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);
  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 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 ):
    Integrator( 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);
  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;

};


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;
  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 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);
  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]);

  double eta, oldEta, prevEta;
};

class NPTf : public NPT{

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]);

  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 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]);

  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:	849
Committed:	Fri Oct 31 21:06:47 2003 UTC (21 years, 8 months ago) by mmeineke
File size:	12607 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	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 void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
49
50	void checkConstraints( void );
51	void rotate( int axes1, int axes2, double angle, double j[3],
52	double A[3][3] );
53
54	ForceFields* myFF;
55
56	SimInfo *info; // all the info we'll ever need
57	int nAtoms; /* the number of atoms */
58	int oldAtoms;
59	Atom *atoms; / array of atom pointers */
60	Molecule* molecules;
61	int nMols;
62
63	int isConstrained; // boolean to know whether the systems contains
64	// constraints.
65	int nConstrained; // counter for number of constraints
66	int *constrainedA; // the i of a constraint pair
67	int *constrainedB; // the j of a constraint pair
68	double *constrainedDsqr; // the square of the constraint distance
69
70	int* moving; // tells whether we are moving atom i
71	int* moved; // tells whether we have moved atom i
72	double* oldPos; // pre constrained positions
73
74	short isFirst; /boolean for the first time integrate is called /
75
76	double dt;
77	double dt2;
78
79	Thermo *tStats;
80	StatWriter* statOut;
81	DumpWriter* dumpOut;
82
83	};
84
85	class NVE : public Integrator {
86
87	public:
88	NVE ( SimInfo theInfo, ForceFields the_ff ):
89	Integrator( theInfo, the_ff ){}
90	virtual ~NVE(){}
91	};
92
93
94	class NVT : public Integrator {
95
96	public:
97
98	NVT ( SimInfo theInfo, ForceFields the_ff);
99	virtual ~NVT();
100
101	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
102	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
103	void setChiTolerance(double tol) {chiTolerance = tol;}
104	virtual double getConservedQuantity(void);
105	virtual string getAdditionalParameters(void);
106
107	protected:
108
109	virtual void moveA( void );
110	virtual void moveB( void );
111
112	virtual int readyCheck();
113
114	virtual void resetIntegrator( void );
115
116	// chi is a propagated degree of freedom.
117
118	double chi;
119
120	//integral of chi(t)dt
121	double integralOfChidt;
122
123	// targetTemp must be set. tauThermostat must also be set;
124
125	double targetTemp;
126	double tauThermostat;
127
128	short int have_tau_thermostat, have_target_temp;
129
130	double *oldVel;
131	double *oldJi;
132
133	double chiTolerance;
134	short int have_chi_tolerance;
135
136	};
137
138
139
140	class NPT : public Integrator{
141
142	public:
143
144	NPT ( SimInfo theInfo, ForceFields the_ff);
145	virtual ~NPT();
146
147	virtual void integrateStep( int calcPot, int calcStress ){
148	calcStress = 1;
149	T::integrateStep( calcPot, calcStress );
150	}
151
152	virtual double getConservedQuantity(void) = 0;
153	virtual string getAdditionalParameters(void) = 0;
154
155	double myTauThermo( void ) { return tauThermostat; }
156	double myTauBaro( void ) { return tauBarostat; }
157
158	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
159	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
160	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
161	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
162	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
163	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
164	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
165
166	protected:
167
168	virtual void moveA( void );
169	virtual void moveB( void );
170
171	virtual int readyCheck();
172
173	virtual void resetIntegrator( void );
174
175	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
176	virtual void getVelScaleB( double sc[3], int index ) = 0;
177	virtual void getPosScale(double pos[3], double COM[3],
178	int index, double sc[3]) = 0;
179
180	virtual bool chiConverged( void );
181	virtual bool etaConverged( void ) = 0;
182
183	virtual void evolveChiA( void );
184	virtual void evolveEtaA( void ) = 0;
185	virtual void evolveChiB( void );
186	virtual void evolveEtaB( void ) = 0;
187
188	virtual void scaleSimBox( void ) = 0;
189
190	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
191
192	// chi and eta are the propagated degrees of freedom
193
194	double oldChi;
195	double prevChi;
196	double chi;
197	double NkBT;
198	double fkBT;
199
200	double tt2, tb2;
201	double instaTemp, instaPress, instaVol;
202	double press[3][3];
203
204	int Nparticles;
205
206	double integralOfChidt;
207
208	// targetTemp, targetPressure, and tauBarostat must be set.
209	// One of qmass or tauThermostat must be set;
210
211	double targetTemp;
212	double targetPressure;
213	double tauThermostat;
214	double tauBarostat;
215
216	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
217	short int have_target_pressure;
218
219	double *oldPos;
220	double *oldVel;
221	double *oldJi;
222
223	double chiTolerance;
224	short int have_chi_tolerance;
225	double posIterTolerance;
226	short int have_pos_iter_tolerance;
227	double etaTolerance;
228	short int have_eta_tolerance;
229
230	};
231
232	class NPTi : public NPT{
233
234	public:
235	NPTi( SimInfo theInfo, ForceFields the_ff);
236	~NPTi();
237
238	virtual double getConservedQuantity(void);
239	virtual void resetIntegrator(void);
240	virtual string getAdditionalParameters(void);
241	protected:
242
243
244
245	virtual void evolveEtaA(void);
246	virtual void evolveEtaB(void);
247
248	virtual bool etaConverged( void );
249
250	virtual void scaleSimBox( void );
251
252	virtual void getVelScaleA( double sc[3], double vel[3] );
253	virtual void getVelScaleB( double sc[3], int index );
254	virtual void getPosScale(double pos[3], double COM[3],
255	int index, double sc[3]);
256
257	double eta, oldEta, prevEta;
258	};
259
260	class NPTf : public NPT{
261
262	public:
263
264	NPTf ( SimInfo theInfo, ForceFields the_ff);
265	virtual ~NPTf();
266
267	virtual double getConservedQuantity(void);
268	virtual string getAdditionalParameters(void);
269	virtual void resetIntegrator(void);
270
271	protected:
272
273	virtual void evolveEtaA(void);
274	virtual void evolveEtaB(void);
275
276	virtual bool etaConverged( void );
277
278	virtual void scaleSimBox( void );
279
280	virtual void getVelScaleA( double sc[3], double vel[3] );
281	virtual void getVelScaleB( double sc[3], int index );
282	virtual void getPosScale(double pos[3], double COM[3],
283	int index, double sc[3]);
284
285	double eta[3][3];
286	double oldEta[3][3];
287	double prevEta[3][3];
288	};
289
290	class NPTxyz : public NPT{
291
292	public:
293
294	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
295	virtual ~NPTxyz();
296
297	virtual double getConservedQuantity(void);
298	virtual string getAdditionalParameters(void);
299	virtual void resetIntegrator(void);
300
301	protected:
302
303	virtual void evolveEtaA(void);
304	virtual void evolveEtaB(void);
305
306	virtual bool etaConverged( void );
307
308	virtual void scaleSimBox( void );
309
310	virtual void getVelScaleA( double sc[3], double vel[3] );
311	virtual void getVelScaleB( double sc[3], int index );
312	virtual void getPosScale(double pos[3], double COM[3],
313	int index, double sc[3]);
314
315	double eta[3][3];
316	double oldEta[3][3];
317	double prevEta[3][3];
318	};
319
320
321	// template<typename T> class ZConstraint : public T {
322
323	// public:
324	// class ForceSubtractionPolicy{
325	// public:
326	// ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
327
328	// virtual void update() = 0;
329	// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
330	// virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
331	// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
332	// virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
333
334	// protected:
335	// ZConstraint<T>* zconsIntegrator;
336	// };
337
338	// class PolicyByNumber : public ForceSubtractionPolicy{
339
340	// public:
341	// PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
342	// virtual void update();
343	// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
344	// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
345	// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
346	// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
347
348	// private:
349	// int totNumOfMovingAtoms;
350	// };
351
352	// class PolicyByMass : public ForceSubtractionPolicy{
353
354	// public:
355	// PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
356
357	// virtual void update();
358	// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
359	// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
360	// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
361	// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
362
363	// private:
364	// double totMassOfMovingAtoms;
365	// };
366
367	// public:
368
369	// ZConstraint( SimInfo theInfo, ForceFields the_ff);
370	// ~ZConstraint();
371
372	// void setZConsTime(double time) {this->zconsTime = time;}
373	// void getZConsTime() {return zconsTime;}
374
375	// void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
376	// void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
377
378	// void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
379	// string getZConsOutput() {return zconsOutput;}
380
381	// virtual void integrate();
382
383
384	// #ifdef IS_MPI
385	// virtual void update(); //which is called to indicate the molecules' migration
386	// #endif
387
388	// enum ZConsState {zcsMoving, zcsFixed};
389
390	// vector<Molecule*> zconsMols; //z-constraint molecules array
391	// vector<ZConsState> states; //state of z-constraint molecules
392
393
394
395	// int totNumOfUnconsAtoms; //total number of uncontraint atoms
396	// double totalMassOfUncons; //total mas of unconstraint molecules
397
398
399	// protected:
400
401
402
403	// virtual void calcForce( int calcPot, int calcStress );
404	// virtual void thermalize(void);
405
406	// void zeroOutVel();
407	// void doZconstraintForce();
408	// void doHarmonic();
409	// bool checkZConsState();
410
411	// bool haveFixedZMols();
412	// bool haveMovingZMols();
413
414	// double calcZSys();
415
416	// int isZConstraintMol(Molecule* mol);
417
418
419	// double zconsTime; //sample time
420	// double zconsTol; //tolerance of z-contratint
421	// double zForceConst; //base force constant term
422	// //which is estimate by OOPSE
423
424
425	// vector<double> massOfZConsMols; //mass of z-constraint molecule
426	// vector<double> kz; //force constant array
427
428	// vector<double> zPos; //
429
430
431	// vector<Molecule*> unconsMols; //unconstraint molecules array
432	// vector<double> massOfUnconsMols; //mass array of unconstraint molecules
433
434
435	// vector<ZConsParaItem>* parameters; //
436
437	// vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
438
439	// int* indexOfZConsMols; //index of local Z-Constraint Molecules
440	// double* fz;
441	// double* curZPos;
442
443
444
445	// int whichDirection; //constraint direction
446
447	// private:
448
449	// string zconsOutput; //filename of zconstraint output
450	// ZConsWriter* fzOut; //z-constraint writer
451
452	// double curZconsTime;
453
454	// double calcMovingMolsCOMVel();
455	// double calcSysCOMVel();
456	// double calcTotalForce();
457
458	// ForceSubtractionPolicy* forcePolicy; //force subtraction policy
459	// friend class ForceSubtractionPolicy;
460
461	// };
462
463	#endif