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;


class Integrator : public BaseIntegrator {

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;
  
};

class NVE : public Integrator {

public:
  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
    T( theInfo, the_ff ){}
  virtual ~NVE(){}  
};


class NVT : public Integrator {

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;

};


class NPT : public Integrator{

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;

};

class NPTi : public NPT{
  
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;
};

class NPTf : public NPT{

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];
};

class NPTxyz : public NPT{

public:

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

  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 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();
//   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

//   int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
//   double* fz;
//   double* curZPos;
  

//   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:	833
Committed:	Tue Oct 28 17:08:18 2003 UTC (21 years, 6 months ago) by mmeineke
File size:	12338 byte(s)
Log Message:	started work on template removal
#	Content
1	#ifndef _INTEGRATOR_H_
2	#define _INTEGRATOR_H_
3
4	#include <string>
5	// #include <vector>
6	#include "Atom.hpp"
7	#include "Molecule.hpp"
8	#include "SRI.hpp"
9	#include "AbstractClasses.hpp"
10	#include "SimInfo.hpp"
11	#include "ForceFields.hpp"
12	#include "Thermo.hpp"
13	#include "ReadWrite.hpp"
14	// #include "ZConsWriter.hpp"
15
16	using namespace std;
17	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
18	const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
20	const int maxIteration = 300;
21	const double tol = 1.0e-6;
22
23
24	class Integrator : public BaseIntegrator {
25
26	public:
27	Integrator( SimInfo theInfo, ForceFields the_ff );
28	virtual ~Integrator();
29	void integrate( void );
30	virtual double getConservedQuantity(void);
31
32	protected:
33
34	virtual void integrateStep( int calcPot, int calcStress );
35	virtual void preMove( void );
36	virtual void moveA( void );
37	virtual void moveB( void );
38	virtual void constrainA( void );
39	virtual void constrainB( void );
40	virtual int readyCheck( void ) { return 1; }
41
42	virtual void resetIntegrator( void ) { }
43
44	virtual void calcForce( int calcPot, int calcStress );
45	virtual void thermalize();
46
47	virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48
49	void checkConstraints( void );
50	void rotate( int axes1, int axes2, double angle, double j[3],
51	double A[3][3] );
52
53	ForceFields* myFF;
54
55	SimInfo *info; // all the info we'll ever need
56	int nAtoms; /* the number of atoms */
57	int oldAtoms;
58	Atom *atoms; / array of atom pointers */
59	Molecule* molecules;
60	int nMols;
61
62	int isConstrained; // boolean to know whether the systems contains
63	// constraints.
64	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	double* oldPos; // pre constrained positions
72
73	short isFirst; /boolean for the first time integrate is called /
74
75	double dt;
76	double dt2;
77
78	Thermo *tStats;
79	StatWriter* statOut;
80	DumpWriter* dumpOut;
81
82	};
83
84	class NVE : public Integrator {
85
86	public:
87	NVE ( SimInfo theInfo, ForceFields the_ff ):
88	T( theInfo, the_ff ){}
89	virtual ~NVE(){}
90	};
91
92
93	class NVT : public Integrator {
94
95	public:
96
97	NVT ( SimInfo theInfo, ForceFields the_ff);
98	virtual ~NVT();
99
100	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
101	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
102	void setChiTolerance(double tol) {chiTolerance = tol;}
103	virtual double getConservedQuantity(void);
104
105	protected:
106
107	virtual void moveA( void );
108	virtual void moveB( void );
109
110	virtual int readyCheck();
111
112	virtual void resetIntegrator( void );
113
114	// chi is a propagated degree of freedom.
115
116	double chi;
117
118	//integral of chi(t)dt
119	double integralOfChidt;
120
121	// targetTemp must be set. tauThermostat must also be set;
122
123	double targetTemp;
124	double tauThermostat;
125
126	short int have_tau_thermostat, have_target_temp;
127
128	double *oldVel;
129	double *oldJi;
130
131	double chiTolerance;
132	short int have_chi_tolerance;
133
134	};
135
136
137
138	class NPT : public Integrator{
139
140	public:
141
142	NPT ( SimInfo theInfo, ForceFields the_ff);
143	virtual ~NPT();
144
145	virtual void integrateStep( int calcPot, int calcStress ){
146	calcStress = 1;
147	T::integrateStep( calcPot, calcStress );
148	}
149
150	virtual double getConservedQuantity(void) = 0;
151
152	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
153	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
154	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
155	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
156	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
157	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
158	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
159
160	protected:
161
162	virtual void moveA( void );
163	virtual void moveB( void );
164
165	virtual int readyCheck();
166
167	virtual void resetIntegrator( void );
168
169	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
170	virtual void getVelScaleB( double sc[3], int index ) = 0;
171	virtual void getPosScale(double pos[3], double COM[3],
172	int index, double sc[3]) = 0;
173
174	virtual bool chiConverged( void );
175	virtual bool etaConverged( void ) = 0;
176
177	virtual void evolveChiA( void );
178	virtual void evolveEtaA( void ) = 0;
179	virtual void evolveChiB( void );
180	virtual void evolveEtaB( void ) = 0;
181
182	virtual void scaleSimBox( void ) = 0;
183
184	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
185
186	// chi and eta are the propagated degrees of freedom
187
188	double oldChi;
189	double prevChi;
190	double chi;
191	double NkBT;
192	double fkBT;
193
194	double tt2, tb2;
195	double instaTemp, instaPress, instaVol;
196	double press[3][3];
197
198	int Nparticles;
199
200	double integralOfChidt;
201
202	// targetTemp, targetPressure, and tauBarostat must be set.
203	// One of qmass or tauThermostat must be set;
204
205	double targetTemp;
206	double targetPressure;
207	double tauThermostat;
208	double tauBarostat;
209
210	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
211	short int have_target_pressure;
212
213	double *oldPos;
214	double *oldVel;
215	double *oldJi;
216
217	double chiTolerance;
218	short int have_chi_tolerance;
219	double posIterTolerance;
220	short int have_pos_iter_tolerance;
221	double etaTolerance;
222	short int have_eta_tolerance;
223
224	};
225
226	class NPTi : public NPT{
227
228	public:
229	NPTi( SimInfo theInfo, ForceFields the_ff);
230	~NPTi();
231
232	virtual double getConservedQuantity(void);
233	virtual void resetIntegrator(void);
234
235	protected:
236
237
238
239	virtual void evolveEtaA(void);
240	virtual void evolveEtaB(void);
241
242	virtual bool etaConverged( void );
243
244	virtual void scaleSimBox( void );
245
246	virtual void getVelScaleA( double sc[3], double vel[3] );
247	virtual void getVelScaleB( double sc[3], int index );
248	virtual void getPosScale(double pos[3], double COM[3],
249	int index, double sc[3]);
250
251	double eta, oldEta, prevEta;
252	};
253
254	class NPTf : public NPT{
255
256	public:
257
258	NPTf ( SimInfo theInfo, ForceFields the_ff);
259	virtual ~NPTf();
260
261	virtual double getConservedQuantity(void);
262	virtual void resetIntegrator(void);
263
264	protected:
265
266	virtual void evolveEtaA(void);
267	virtual void evolveEtaB(void);
268
269	virtual bool etaConverged( void );
270
271	virtual void scaleSimBox( void );
272
273	virtual void getVelScaleA( double sc[3], double vel[3] );
274	virtual void getVelScaleB( double sc[3], int index );
275	virtual void getPosScale(double pos[3], double COM[3],
276	int index, double sc[3]);
277
278	double eta[3][3];
279	double oldEta[3][3];
280	double prevEta[3][3];
281	};
282
283	class NPTxyz : public NPT{
284
285	public:
286
287	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
288	virtual ~NPTxyz();
289
290	virtual double getConservedQuantity(void);
291	virtual void resetIntegrator(void);
292
293	protected:
294
295	virtual void evolveEtaA(void);
296	virtual void evolveEtaB(void);
297
298	virtual bool etaConverged( void );
299
300	virtual void scaleSimBox( void );
301
302	virtual void getVelScaleA( double sc[3], double vel[3] );
303	virtual void getVelScaleB( double sc[3], int index );
304	virtual void getPosScale(double pos[3], double COM[3],
305	int index, double sc[3]);
306
307	double eta[3][3];
308	double oldEta[3][3];
309	double prevEta[3][3];
310	};
311
312
313	// template<typename T> class ZConstraint : public T {
314
315	// public:
316	// class ForceSubtractionPolicy{
317	// public:
318	// ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
319
320	// virtual void update() = 0;
321	// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
322	// virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
323	// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
324	// virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
325
326	// protected:
327	// ZConstraint<T>* zconsIntegrator;
328	// };
329
330	// class PolicyByNumber : public ForceSubtractionPolicy{
331
332	// public:
333	// PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
334	// virtual void update();
335	// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
336	// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
337	// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
338	// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
339
340	// private:
341	// int totNumOfMovingAtoms;
342	// };
343
344	// class PolicyByMass : public ForceSubtractionPolicy{
345
346	// public:
347	// PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
348
349	// virtual void update();
350	// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
351	// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
352	// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
353	// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
354
355	// private:
356	// double totMassOfMovingAtoms;
357	// };
358
359	// public:
360
361	// ZConstraint( SimInfo theInfo, ForceFields the_ff);
362	// ~ZConstraint();
363
364	// void setZConsTime(double time) {this->zconsTime = time;}
365	// void getZConsTime() {return zconsTime;}
366
367	// void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
368	// void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
369
370	// void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
371	// string getZConsOutput() {return zconsOutput;}
372
373	// virtual void integrate();
374
375
376	// #ifdef IS_MPI
377	// virtual void update(); //which is called to indicate the molecules' migration
378	// #endif
379
380	// enum ZConsState {zcsMoving, zcsFixed};
381
382	// vector<Molecule*> zconsMols; //z-constraint molecules array
383	// vector<ZConsState> states; //state of z-constraint molecules
384
385
386
387	// int totNumOfUnconsAtoms; //total number of uncontraint atoms
388	// double totalMassOfUncons; //total mas of unconstraint molecules
389
390
391	// protected:
392
393
394
395	// virtual void calcForce( int calcPot, int calcStress );
396	// virtual void thermalize(void);
397
398	// void zeroOutVel();
399	// void doZconstraintForce();
400	// void doHarmonic();
401	// bool checkZConsState();
402
403	// bool haveFixedZMols();
404	// bool haveMovingZMols();
405
406	// double calcZSys();
407
408	// int isZConstraintMol(Molecule* mol);
409
410
411	// double zconsTime; //sample time
412	// double zconsTol; //tolerance of z-contratint
413	// double zForceConst; //base force constant term
414	// //which is estimate by OOPSE
415
416
417	// vector<double> massOfZConsMols; //mass of z-constraint molecule
418	// vector<double> kz; //force constant array
419
420	// vector<double> zPos; //
421
422
423	// vector<Molecule*> unconsMols; //unconstraint molecules array
424	// vector<double> massOfUnconsMols; //mass array of unconstraint molecules
425
426
427	// vector<ZConsParaItem>* parameters; //
428
429	// vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
430
431	// int* indexOfZConsMols; //index of local Z-Constraint Molecules
432	// double* fz;
433	// double* curZPos;
434
435
436
437	// int whichDirection; //constraint direction
438
439	// private:
440
441	// string zconsOutput; //filename of zconstraint output
442	// ZConsWriter* fzOut; //z-constraint writer
443
444	// double curZconsTime;
445
446	// double calcMovingMolsCOMVel();
447	// double calcSysCOMVel();
448	// double calcTotalForce();
449
450	// ForceSubtractionPolicy* forcePolicy; //force subtraction policy
451	// friend class ForceSubtractionPolicy;
452
453	// };
454
455	#endif