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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC vs.
Revision 837 by tim, Wed Oct 29 00:19:10 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  
# 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 61 | 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 88 | 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 103 | 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 124 | 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 143 | Line 145 | template<typename T> class NPT : public T{ (public)
145  
146    NPT ( SimInfo *theInfo, ForceFields* the_ff);
147    virtual ~NPT();
148 <  
148 >
149    virtual void integrateStep( int calcPot, int calcStress ){
150      calcStress = 1;
151      T::integrateStep( calcPot, calcStress );
152    }
153  
154    virtual double getConservedQuantity(void) = 0;
155 <
155 >  virtual string getAdditionalParameters(void) = 0;
156    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
157    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
158    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 170 | Line 172 | template<typename T> class NPT : public T{ (public)
172  
173    virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
174    virtual void getVelScaleB( double sc[3], int index ) = 0;
175 <  virtual void getPosScale(double pos[3], double COM[3],
175 >  virtual void getPosScale(double pos[3], double COM[3],
176                             int index, double sc[3]) = 0;
177  
178    virtual bool chiConverged( void );
179    virtual bool etaConverged( void ) = 0;
180 <  
180 >
181    virtual void evolveChiA( void );
182    virtual void evolveEtaA( void ) = 0;
183    virtual void evolveChiB( void );
# Line 195 | Line 197 | template<typename T> class NPT : public T{ (public)
197  
198    double tt2, tb2;
199    double instaTemp, instaPress, instaVol;
200 +  double press[3][3];
201  
202    int Nparticles;
203  
204    double integralOfChidt;
205  
206 <  // targetTemp, targetPressure, and tauBarostat must be set.  
206 >  // targetTemp, targetPressure, and tauBarostat must be set.
207    // One of qmass or tauThermostat must be set;
208  
209    double targetTemp;
# Line 225 | Line 228 | template<typename T> class NPTi : public T{
228   };
229  
230   template<typename T> class NPTi : public T{
231 <  
231 >
232   public:
233    NPTi( SimInfo *theInfo, ForceFields* the_ff);
234    ~NPTi();
235  
236    virtual double getConservedQuantity(void);
237    virtual void resetIntegrator(void);
238 <
238 >  virtual string getAdditionalParameters(void);
239   protected:
240  
238 –
241  
242 +
243    virtual void evolveEtaA(void);
244    virtual void evolveEtaB(void);
245  
# Line 246 | Line 249 | template<typename T> class NPTi : public T{
249  
250    virtual void getVelScaleA( double sc[3], double vel[3] );
251    virtual void getVelScaleB( double sc[3], int index );
252 <  virtual void getPosScale(double pos[3], double COM[3],
252 >  virtual void getPosScale(double pos[3], double COM[3],
253                             int index, double sc[3]);
254  
255    double eta, oldEta, prevEta;
256   };
257  
258 + template<typename T> class NPTf : public T{
259  
256 – template<typename T> class NPTim : public T{
257 –
260   public:
261  
262 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
263 <  virtual ~NPTim() {}
262 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
263 >  virtual ~NPTf();
264  
263 –  virtual void integrateStep( int calcPot, int calcStress ){
264 –    calcStress = 1;
265 –    T::integrateStep( calcPot, calcStress );
266 –    accIntegralOfChidt();  
267 –  }
268 –
265    virtual double getConservedQuantity(void);
266 <
267 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
272 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
273 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
274 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
275 <  void setChiTolerance(double tol) {chiTolerance = tol;}
276 <  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
266 >  virtual string getAdditionalParameters(void);
267 >  virtual void resetIntegrator(void);
268  
269   protected:
270  
271 <  virtual void moveA( void );
272 <  virtual void moveB( void );
271 >  virtual void evolveEtaA(void);
272 >  virtual void evolveEtaB(void);
273  
274 <  virtual int readyCheck();
274 >  virtual bool etaConverged( void );
275  
276 <  virtual void resetIntegrator( void );
276 >  virtual void scaleSimBox( void );
277  
278 <  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
279 <  
280 <  Molecule* myMolecules;
281 <  Atom** myAtoms;
278 >  virtual void getVelScaleA( double sc[3], double vel[3] );
279 >  virtual void getVelScaleB( double sc[3], int index );
280 >  virtual void getPosScale(double pos[3], double COM[3],
281 >                           int index, double sc[3]);
282  
283 <  // chi and eta are the propagated degrees of freedom
284 <
285 <  double chi;
295 <  double eta;
296 <  double NkBT;
297 <  double integralOfChidt;
298 <
299 <  // targetTemp, targetPressure, and tauBarostat must be set.  
300 <  // One of qmass or tauThermostat must be set;
301 <
302 <  double targetTemp;
303 <  double targetPressure;
304 <  double tauThermostat;
305 <  double tauBarostat;
306 <
307 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
308 <  short int have_target_pressure;
309 <  double chiTolerance;
310 <  short int have_chi_tolerance;
311 <  double posIterTolerance;
312 <  short int have_pos_iter_tolerance;
313 <
283 >  double eta[3][3];
284 >  double oldEta[3][3];
285 >  double prevEta[3][3];
286   };
287  
288 < template<typename T> class NPTzm : public T{
288 > template<typename T> class NPTxyz : public T{
289  
290   public:
291  
292 <  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
293 <  virtual ~NPTzm() {};
292 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
293 >  virtual ~NPTxyz();
294  
323 –  virtual void integrateStep( int calcPot, int calcStress ){
324 –    calcStress = 1;
325 –    T::integrateStep( calcPot, calcStress );
326 –  }
327 –
328 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
329 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
330 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
331 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
332 –
333 – protected:
334 –
335 –  virtual void moveA( void );
336 –  virtual void moveB( void );
337 –
338 –  virtual int readyCheck();
339 –
340 –  virtual void resetIntegrator( void );
341 –
342 –  Molecule* myMolecules;
343 –  Atom** myAtoms;
344 –
345 –  // chi and eta are the propagated degrees of freedom
346 –
347 –  double chi;
348 –  double eta;
349 –  double etaZ;
350 –  double NkBT;
351 –
352 –  // targetTemp, targetPressure, and tauBarostat must be set.  
353 –  // One of qmass or tauThermostat must be set;
354 –
355 –  double targetTemp;
356 –  double targetPressure;
357 –  double tauThermostat;
358 –  double tauBarostat;
359 –
360 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
361 –  short int have_target_pressure;
362 –
363 – };
364 –
365 – template<typename T> class NPTf : public T{
366 –
367 – public:
368 –
369 –  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
370 –  virtual ~NPTf();
371 –
372 –  virtual void integrateStep( int calcPot, int calcStress ){
373 –    calcStress = 1;
374 –    T::integrateStep( calcPot, calcStress );
375 –  }
376 –  
295    virtual double getConservedQuantity(void);
296 +  virtual string getAdditionalParameters(void);
297 +  virtual void resetIntegrator(void);
298  
379 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
380 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
381 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
382 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
383 –  void setChiTolerance(double tol) {chiTolerance = tol;}
384 –  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
385 –
299   protected:
300  
301 <  virtual void  moveA( void );
302 <  virtual void moveB( void );
301 >  virtual void evolveEtaA(void);
302 >  virtual void evolveEtaB(void);
303  
304 <  virtual void resetIntegrator( void );
392 <
393 <  virtual int readyCheck();
394 <
395 <
396 <  // chi and eta are the propagated degrees of freedom
397 <
398 <  double chi;
399 <  double eta[3][3];
400 <  double NkBT;
401 <  double fkBT;
402 <
403 <  int Nparticles;
404 <
405 <  double *oldPos;
406 <  double *oldVel;
407 <  double *oldJi;
408 <
409 <  double integralOfChidt;
410 <  
411 <  // targetTemp, targetPressure, and tauBarostat must be set.  
412 <  // One of qmass or tauThermostat must be set;
413 <
414 <  double targetTemp;
415 <  double targetPressure;
416 <  double tauThermostat;
417 <  double tauBarostat;
418 <
419 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
420 <  short int have_target_pressure;
421 <  double chiTolerance;
422 <  short int have_chi_tolerance;
423 <  double posIterTolerance;
424 <  short int have_pos_iter_tolerance;
425 <  double etaTolerance;
426 <  short int have_eta_tolerance;
427 < };
428 <
429 < template<typename T> class NPTxym : public T{
430 <
431 < public:
432 <
433 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
434 <  virtual ~NPTxym() {};
435 <
436 <  virtual void integrateStep( int calcPot, int calcStress ){
437 <    calcStress = 1;
438 <    T::integrateStep( calcPot, calcStress );
439 <  }
440 <
441 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
442 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
443 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
444 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
445 <
446 < protected:
447 <
448 <  virtual void moveA( void );
449 <  virtual void moveB( void );
450 <
451 <  virtual int readyCheck();
452 <
453 <  virtual void resetIntegrator( void );
304 >  virtual bool etaConverged( void );
305  
306 <  Molecule* myMolecules;
456 <  Atom** myAtoms;
306 >  virtual void scaleSimBox( void );
307  
308 <  // chi and eta are the propagated degrees of freedom
308 >  virtual void getVelScaleA( double sc[3], double vel[3] );
309 >  virtual void getVelScaleB( double sc[3], int index );
310 >  virtual void getPosScale(double pos[3], double COM[3],
311 >                           int index, double sc[3]);
312  
460 –  double chi;
461 –  double eta;
462 –  double etaX;
463 –  double etaY;
464 –  double NkBT;
465 –
466 –  // targetTemp, targetPressure, and tauBarostat must be set.  
467 –  // One of qmass or tauThermostat must be set;
468 –
469 –  double targetTemp;
470 –  double targetPressure;
471 –  double tauThermostat;
472 –  double tauBarostat;
473 –
474 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
475 –  short int have_target_pressure;
476 –
477 – };
478 –
479 –
480 – template<typename T> class NPTfm : public T{
481 –
482 – public:
483 –
484 –  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
485 –  virtual ~NPTfm() {};
486 –
487 –  virtual void integrateStep( int calcPot, int calcStress ){
488 –    calcStress = 1;
489 –    T::integrateStep( calcPot, calcStress );
490 –    accIntegralOfChidt();
491 –  }
492 –
493 –  virtual double getConservedQuantity(void);
494 –  
495 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
496 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
497 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
498 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
499 –  void setChiTolerance(double tol) {chiTolerance = tol;}
500 –  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
501 –
502 – protected:
503 –
504 –  virtual void  moveA( void );
505 –  virtual void moveB( void );
506 –
507 –  virtual void resetIntegrator( void );
508 –
509 –  virtual int readyCheck();
510 –
511 –  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
512 –
513 –  Molecule* myMolecules;
514 –  Atom** myAtoms;
515 –
516 –  // chi and eta are the propagated degrees of freedom
517 –
518 –  double chi;
313    double eta[3][3];
314 <  double NkBT;
315 <  double integralOfChidt;
522 <
523 <  // targetTemp, targetPressure, and tauBarostat must be set.  
524 <  // One of qmass or tauThermostat must be set;
525 <
526 <  double targetTemp;
527 <  double targetPressure;
528 <  double tauThermostat;
529 <  double tauBarostat;
530 <
531 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
532 <  short int have_target_pressure;
533 <  double chiTolerance;
534 <  short int have_chi_tolerance;
535 <  double posIterTolerance;
536 <  short int have_pos_iter_tolerance;
537 <
314 >  double oldEta[3][3];
315 >  double prevEta[3][3];
316   };
317  
318  
541 – template<typename T> class NPTpr : public T{
542 –
543 – public:
544 –
545 –  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
546 –  virtual ~NPTpr() {};
547 –
548 –  virtual void integrateStep( int calcPot, int calcStress ){
549 –    calcStress = 1;
550 –    T::integrateStep( calcPot, calcStress );
551 –  }
552 –
553 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
554 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
555 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
556 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
557 –  void setChiTolerance(double tol) {chiTolerance = tol;}
558 –  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
559 –
560 – protected:
561 –
562 –  virtual void  moveA( void );
563 –  virtual void moveB( void );
564 –
565 –  virtual int readyCheck();
566 –
567 –  virtual void resetIntegrator( void );
568 –
569 –  // chi and eta are the propagated degrees of freedom
570 –
571 –  double chi;
572 –  double eta[3][3];
573 –  double NkBT;
574 –
575 –  // targetTemp, targetPressure, and tauBarostat must be set.  
576 –  // One of qmass or tauThermostat must be set;
577 –
578 –  double targetTemp;
579 –  double targetPressure;
580 –  double tauThermostat;
581 –  double tauBarostat;
582 –
583 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
584 –  short int have_target_pressure;
585 –  double chiTolerance;
586 –  short int have_chi_tolerance;
587 –  double posIterTolerance;
588 –  short int have_pos_iter_tolerance;
589 –
590 – };
591 –
592 –
319   template<typename T> class ZConstraint : public T {
320 <  
321 <  public:
320 >
321 >  public:
322    class ForceSubtractionPolicy{
323      public:
324        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
325  
326 <      virtual void update() = 0;    
326 >      virtual void update() = 0;
327        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
328        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
329        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
330        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
331 <    
331 >
332     protected:
333 <     ZConstraint<T>* zconsIntegrator;;
333 >     ZConstraint<T>* zconsIntegrator;
334    };
335  
336    class PolicyByNumber : public ForceSubtractionPolicy{
337  
338      public:
339 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
340 <      virtual void update();    
339 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
340 >      virtual void update();
341        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
342        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
343        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
344        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
345 <    
345 >
346      private:
347        int totNumOfMovingAtoms;
348    };
# Line 624 | Line 350 | template<typename T> class ZConstraint : public T {
350    class PolicyByMass : public ForceSubtractionPolicy{
351  
352      public:
353 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
354 <      
355 <      virtual void update();    
353 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
354 >
355 >      virtual void update();
356        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
357        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
358        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 640 | Line 366 | template<typename T> class ZConstraint : public T {
366  
367    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
368    ~ZConstraint();
369 <    
369 >
370    void setZConsTime(double time)                  {this->zconsTime = time;}
371    void getZConsTime()                             {return zconsTime;}
372 <  
372 >
373    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
374    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
375 <  
375 >
376    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
377    string getZConsOutput()                         {return zconsOutput;}
378 <  
378 >
379    virtual void integrate();
654 –  
380  
381 +
382   #ifdef IS_MPI
383    virtual void update();                      //which is called to indicate the molecules' migration
384   #endif
385  
386 +  enum ZConsState {zcsMoving, zcsFixed};
387 +
388 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
389 +  vector<ZConsState> states;                 //state of z-constraint molecules
390 +
391 +
392 +
393 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
394 +  double totalMassOfUncons;                //total mas of unconstraint molecules
395 +
396 +
397   protected:
398  
399 <  enum ZConsState {zcsMoving, zcsFixed};  
400 <
401 <  virtual void calcForce( int calcPot, int calcStress );
399 >
400 >
401 >  virtual void calcForce( int calcPot, int calcStress );
402    virtual void thermalize(void);
403 <  
403 >
404    void zeroOutVel();
405    void doZconstraintForce();
406    void doHarmonic();
# Line 681 | Line 418 | template<typename T> class ZConstraint : public T {
418    double zconsTol;                                 //tolerance of z-contratint
419    double zForceConst;                           //base force constant term
420                                                            //which is estimate by OOPSE
421 <  
422 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
423 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
421 >
422 >
423 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
424    vector<double> kz;                              //force constant array
425 <  vector<ZConsState> states;                 //state of z-constraint molecules
425 >
426    vector<double> zPos;                          //
427 <  
428 <  
427 >
428 >
429    vector<Molecule*> unconsMols;           //unconstraint molecules array
430    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
694 –  double totalMassOfUncons;                //total mas of unconstraint molecules
431  
432 +
433    vector<ZConsParaItem>* parameters; //
434 <  
434 >
435    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
436  
437 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
437 >  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
438    double* fz;
439    double* curZPos;
703 –  
704 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
440  
441 <  int whichDirection;                           //constraint direction
442 <  
441 >
442 >
443 >  int whichDirection;                           //constraint direction
444 >
445   private:
446 <  
446 >
447    string zconsOutput;                         //filename of zconstraint output
448    ZConsWriter* fzOut;                         //z-constraint writer
449  
450 <  double curZconsTime;                      
450 >  double curZconsTime;
451  
452    double calcMovingMolsCOMVel();
453    double calcSysCOMVel();
454    double calcTotalForce();
455 <  
455 >
456    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
457    friend class ForceSubtractionPolicy;
458  

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