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;

// ansi instantiation
template class Integrator<BaseIntegrator>;

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:	1161
Committed:	Tue May 11 21:44:05 2004 UTC (20 years, 1 month ago) by tim
File size:	14356 byte(s)
Log Message:	adding instantiation of Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8
#	Content
1	#ifndef _INTEGRATOR_H_
2	#define _INTEGRATOR_H_
3
4	#include <string>
5	#include <vector>
6	#include "Atom.hpp"
7	#include "StuntDouble.hpp"
8	#include "Molecule.hpp"
9	#include "SRI.hpp"
10	#include "AbstractClasses.hpp"
11	#include "SimInfo.hpp"
12	#include "ForceFields.hpp"
13	#include "Thermo.hpp"
14	#include "ReadWrite.hpp"
15	#include "ZConsWriter.hpp"
16
17	using namespace std;
18	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	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
21	const int maxIteration = 300;
22	const double tol = 1.0e-6;
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	virtual string getAdditionalParameters(void);
32
33	protected:
34
35	virtual void integrateStep( int calcPot, int calcStress );
36	virtual void preMove( void );
37	virtual void moveA( void );
38	virtual void moveB( void );
39	virtual void constrainA( void );
40	virtual void constrainB( void );
41	virtual int readyCheck( void ) { return 1; }
42
43	virtual void resetIntegrator( void ) { }
44
45	virtual void calcForce( int calcPot, int calcStress );
46	virtual void thermalize();
47
48	virtual bool stopIntegrator() {return false;}
49
50	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
51
52	void checkConstraints( void );
53	void rotate( int axes1, int axes2, double angle, double j[3],
54	double A[3][3] );
55
56	ForceFields* myFF;
57
58	SimInfo *info; // all the info we'll ever need
59	vector<StuntDouble*> integrableObjects;
60	int nAtoms; /* the number of atoms */
61	int oldAtoms;
62	Atom *atoms; / array of atom pointers */
63	Molecule* molecules;
64	int nMols;
65
66	int isConstrained; // boolean to know whether the systems contains
67	// constraints.
68	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	int* moving; // tells whether we are moving atom i
74	int* moved; // tells whether we have moved atom i
75	double* oldPos; // pre constrained positions
76
77	short isFirst; /boolean for the first time integrate is called /
78
79	double dt;
80	double dt2;
81
82	Thermo *tStats;
83	StatWriter* statOut;
84	DumpWriter* dumpOut;
85
86	};
87
88	typedef Integrator<BaseIntegrator> RealIntegrator;
89
90	// ansi instantiation
91	template class Integrator<BaseIntegrator>;
92
93	template<typename T> class NVE : public T {
94
95	public:
96	NVE ( SimInfo theInfo, ForceFields the_ff ):
97	T( theInfo, the_ff ){}
98	virtual ~NVE(){}
99	};
100
101
102	template<typename T> class NVT : public T {
103
104	public:
105
106	NVT ( SimInfo theInfo, ForceFields the_ff);
107	virtual ~NVT();
108
109	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
110	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
111	void setChiTolerance(double tol) {chiTolerance = tol;}
112	virtual double getConservedQuantity(void);
113	virtual string getAdditionalParameters(void);
114
115	protected:
116
117	virtual void moveA( void );
118	virtual void moveB( void );
119
120	virtual int readyCheck();
121
122	virtual void resetIntegrator( void );
123
124	// chi is a propagated degree of freedom.
125
126	double chi;
127
128	//integral of chi(t)dt
129	double integralOfChidt;
130
131	// targetTemp must be set. tauThermostat must also be set;
132
133	double targetTemp;
134	double tauThermostat;
135
136	short int have_tau_thermostat, have_target_temp;
137
138	double *oldVel;
139	double *oldJi;
140
141	double chiTolerance;
142	short int have_chi_tolerance;
143
144	};
145
146
147
148	template<typename T> class NPT : public T{
149
150	public:
151
152	NPT ( SimInfo theInfo, ForceFields the_ff);
153	virtual ~NPT();
154
155	virtual void integrateStep( int calcPot, int calcStress ){
156	calcStress = 1;
157	T::integrateStep( calcPot, calcStress );
158	}
159
160	virtual double getConservedQuantity(void) = 0;
161	virtual string getAdditionalParameters(void) = 0;
162
163	double myTauThermo( void ) { return tauThermostat; }
164	double myTauBaro( void ) { return tauBarostat; }
165
166	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
167	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
168	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
169	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
170	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
171	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
172	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
173
174	protected:
175
176	virtual void moveA( void );
177	virtual void moveB( void );
178
179	virtual int readyCheck();
180
181	virtual void resetIntegrator( void );
182
183	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
184	virtual void getVelScaleB( double sc[3], int index ) = 0;
185	virtual void getPosScale(double pos[3], double COM[3],
186	int index, double sc[3]) = 0;
187
188	virtual void calcVelScale( void ) = 0;
189
190	virtual bool chiConverged( void );
191	virtual bool etaConverged( void ) = 0;
192
193	virtual void evolveChiA( void );
194	virtual void evolveEtaA( void ) = 0;
195	virtual void evolveChiB( void );
196	virtual void evolveEtaB( void ) = 0;
197
198	virtual void scaleSimBox( void ) = 0;
199
200	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
201
202	// chi and eta are the propagated degrees of freedom
203
204	double oldChi;
205	double prevChi;
206	double chi;
207	double NkBT;
208	double fkBT;
209
210	double tt2, tb2;
211	double instaTemp, instaPress, instaVol;
212	double press[3][3];
213
214	int Nparticles;
215
216	double integralOfChidt;
217
218	// targetTemp, targetPressure, and tauBarostat must be set.
219	// One of qmass or tauThermostat must be set;
220
221	double targetTemp;
222	double targetPressure;
223	double tauThermostat;
224	double tauBarostat;
225
226	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
227	short int have_target_pressure;
228
229	double *oldPos;
230	double *oldVel;
231	double *oldJi;
232
233	double chiTolerance;
234	short int have_chi_tolerance;
235	double posIterTolerance;
236	short int have_pos_iter_tolerance;
237	double etaTolerance;
238	short int have_eta_tolerance;
239
240	};
241
242	template<typename T> class NPTi : public T{
243
244	public:
245	NPTi( SimInfo theInfo, ForceFields the_ff);
246	~NPTi();
247
248	virtual double getConservedQuantity(void);
249	virtual void resetIntegrator(void);
250	virtual string getAdditionalParameters(void);
251	protected:
252
253
254
255	virtual void evolveEtaA(void);
256	virtual void evolveEtaB(void);
257
258	virtual bool etaConverged( void );
259
260	virtual void scaleSimBox( void );
261
262	virtual void getVelScaleA( double sc[3], double vel[3] );
263	virtual void getVelScaleB( double sc[3], int index );
264	virtual void getPosScale(double pos[3], double COM[3],
265	int index, double sc[3]);
266
267	virtual void calcVelScale( void );
268
269	double eta, oldEta, prevEta;
270	double vScale;
271	};
272
273	template<typename T> class NPTf : public T{
274
275	public:
276
277	NPTf ( SimInfo theInfo, ForceFields the_ff);
278	virtual ~NPTf();
279
280	virtual double getConservedQuantity(void);
281	virtual string getAdditionalParameters(void);
282	virtual void resetIntegrator(void);
283
284	protected:
285
286	virtual void evolveEtaA(void);
287	virtual void evolveEtaB(void);
288
289	virtual bool etaConverged( void );
290
291	virtual void scaleSimBox( void );
292
293	virtual void getVelScaleA( double sc[3], double vel[3] );
294	virtual void getVelScaleB( double sc[3], int index );
295	virtual void getPosScale(double pos[3], double COM[3],
296	int index, double sc[3]);
297
298	virtual void calcVelScale( void );
299
300	double eta[3][3];
301	double oldEta[3][3];
302	double prevEta[3][3];
303	double vScale[3][3];
304	};
305
306	template<typename T> class NPTxyz : public T{
307
308	public:
309
310	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
311	virtual ~NPTxyz();
312
313	virtual double getConservedQuantity(void);
314	virtual string getAdditionalParameters(void);
315	virtual void resetIntegrator(void);
316
317	protected:
318
319	virtual void evolveEtaA(void);
320	virtual void evolveEtaB(void);
321
322	virtual bool etaConverged( void );
323
324	virtual void scaleSimBox( void );
325
326	virtual void getVelScaleA( double sc[3], double vel[3] );
327	virtual void getVelScaleB( double sc[3], int index );
328	virtual void getPosScale(double pos[3], double COM[3],
329	int index, double sc[3]);
330
331	virtual void calcVelScale( void );
332
333	double eta[3][3];
334	double oldEta[3][3];
335	double prevEta[3][3];
336	double vScale[3][3];
337	};
338
339
340	template<typename T> class ZConstraint : public T {
341
342	public:
343	class ForceSubtractionPolicy{
344	public:
345	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
346
347	virtual void update() = 0;
348	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
349	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
350	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
351	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
352
353	protected:
354	ZConstraint<T>* zconsIntegrator;
355	};
356
357	class PolicyByNumber : public ForceSubtractionPolicy{
358
359	public:
360	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
361	virtual void update();
362	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
363	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
364	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
365	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
366
367	private:
368	int totNumOfMovingAtoms;
369	};
370
371	class PolicyByMass : public ForceSubtractionPolicy{
372
373	public:
374	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
375
376	virtual void update();
377	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
378	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
379	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
380	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
381
382	private:
383	double totMassOfMovingAtoms;
384	};
385
386	public:
387
388	ZConstraint( SimInfo theInfo, ForceFields the_ff);
389	~ZConstraint();
390
391	void setZConsTime(double time) {this->zconsTime = time;}
392	void getZConsTime() {return zconsTime;}
393
394	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
395	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
396
397	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
398	string getZConsOutput() {return zconsOutput;}
399
400	virtual void integrate();
401
402
403	#ifdef IS_MPI
404	virtual void update(); //which is called to indicate the molecules' migration
405	#endif
406
407	enum ZConsState {zcsMoving, zcsFixed};
408
409	vector<Molecule*> zconsMols; //z-constraint molecules array
410	vector<ZConsState> states; //state of z-constraint molecules
411
412
413
414	int totNumOfUnconsAtoms; //total number of uncontraint atoms
415	double totalMassOfUncons; //total mas of unconstraint molecules
416
417
418	protected:
419
420
421
422	virtual void calcForce( int calcPot, int calcStress );
423	virtual void thermalize(void);
424
425	void zeroOutVel();
426	void doZconstraintForce();
427	void doHarmonic(vector<double>& resPos);
428	bool checkZConsState();
429
430	bool haveFixedZMols();
431	bool haveMovingZMols();
432
433	double calcZSys();
434
435	int isZConstraintMol(Molecule* mol);
436
437
438	double zconsTime; //sample time
439	double zconsTol; //tolerance of z-contratint
440	double zForceConst; //base force constant term
441	//which is estimate by OOPSE
442
443
444	vector<double> massOfZConsMols; //mass of z-constraint molecule
445	vector<double> kz; //force constant array
446
447	vector<double> zPos; //
448
449
450	vector<Molecule*> unconsMols; //unconstraint molecules array
451	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
452
453
454	vector<ZConsParaItem>* parameters; //
455
456	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
457
458	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
459	vector<double> fz;
460	vector<double> curZPos;
461
462	bool usingSMD;
463	vector<double> prevCantPos;
464	vector<double> cantPos;
465	vector<double> cantVel;
466
467	double zconsFixTime;
468	double zconsGap;
469	bool hasZConsGap;
470	vector<double> endFixTime;
471
472	int whichDirection; //constraint direction
473
474	private:
475
476	string zconsOutput; //filename of zconstraint output
477	ZConsWriter* fzOut; //z-constraint writer
478
479	double curZconsTime;
480
481	double calcMovingMolsCOMVel();
482	double calcSysCOMVel();
483	double calcTotalForce();
484	void updateZPos();
485	void updateCantPos();
486
487	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
488	friend class ForceSubtractionPolicy;
489
490	};
491
492	/*
493	template<typename T> class SingleZConstrain : public T{
494
495
496	};
497	*/
498
499	template<typename T> class NonEquMD : public T {
500	public:
501
502
503
504	};
505
506
507	//
508	template<typename T> class SingleZConstraint : public T{
509	public:
510	SingleZConstraint(SimInfo theInfo, ForceFields the_ff);
511	~SingleZConstraint();
512
513	bool stopIntegrator();
514
515	protected:
516
517	};
518
519	//Steered Molecular Dynamics, curret implement only support one steered molecule
520	template<typename T> class SMD : public T{
521	public:
522	SMD( SimInfo theInfo, ForceFields the_ff);
523	~SMD();
524
525	virtual void integrate();
526	virtual void calcForce( int calcPot, int calcStress );
527	bool stopIntegrator();
528	private:
529
530	};
531
532	//By using state pattern, Coordinate Drive is responsible for switching back and forth between
533	//Driven Molecular Dynamics and ZConstraint Method.
534	template<typename T> class CoordinateDriver : public T {
535	public:
536	typedef T ParentIntegrator;
537
538	CoordinateDriver(SimInfo, ForceFields, BaseIntegrator, BaseIntegrator);
539	~CoordinateDriver();
540
541	virtual void integrate();
542
543	private:
544	BaseIntegrator* zconsIntegrator;
545	BaseIntegrator* drivenIntegrator;
546
547	};
548
549	#endif