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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 767 by tim, Tue Sep 16 20:02:11 2003 UTC vs.
Revision 843 by mmeineke, Wed Oct 29 20:41:39 2003 UTC

# Line 28 | Line 28 | template<typename T = BaseIntegrator> class Integrator
28    virtual ~Integrator();
29    void integrate( void );
30    virtual double  getConservedQuantity(void);
31 +  virtual string getAdditionalParameters(void);
32  
33   protected:
34 <  
34 >
35    virtual void integrateStep( int calcPot, int calcStress );
36    virtual void preMove( void );
37    virtual void moveA( void );
# Line 40 | Line 41 | template<typename T = BaseIntegrator> class Integrator
41    virtual int  readyCheck( void ) { return 1; }
42  
43    virtual void resetIntegrator( void ) { }
44 <
45 <  virtual void calcForce( int calcPot, int calcStress );  
44 >
45 >  virtual void calcForce( int calcPot, int calcStress );
46    virtual void thermalize();
47 <  
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],
51 >  void rotate( int axes1, int axes2, double angle, double j[3],
52           double A[3][3] );
53 <        
53 >
54    ForceFields* myFF;
55  
56    SimInfo *info; // all the info we'll ever need
# Line 59 | Line 62 | template<typename T = BaseIntegrator> class Integrator
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 <  
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
72 >  double* oldPos; // pre constrained positions
73  
74    short isFirst; /*boolean for the first time integrate is called */
75 <  
75 >
76    double dt;
77    double dt2;
78  
79    Thermo *tStats;
80    StatWriter*  statOut;
81    DumpWriter*  dumpOut;
82 <  
82 >
83   };
84  
85   typedef Integrator<BaseIntegrator> RealIntegrator;
# Line 86 | Line 89 | template<typename T> class NVE : public T { (public)
89   public:
90    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
91      T( theInfo, the_ff ){}
92 <  virtual ~NVE(){}  
92 >  virtual ~NVE(){}
93   };
94  
95  
# Line 101 | Line 104 | template<typename T> class NVT : public T { (public)
104    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
105    void setChiTolerance(double tol) {chiTolerance = tol;}
106    virtual double  getConservedQuantity(void);
107 +  virtual string getAdditionalParameters(void);
108  
109   protected:
110  
# Line 122 | Line 126 | template<typename T> class NVT : public T { (public)
126  
127    double targetTemp;
128    double tauThermostat;
129 <  
129 >
130    short int have_tau_thermostat, have_target_temp;
131  
132    double *oldVel;
# Line 135 | Line 139 | template<typename T> class NPTi : public T{
139  
140  
141  
142 < template<typename T> class NPTi : public T{
142 > template<typename T> class NPT : public T{
143  
144   public:
145  
146 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
147 <  virtual ~NPTi();
148 <  
146 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
147 >  virtual ~NPT();
148 >
149    virtual void integrateStep( int calcPot, int calcStress ){
150      calcStress = 1;
151      T::integrateStep( calcPot, calcStress );
148 –    /* accIntegralOfChidt(); */
152    }
153  
154 <  virtual double getConservedQuantity(void);
154 >  virtual double getConservedQuantity(void) = 0;
155 >  virtual string getAdditionalParameters(void) = 0;
156 >  
157 >  double myTauThermo( void ) { return tauThermostat; }
158 >  double myTauBaro( void ) { return tauBarostat; }
159  
160    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
161    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
# Line 167 | Line 174 | template<typename T> class NPTi : public T{ (protected
174  
175    virtual void resetIntegrator( void );
176  
177 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
178 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
179 +  virtual void getPosScale(double pos[3], double COM[3],
180 +                           int index, double sc[3]) = 0;
181 +
182 +  virtual bool chiConverged( void );
183 +  virtual bool etaConverged( void ) = 0;
184 +
185 +  virtual void evolveChiA( void );
186 +  virtual void evolveEtaA( void ) = 0;
187 +  virtual void evolveChiB( void );
188 +  virtual void evolveEtaB( void ) = 0;
189 +
190 +  virtual void scaleSimBox( void ) = 0;
191 +
192    void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
193  
194    // chi and eta are the propagated degrees of freedom
195  
196 +  double oldChi;
197 +  double prevChi;
198    double chi;
175 –  double eta;
199    double NkBT;
200    double fkBT;
201 +
202 +  double tt2, tb2;
203 +  double instaTemp, instaPress, instaVol;
204 +  double press[3][3];
205  
206    int Nparticles;
207  
208    double integralOfChidt;
209  
210 <  // targetTemp, targetPressure, and tauBarostat must be set.  
210 >  // targetTemp, targetPressure, and tauBarostat must be set.
211    // One of qmass or tauThermostat must be set;
212  
213    double targetTemp;
# Line 204 | Line 231 | template<typename T> class NPTim : public T{
231  
232   };
233  
234 < template<typename T> class NPTim : public T{
234 > template<typename T> class NPTi : public T{
235  
236   public:
237 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
238 +  ~NPTi();
239  
211 –  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
212 –  virtual ~NPTim() {}
213 –
214 –  virtual void integrateStep( int calcPot, int calcStress ){
215 –    calcStress = 1;
216 –    T::integrateStep( calcPot, calcStress );
217 –    accIntegralOfChidt();  
218 –  }
219 –
240    virtual double getConservedQuantity(void);
241 <
242 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
223 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
224 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
225 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
226 <  void setChiTolerance(double tol) {chiTolerance = tol;}
227 <  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
228 <
241 >  virtual void resetIntegrator(void);
242 >  virtual string getAdditionalParameters(void);
243   protected:
244  
231 –  virtual void moveA( void );
232 –  virtual void moveB( void );
245  
234 –  virtual int readyCheck();
246  
247 <  virtual void resetIntegrator( void );
247 >  virtual void evolveEtaA(void);
248 >  virtual void evolveEtaB(void);
249  
250 <  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
239 <  
240 <  Molecule* myMolecules;
241 <  Atom** myAtoms;
250 >  virtual bool etaConverged( void );
251  
252 <  // chi and eta are the propagated degrees of freedom
252 >  virtual void scaleSimBox( void );
253  
254 <  double chi;
255 <  double eta;
256 <  double NkBT;
257 <  double integralOfChidt;
249 <
250 <  // targetTemp, targetPressure, and tauBarostat must be set.  
251 <  // One of qmass or tauThermostat must be set;
252 <
253 <  double targetTemp;
254 <  double targetPressure;
255 <  double tauThermostat;
256 <  double tauBarostat;
257 <
258 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
259 <  short int have_target_pressure;
260 <  double chiTolerance;
261 <  short int have_chi_tolerance;
262 <  double posIterTolerance;
263 <  short int have_pos_iter_tolerance;
264 <
265 < };
254 >  virtual void getVelScaleA( double sc[3], double vel[3] );
255 >  virtual void getVelScaleB( double sc[3], int index );
256 >  virtual void getPosScale(double pos[3], double COM[3],
257 >                           int index, double sc[3]);
258  
259 < template<typename T> class NPTzm : public T{
268 <
269 < public:
270 <
271 <  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
272 <  virtual ~NPTzm() {};
273 <
274 <  virtual void integrateStep( int calcPot, int calcStress ){
275 <    calcStress = 1;
276 <    T::integrateStep( calcPot, calcStress );
277 <  }
278 <
279 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
280 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
281 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
282 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
283 <
284 < protected:
285 <
286 <  virtual void moveA( void );
287 <  virtual void moveB( void );
288 <
289 <  virtual int readyCheck();
290 <
291 <  virtual void resetIntegrator( void );
292 <
293 <  Molecule* myMolecules;
294 <  Atom** myAtoms;
295 <
296 <  // chi and eta are the propagated degrees of freedom
297 <
298 <  double chi;
299 <  double eta;
300 <  double etaZ;
301 <  double NkBT;
302 <
303 <  // targetTemp, targetPressure, and tauBarostat must be set.  
304 <  // One of qmass or tauThermostat must be set;
305 <
306 <  double targetTemp;
307 <  double targetPressure;
308 <  double tauThermostat;
309 <  double tauBarostat;
310 <
311 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
312 <  short int have_target_pressure;
313 <
259 >  double eta, oldEta, prevEta;
260   };
261  
262   template<typename T> class NPTf : public T{
# Line 320 | Line 266 | template<typename T> class NPTf : public T{ (public)
266    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
267    virtual ~NPTf();
268  
323 –  virtual void integrateStep( int calcPot, int calcStress ){
324 –    calcStress = 1;
325 –    T::integrateStep( calcPot, calcStress );
326 –  }
327 –  
269    virtual double getConservedQuantity(void);
270 +  virtual string getAdditionalParameters(void);
271 +  virtual void resetIntegrator(void);
272  
330 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
331 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
332 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
333 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
334 –  void setChiTolerance(double tol) {chiTolerance = tol;}
335 –  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
336 –
273   protected:
274  
275 <  virtual void  moveA( void );
276 <  virtual void moveB( void );
275 >  virtual void evolveEtaA(void);
276 >  virtual void evolveEtaB(void);
277  
278 <  virtual void resetIntegrator( void );
278 >  virtual bool etaConverged( void );
279  
280 <  virtual int readyCheck();
280 >  virtual void scaleSimBox( void );
281  
282 +  virtual void getVelScaleA( double sc[3], double vel[3] );
283 +  virtual void getVelScaleB( double sc[3], int index );
284 +  virtual void getPosScale(double pos[3], double COM[3],
285 +                           int index, double sc[3]);
286  
347 –  // chi and eta are the propagated degrees of freedom
348 –
349 –  double chi;
287    double eta[3][3];
288 <  double NkBT;
289 <  double fkBT;
353 <
354 <  int Nparticles;
355 <
356 <  double *oldPos;
357 <  double *oldVel;
358 <  double *oldJi;
359 <
360 <  double integralOfChidt;
361 <  
362 <  // targetTemp, targetPressure, and tauBarostat must be set.  
363 <  // One of qmass or tauThermostat must be set;
364 <
365 <  double targetTemp;
366 <  double targetPressure;
367 <  double tauThermostat;
368 <  double tauBarostat;
369 <
370 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
371 <  short int have_target_pressure;
372 <  double chiTolerance;
373 <  short int have_chi_tolerance;
374 <  double posIterTolerance;
375 <  short int have_pos_iter_tolerance;
376 <  double etaTolerance;
377 <  short int have_eta_tolerance;
378 < };
379 <
380 < template<typename T> class NPTxym : public T{
381 <
382 < public:
383 <
384 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
385 <  virtual ~NPTxym() {};
386 <
387 <  virtual void integrateStep( int calcPot, int calcStress ){
388 <    calcStress = 1;
389 <    T::integrateStep( calcPot, calcStress );
390 <  }
391 <
392 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
393 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
394 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
395 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
396 <
397 < protected:
398 <
399 <  virtual void moveA( void );
400 <  virtual void moveB( void );
401 <
402 <  virtual int readyCheck();
403 <
404 <  virtual void resetIntegrator( void );
405 <
406 <  Molecule* myMolecules;
407 <  Atom** myAtoms;
408 <
409 <  // chi and eta are the propagated degrees of freedom
410 <
411 <  double chi;
412 <  double eta;
413 <  double etaX;
414 <  double etaY;
415 <  double NkBT;
416 <
417 <  // targetTemp, targetPressure, and tauBarostat must be set.  
418 <  // One of qmass or tauThermostat must be set;
419 <
420 <  double targetTemp;
421 <  double targetPressure;
422 <  double tauThermostat;
423 <  double tauBarostat;
424 <
425 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
426 <  short int have_target_pressure;
427 <
288 >  double oldEta[3][3];
289 >  double prevEta[3][3];
290   };
291  
292 + template<typename T> class NPTxyz : public T{
293  
431 – template<typename T> class NPTfm : public T{
432 –
294   public:
295  
296 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
297 <  virtual ~NPTfm() {};
296 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
297 >  virtual ~NPTxyz();
298  
438 –  virtual void integrateStep( int calcPot, int calcStress ){
439 –    calcStress = 1;
440 –    T::integrateStep( calcPot, calcStress );
441 –    accIntegralOfChidt();
442 –  }
443 –
299    virtual double getConservedQuantity(void);
300 <  
301 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
447 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
448 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
449 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
450 <  void setChiTolerance(double tol) {chiTolerance = tol;}
451 <  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
300 >  virtual string getAdditionalParameters(void);
301 >  virtual void resetIntegrator(void);
302  
303   protected:
304  
305 <  virtual void  moveA( void );
306 <  virtual void moveB( void );
305 >  virtual void evolveEtaA(void);
306 >  virtual void evolveEtaB(void);
307  
308 <  virtual void resetIntegrator( void );
308 >  virtual bool etaConverged( void );
309  
310 <  virtual int readyCheck();
310 >  virtual void scaleSimBox( void );
311  
312 <  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
312 >  virtual void getVelScaleA( double sc[3], double vel[3] );
313 >  virtual void getVelScaleB( double sc[3], int index );
314 >  virtual void getPosScale(double pos[3], double COM[3],
315 >                           int index, double sc[3]);
316  
464 –  Molecule* myMolecules;
465 –  Atom** myAtoms;
466 –
467 –  // chi and eta are the propagated degrees of freedom
468 –
469 –  double chi;
317    double eta[3][3];
318 <  double NkBT;
319 <  double integralOfChidt;
473 <
474 <  // targetTemp, targetPressure, and tauBarostat must be set.  
475 <  // One of qmass or tauThermostat must be set;
476 <
477 <  double targetTemp;
478 <  double targetPressure;
479 <  double tauThermostat;
480 <  double tauBarostat;
481 <
482 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
483 <  short int have_target_pressure;
484 <  double chiTolerance;
485 <  short int have_chi_tolerance;
486 <  double posIterTolerance;
487 <  short int have_pos_iter_tolerance;
488 <
318 >  double oldEta[3][3];
319 >  double prevEta[3][3];
320   };
321  
322  
492 – template<typename T> class NPTpr : public T{
493 –
494 – public:
495 –
496 –  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
497 –  virtual ~NPTpr() {};
498 –
499 –  virtual void integrateStep( int calcPot, int calcStress ){
500 –    calcStress = 1;
501 –    T::integrateStep( calcPot, calcStress );
502 –  }
503 –
504 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
505 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
506 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
507 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
508 –  void setChiTolerance(double tol) {chiTolerance = tol;}
509 –  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
510 –
511 – protected:
512 –
513 –  virtual void  moveA( void );
514 –  virtual void moveB( void );
515 –
516 –  virtual int readyCheck();
517 –
518 –  virtual void resetIntegrator( void );
519 –
520 –  // chi and eta are the propagated degrees of freedom
521 –
522 –  double chi;
523 –  double eta[3][3];
524 –  double NkBT;
525 –
526 –  // targetTemp, targetPressure, and tauBarostat must be set.  
527 –  // One of qmass or tauThermostat must be set;
528 –
529 –  double targetTemp;
530 –  double targetPressure;
531 –  double tauThermostat;
532 –  double tauBarostat;
533 –
534 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
535 –  short int have_target_pressure;
536 –  double chiTolerance;
537 –  short int have_chi_tolerance;
538 –  double posIterTolerance;
539 –  short int have_pos_iter_tolerance;
540 –
541 – };
542 –
543 –
323   template<typename T> class ZConstraint : public T {
324 <  
325 <  public:
324 >
325 >  public:
326    class ForceSubtractionPolicy{
327      public:
328        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
329  
330 <      virtual void update() = 0;    
330 >      virtual void update() = 0;
331        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
332        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
333        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
334        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
335 <    
335 >
336     protected:
337 <     ZConstraint<T>* zconsIntegrator;;
337 >     ZConstraint<T>* zconsIntegrator;
338    };
339  
340    class PolicyByNumber : public ForceSubtractionPolicy{
341  
342      public:
343 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
344 <      virtual void update();    
343 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
344 >      virtual void update();
345        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
346        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
347        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
348        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
349 <    
349 >
350      private:
351        int totNumOfMovingAtoms;
352    };
# Line 575 | Line 354 | template<typename T> class ZConstraint : public T {
354    class PolicyByMass : public ForceSubtractionPolicy{
355  
356      public:
357 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
358 <      
359 <      virtual void update();    
357 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358 >
359 >      virtual void update();
360        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
361        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
362        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 591 | Line 370 | template<typename T> class ZConstraint : public T {
370  
371    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
372    ~ZConstraint();
373 <    
373 >
374    void setZConsTime(double time)                  {this->zconsTime = time;}
375    void getZConsTime()                             {return zconsTime;}
376 <  
376 >
377    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
378    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
379 <  
379 >
380    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
381    string getZConsOutput()                         {return zconsOutput;}
382 <  
382 >
383    virtual void integrate();
605 –  
384  
385 +
386   #ifdef IS_MPI
387    virtual void update();                      //which is called to indicate the molecules' migration
388   #endif
389  
390 +  enum ZConsState {zcsMoving, zcsFixed};
391 +
392 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
393 +  vector<ZConsState> states;                 //state of z-constraint molecules
394 +
395 +
396 +
397 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
398 +  double totalMassOfUncons;                //total mas of unconstraint molecules
399 +
400 +
401   protected:
402  
403 <  enum ZConsState {zcsMoving, zcsFixed};  
404 <
405 <  virtual void calcForce( int calcPot, int calcStress );
403 >
404 >
405 >  virtual void calcForce( int calcPot, int calcStress );
406    virtual void thermalize(void);
407 <  
407 >
408    void zeroOutVel();
409    void doZconstraintForce();
410    void doHarmonic();
# Line 632 | Line 422 | template<typename T> class ZConstraint : public T {
422    double zconsTol;                                 //tolerance of z-contratint
423    double zForceConst;                           //base force constant term
424                                                            //which is estimate by OOPSE
425 <  
426 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
427 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
425 >
426 >
427 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
428    vector<double> kz;                              //force constant array
429 <  vector<ZConsState> states;                 //state of z-constraint molecules
429 >
430    vector<double> zPos;                          //
431 <  
432 <  
431 >
432 >
433    vector<Molecule*> unconsMols;           //unconstraint molecules array
434    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
645 –  double totalMassOfUncons;                //total mas of unconstraint molecules
435  
436 +
437    vector<ZConsParaItem>* parameters; //
438 <  
438 >
439    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
440  
441 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
441 >  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
442    double* fz;
443    double* curZPos;
654 –  
655 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
444  
445 <  int whichDirection;                           //constraint direction
446 <  
445 >
446 >
447 >  int whichDirection;                           //constraint direction
448 >
449   private:
450 <  
450 >
451    string zconsOutput;                         //filename of zconstraint output
452    ZConsWriter* fzOut;                         //z-constraint writer
453  
454 <  double curZconsTime;                      
454 >  double curZconsTime;
455  
456    double calcMovingMolsCOMVel();
457    double calcSysCOMVel();
458    double calcTotalForce();
459 <  
459 >
460    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
461    friend class ForceSubtractionPolicy;
462  

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