleB( double sc[3], int index );
  virtual void getPosScale(double pos[3], double COM[3],
                           int index, double sc[3]);

  virtual void calcVelScale( void );

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


template<typename T> class ZConstraint : public T {

  public:
  class ForceSubtractionPolicy{
    public:
      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}

      virtual void update() = 0;
      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;

   protected:
     ZConstraint<T>* zconsIntegrator;
  };

  class PolicyByNumber : public ForceSubtractionPolicy{

    public:
      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
      virtual void update();
      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);

    private:
      int totNumOfMovingAtoms;
  };

  class PolicyByMass : public ForceSubtractionPolicy{

    public:
      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}

      virtual void update();
      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);

   private:
     double totMassOfMovingAtoms;
  };

public:

  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
  ~ZConstraint();

  void setZConsTime(double time)                  {this->zconsTime = time;}
  void getZConsTime()                             {return zconsTime;}

  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}

  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
  string getZConsOutput()                         {return zconsOutput;}

  virtual void integrate();


#ifdef IS_MPI
  virtual void update();                      //which is called to indicate the molecules' migration
#endif

  enum ZConsState {zcsMoving, zcsFixed};

  vector<Molecule*> zconsMols;              //z-constraint molecules array
  vector<ZConsState> states;                 //state of z-constraint molecules


  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
  double totalMassOfUncons;                //total mas of unconstraint molecules


protected:


  virtual void calcForce( int calcPot, int calcStress );
  virtual void thermalize(void);

  void zeroOutVel();
  void doZconstraintForce();
  void doHarmonic(vector<double>& resPos);
  bool checkZConsState();

  bool haveFixedZMols();
  bool haveMovingZMols();

  double calcZSys();

  int isZConstraintMol(Molecule* mol);


  double zconsTime;                              //sample time
  double zconsTol;                                 //tolerance of z-contratint
  double zForceConst;                           //base force constant term
                                                          //which is estimate by OOPSE


  vector<double> massOfZConsMols;       //mass of z-constraint molecule
  vector<double> kz;                              //force constant array

  vector<double> zPos;                          //


  vector<Molecule*> unconsMols;           //unconstraint molecules array
  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules


  vector<ZConsParaItem>* parameters; //

  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels

  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
  vector<double> fz;
  vector<double> curZPos;

  bool usingSMD;
  vector<double> prevCantPos;
  vector<double> cantPos;
  vector<double> cantVel;

  double zconsFixTime;  
  double zconsGap;
  bool hasZConsGap;
  vector<double> endFixTime;
  
  int whichDirection;                           //constraint direction

private:

  string zconsOutput;                         //filename of zconstraint output
  ZConsWriter* fzOut;                         //z-constraint writer

  double curZconsTime;

  double calcMovingMolsCOMVel();
  double calcSysCOMVel();
  double calcTotalForce();
  void updateZPos();
  void updateCantPos();
  
  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
  friend class ForceSubtractionPolicy;

};

/*
template<typename T> class SingleZConstrain : public T{


};
*/

template<typename T> class NonEquMD : public T {
  public:
    

};


//
template<typename T> class SingleZConstraint : public T{
  public:
    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
    ~SingleZConstraint();
    
    bool stopIntegrator();
    
  protected:
    
};

//Steered Molecular Dynamics, curret implement only support one steered molecule
 template<typename T> class SMD : public T{
  public:
    SMD( SimInfo *theInfo, ForceFields* the_ff);
    ~SMD();
  
    virtual void integrate();
    virtual void calcForce( int calcPot, int calcStress );  
    bool stopIntegrator();
  private:
    
};

//By using state pattern, Coordinate Drive is responsible for switching back and forth between
//Driven Molecular Dynamics and ZConstraint Method. 
template<typename T> class CoordinateDriver : public T {
  public:
    typedef T ParentIntegrator;

    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
    ~CoordinateDriver();
    
    virtual void integrate();

  private:    
    BaseIntegrator* zconsIntegrator;
    BaseIntegrator* drivenIntegrator;
    
};

#endif
Revision:	1141
Committed:	Wed Apr 28 23:09:32 2004 UTC (20 years, 2 months ago) by tim
File size:	14290 byte(s)
Log Message:	keep the previous position of cantilever in SMD
#	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	1097	#include "StuntDouble.hpp"
8	gezelter	604	#include "Molecule.hpp"
9	mmeineke	377	#include "SRI.hpp"
10			#include "AbstractClasses.hpp"
11			#include "SimInfo.hpp"
12			#include "ForceFields.hpp"
13	mmeineke	540	#include "Thermo.hpp"
14			#include "ReadWrite.hpp"
15	tim	658	#include "ZConsWriter.hpp"
16	mmeineke	377
17	tim	658	using namespace std;
18	mmeineke	561	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
19			const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
20	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
21	mmeineke	561	const int maxIteration = 300;
22			const double tol = 1.0e-6;
23
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	tim	837	virtual string getAdditionalParameters(void);
32	mmeineke	377
33	mmeineke	540	protected:
34	mmeineke	778
35	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
36	mmeineke	548	virtual void preMove( void );
37	mmeineke	540	virtual void moveA( void );
38			virtual void moveB( void );
39			virtual void constrainA( void );
40			virtual void constrainB( void );
41	mmeineke	559	virtual int readyCheck( void ) { return 1; }
42	tim	677
43	mmeineke	746	virtual void resetIntegrator( void ) { }
44	tim	837
45			virtual void calcForce( int calcPot, int calcStress );
46	tim	677	virtual void thermalize();
47	tim	837
48	tim	1108	virtual bool stopIntegrator() {return false;}
49
50	gezelter	1097	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
51	mmeineke	778
52	mmeineke	540	void checkConstraints( void );
53	tim	837	void rotate( int axes1, int axes2, double angle, double j[3],
54	tim	701	double A[3][3] );
55	tim	837
56	mmeineke	377	ForceFields* myFF;
57
58	mmeineke	540	SimInfo *info; // all the info we'll ever need
59	gezelter	1097	vector<StuntDouble*> integrableObjects;
60	mmeineke	540	int nAtoms; /* the number of atoms */
61	mmeineke	548	int oldAtoms;
62	mmeineke	540	Atom *atoms; / array of atom pointers */
63	mmeineke	423	Molecule* molecules;
64			int nMols;
65
66	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
67	tim	701	// constraints.
68	tim	837	int nConstrained; // counter for number of constraints
69			int *constrainedA; // the i of a constraint pair
70			int *constrainedB; // the j of a constraint pair
71			double *constrainedDsqr; // the square of the constraint distance
72
73	mmeineke	548	int* moving; // tells whether we are moving atom i
74			int* moved; // tells whether we have moved atom i
75	tim	837	double* oldPos; // pre constrained positions
76	mmeineke	548
77	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
78	tim	837
79	mmeineke	540	double dt;
80	mmeineke	541	double dt2;
81	gezelter	560
82	mmeineke	540	Thermo *tStats;
83			StatWriter* statOut;
84			DumpWriter* dumpOut;
85	tim	837
86	mmeineke	377	};
87
88	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
89	mmeineke	540
90	tim	645	template<typename T> class NVE : public T {
91
92	mmeineke	561	public:
93			NVE ( SimInfo theInfo, ForceFields the_ff ):
94	tim	645	T( theInfo, the_ff ){}
95	tim	837	virtual ~NVE(){}
96	tim	645	};
97	mmeineke	555
98
99	tim	645	template<typename T> class NVT : public T {
100	mmeineke	555
101	gezelter	560	public:
102
103	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
104	tim	763	virtual ~NVT();
105	mmeineke	540
106	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
107			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
108	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
109			virtual double getConservedQuantity(void);
110	tim	837	virtual string getAdditionalParameters(void);
111	gezelter	560
112	mmeineke	540	protected:
113	gezelter	560
114	mmeineke	561	virtual void moveA( void );
115			virtual void moveB( void );
116	mmeineke	540
117	mmeineke	561	virtual int readyCheck();
118	gezelter	560
119	mmeineke	746	virtual void resetIntegrator( void );
120
121	gezelter	565	// chi is a propagated degree of freedom.
122	gezelter	560
123	gezelter	565	double chi;
124	gezelter	560
125	tim	763	//integral of chi(t)dt
126			double integralOfChidt;
127
128	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
129	gezelter	560
130			double targetTemp;
131			double tauThermostat;
132	tim	837
133	gezelter	565	short int have_tau_thermostat, have_target_temp;
134	gezelter	560
135	tim	763	double *oldVel;
136			double *oldJi;
137
138			double chiTolerance;
139			short int have_chi_tolerance;
140
141	mmeineke	540	};
142
143
144
145	mmeineke	778	template<typename T> class NPT : public T{
146	tim	645
147	gezelter	560	public:
148
149	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
150			virtual ~NPT();
151	tim	837
152	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
153			calcStress = 1;
154	tim	645	T::integrateStep( calcPot, calcStress );
155	mmeineke	594	}
156
157	mmeineke	778	virtual double getConservedQuantity(void) = 0;
158	tim	837	virtual string getAdditionalParameters(void) = 0;
159	mmeineke	843
160			double myTauThermo( void ) { return tauThermostat; }
161			double myTauBaro( void ) { return tauBarostat; }
162
163	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
164			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
165			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
166			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
167	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
168			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
169			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
170	gezelter	560
171			protected:
172
173	mmeineke	561	virtual void moveA( void );
174			virtual void moveB( void );
175	gezelter	560
176	mmeineke	561	virtual int readyCheck();
177	gezelter	560
178	mmeineke	746	virtual void resetIntegrator( void );
179
180	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
181			virtual void getVelScaleB( double sc[3], int index ) = 0;
182	tim	837	virtual void getPosScale(double pos[3], double COM[3],
183	mmeineke	778	int index, double sc[3]) = 0;
184
185	mmeineke	857	virtual void calcVelScale( void ) = 0;
186
187	mmeineke	778	virtual bool chiConverged( void );
188			virtual bool etaConverged( void ) = 0;
189	tim	837
190	mmeineke	778	virtual void evolveChiA( void );
191			virtual void evolveEtaA( void ) = 0;
192			virtual void evolveChiB( void );
193			virtual void evolveEtaB( void ) = 0;
194
195			virtual void scaleSimBox( void ) = 0;
196
197	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
198
199	gezelter	565	// chi and eta are the propagated degrees of freedom
200	gezelter	560
201	mmeineke	778	double oldChi;
202			double prevChi;
203	gezelter	565	double chi;
204	gezelter	574	double NkBT;
205	tim	763	double fkBT;
206	gezelter	560
207	mmeineke	778	double tt2, tb2;
208			double instaTemp, instaPress, instaVol;
209	mmeineke	780	double press[3][3];
210	mmeineke	778
211	tim	763	int Nparticles;
212
213			double integralOfChidt;
214
215	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
216	gezelter	560	// One of qmass or tauThermostat must be set;
217
218			double targetTemp;
219			double targetPressure;
220			double tauThermostat;
221			double tauBarostat;
222
223			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
224	gezelter	565	short int have_target_pressure;
225	gezelter	560
226	tim	763	double *oldPos;
227			double *oldVel;
228			double *oldJi;
229
230			double chiTolerance;
231			short int have_chi_tolerance;
232			double posIterTolerance;
233			short int have_pos_iter_tolerance;
234			double etaTolerance;
235			short int have_eta_tolerance;
236
237	gezelter	560	};
238
239	mmeineke	778	template<typename T> class NPTi : public T{
240	tim	837
241	mmeineke	778	public:
242			NPTi( SimInfo theInfo, ForceFields the_ff);
243			~NPTi();
244
245			virtual double getConservedQuantity(void);
246			virtual void resetIntegrator(void);
247	tim	837	virtual string getAdditionalParameters(void);
248	mmeineke	778	protected:
249
250
251	tim	837
252	mmeineke	778	virtual void evolveEtaA(void);
253			virtual void evolveEtaB(void);
254
255			virtual bool etaConverged( void );
256
257			virtual void scaleSimBox( void );
258
259			virtual void getVelScaleA( double sc[3], double vel[3] );
260			virtual void getVelScaleB( double sc[3], int index );
261	tim	837	virtual void getPosScale(double pos[3], double COM[3],
262	mmeineke	778	int index, double sc[3]);
263
264	mmeineke	857	virtual void calcVelScale( void );
265
266	mmeineke	778	double eta, oldEta, prevEta;
267	mmeineke	857	double vScale;
268	mmeineke	778	};
269
270	tim	645	template<typename T> class NPTf : public T{
271	gezelter	576
272			public:
273
274			NPTf ( SimInfo theInfo, ForceFields the_ff);
275	tim	767	virtual ~NPTf();
276	gezelter	576
277	tim	763	virtual double getConservedQuantity(void);
278	tim	837	virtual string getAdditionalParameters(void);
279	mmeineke	780	virtual void resetIntegrator(void);
280	mmeineke	594
281	gezelter	576	protected:
282
283	mmeineke	780	virtual void evolveEtaA(void);
284			virtual void evolveEtaB(void);
285	gezelter	576
286	mmeineke	780	virtual bool etaConverged( void );
287	mmeineke	746
288	mmeineke	780	virtual void scaleSimBox( void );
289	gezelter	576
290	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
291			virtual void getVelScaleB( double sc[3], int index );
292	tim	837	virtual void getPosScale(double pos[3], double COM[3],
293	mmeineke	780	int index, double sc[3]);
294	tim	763
295	mmeineke	857	virtual void calcVelScale( void );
296
297	gezelter	588	double eta[3][3];
298	mmeineke	780	double oldEta[3][3];
299			double prevEta[3][3];
300	mmeineke	857	double vScale[3][3];
301	gezelter	576	};
302
303	mmeineke	812	template<typename T> class NPTxyz : public T{
304	mmeineke	755
305			public:
306
307	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
308			virtual ~NPTxyz();
309	mmeineke	755
310	mmeineke	812	virtual double getConservedQuantity(void);
311	tim	837	virtual string getAdditionalParameters(void);
312	mmeineke	812	virtual void resetIntegrator(void);
313	mmeineke	755
314			protected:
315
316	mmeineke	812	virtual void evolveEtaA(void);
317			virtual void evolveEtaB(void);
318	mmeineke	755
319	mmeineke	812	virtual bool etaConverged( void );
320	mmeineke	755
321	mmeineke	812	virtual void scaleSimBox( void );
322	mmeineke	755
323	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
324			virtual void getVelScaleB( double sc[3], int index );
325	tim	837	virtual void getPosScale(double pos[3], double COM[3],
326	mmeineke	812	int index, double sc[3]);
327	mmeineke	755
328	mmeineke	857	virtual void calcVelScale( void );
329
330	mmeineke	812	double eta[3][3];
331			double oldEta[3][3];
332			double prevEta[3][3];
333	mmeineke	857	double vScale[3][3];
334	mmeineke	812	};
335	mmeineke	755
336
337	tim	658	template<typename T> class ZConstraint : public T {
338	tim	837
339			public:
340	tim	738	class ForceSubtractionPolicy{
341	tim	699	public:
342	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
343	tim	658
344	tim	837	virtual void update() = 0;
345	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
347	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
348			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
349	tim	837
350	tim	701	protected:
351	mmeineke	788	ZConstraint<T>* zconsIntegrator;
352	tim	699	};
353
354	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
355	gezelter	747
356	tim	699	public:
357	tim	837	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358			virtual void update();
359	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
360			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
361	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
362			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
363	tim	837
364	tim	699	private:
365	tim	763	int totNumOfMovingAtoms;
366	tim	699	};
367
368	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
369	gezelter	747
370	tim	699	public:
371	tim	837	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
372
373			virtual void update();
374	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
375			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
376	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
377			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
378	tim	699
379	tim	701	private:
380			double totMassOfMovingAtoms;
381	tim	699	};
382
383	tim	658	public:
384
385			ZConstraint( SimInfo theInfo, ForceFields the_ff);
386			~ZConstraint();
387	tim	837
388	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
389			void getZConsTime() {return zconsTime;}
390	tim	837
391	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
392			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
393	tim	837
394	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
395	tim	658	string getZConsOutput() {return zconsOutput;}
396	tim	837
397	tim	677	virtual void integrate();
398	tim	658
399	tim	837
400	tim	658	#ifdef IS_MPI
401	tim	701	virtual void update(); //which is called to indicate the molecules' migration
402	mmeineke	377	#endif
403	tim	658
404	tim	837	enum ZConsState {zcsMoving, zcsFixed};
405	mmeineke	790
406			vector<Molecule*> zconsMols; //z-constraint molecules array
407			vector<ZConsState> states; //state of z-constraint molecules
408
409
410	tim	837
411	mmeineke	790	int totNumOfUnconsAtoms; //total number of uncontraint atoms
412			double totalMassOfUncons; //total mas of unconstraint molecules
413
414
415	tim	658	protected:
416
417	mmeineke	790
418	tim	837
419			virtual void calcForce( int calcPot, int calcStress );
420	tim	677	virtual void thermalize(void);
421	tim	837
422	tim	677	void zeroOutVel();
423			void doZconstraintForce();
424	tim	1093	void doHarmonic(vector<double>& resPos);
425	tim	677	bool checkZConsState();
426
427			bool haveFixedZMols();
428			bool haveMovingZMols();
429
430			double calcZSys();
431
432			int isZConstraintMol(Molecule* mol);
433
434
435	tim	701	double zconsTime; //sample time
436			double zconsTol; //tolerance of z-contratint
437			double zForceConst; //base force constant term
438			//which is estimate by OOPSE
439	mmeineke	790
440	tim	837
441			vector<double> massOfZConsMols; //mass of z-constraint molecule
442	tim	701	vector<double> kz; //force constant array
443	mmeineke	790
444	tim	701	vector<double> zPos; //
445	tim	837
446
447	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
448			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
449	tim	682
450	mmeineke	790
451	tim	701	vector<ZConsParaItem>* parameters; //
452	tim	837
453	tim	658	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
454	tim	677
455	tim	1093	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
456			vector<double> fz;
457			vector<double> curZPos;
458	tim	677
459	tim	1093	bool usingSMD;
460	tim	1141	vector<double> prevCantPos;
461	tim	1093	vector<double> cantPos;
462			vector<double> cantVel;
463
464	tim	1091	double zconsFixTime;
465			double zconsGap;
466			bool hasZConsGap;
467			vector<double> endFixTime;
468
469	tim	837	int whichDirection; //constraint direction
470
471	tim	658	private:
472	tim	837
473	tim	701	string zconsOutput; //filename of zconstraint output
474			ZConsWriter* fzOut; //z-constraint writer
475	tim	677
476	tim	837	double curZconsTime;
477	tim	699
478	tim	696	double calcMovingMolsCOMVel();
479			double calcSysCOMVel();
480			double calcTotalForce();
481	tim	1091	void updateZPos();
482	tim	1093	void updateCantPos();
483
484	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
485	tim	738	friend class ForceSubtractionPolicy;
486	tim	677
487	tim	658	};
488
489	tim	1064	/*
490	tim	1108	template<typename T> class SingleZConstrain : public T{
491
492
493			};
494			*/
495
496			template<typename T> class NonEquMD : public T {
497			public:
498
499
500
501			};
502
503
504			//
505			template<typename T> class SingleZConstraint : public T{
506			public:
507			SingleZConstraint(SimInfo theInfo, ForceFields the_ff);
508			~SingleZConstraint();
509
510			bool stopIntegrator();
511
512			protected:
513
514			};
515
516			//Steered Molecular Dynamics, curret implement only support one steered molecule
517	tim	1091	template<typename T> class SMD : public T{
518	tim	969	public:
519	tim	1091	SMD( SimInfo theInfo, ForceFields the_ff);
520			~SMD();
521
522	tim	1108	virtual void integrate();
523			virtual void calcForce( int calcPot, int calcStress );
524			bool stopIntegrator();
525			private:
526
527	tim	969	};
528	tim	1108
529			//By using state pattern, Coordinate Drive is responsible for switching back and forth between
530			//Driven Molecular Dynamics and ZConstraint Method.
531			template<typename T> class CoordinateDriver : public T {
532			public:
533			typedef T ParentIntegrator;
534
535			CoordinateDriver(SimInfo, ForceFields, BaseIntegrator, BaseIntegrator);
536			~CoordinateDriver();
537
538			virtual void integrate();
539
540			private:
541			BaseIntegrator* zconsIntegrator;
542			BaseIntegrator* drivenIntegrator;
543
544			};
545
546	tim	658	#endif