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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 969 by tim, Tue Jan 20 20:32:57 2004 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 +  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 170 | Line 176 | template<typename T> class NPT : public T{ (public)
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],
179 >  virtual void getPosScale(double pos[3], double COM[3],
180                             int index, double sc[3]) = 0;
181  
182 +  virtual void calcVelScale( void ) = 0;
183 +
184    virtual bool chiConverged( void );
185    virtual bool etaConverged( void ) = 0;
186 <  
186 >
187    virtual void evolveChiA( void );
188    virtual void evolveEtaA( void ) = 0;
189    virtual void evolveChiB( void );
# Line 195 | Line 203 | template<typename T> class NPT : public T{ (public)
203  
204    double tt2, tb2;
205    double instaTemp, instaPress, instaVol;
206 +  double press[3][3];
207  
208    int Nparticles;
209  
210    double integralOfChidt;
211  
212 <  // targetTemp, targetPressure, and tauBarostat must be set.  
212 >  // targetTemp, targetPressure, and tauBarostat must be set.
213    // One of qmass or tauThermostat must be set;
214  
215    double targetTemp;
# Line 225 | Line 234 | template<typename T> class NPTi : public T{
234   };
235  
236   template<typename T> class NPTi : public T{
237 <  
237 >
238   public:
239    NPTi( SimInfo *theInfo, ForceFields* the_ff);
240    ~NPTi();
241  
242    virtual double getConservedQuantity(void);
243    virtual void resetIntegrator(void);
244 <
244 >  virtual string getAdditionalParameters(void);
245   protected:
246  
238 –
247  
248 +
249    virtual void evolveEtaA(void);
250    virtual void evolveEtaB(void);
251  
# Line 246 | Line 255 | template<typename T> class NPTi : public T{
255  
256    virtual void getVelScaleA( double sc[3], double vel[3] );
257    virtual void getVelScaleB( double sc[3], int index );
258 <  virtual void getPosScale(double pos[3], double COM[3],
258 >  virtual void getPosScale(double pos[3], double COM[3],
259                             int index, double sc[3]);
260  
261 +  virtual void calcVelScale( void );
262 +
263    double eta, oldEta, prevEta;
264 +  double vScale;
265   };
266  
267 + template<typename T> class NPTf : public T{
268  
256 – template<typename T> class NPTim : public T{
257 –
269   public:
270  
271 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
272 <  virtual ~NPTim() {}
271 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
272 >  virtual ~NPTf();
273  
263 –  virtual void integrateStep( int calcPot, int calcStress ){
264 –    calcStress = 1;
265 –    T::integrateStep( calcPot, calcStress );
266 –    accIntegralOfChidt();  
267 –  }
268 –
274    virtual double getConservedQuantity(void);
275 <
276 <  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;}
275 >  virtual string getAdditionalParameters(void);
276 >  virtual void resetIntegrator(void);
277  
278   protected:
279  
280 <  virtual void moveA( void );
281 <  virtual void moveB( void );
280 >  virtual void evolveEtaA(void);
281 >  virtual void evolveEtaB(void);
282  
283 <  virtual int readyCheck();
283 >  virtual bool etaConverged( void );
284  
285 <  virtual void resetIntegrator( void );
285 >  virtual void scaleSimBox( void );
286  
287 <  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
288 <  
289 <  Molecule* myMolecules;
290 <  Atom** myAtoms;
287 >  virtual void getVelScaleA( double sc[3], double vel[3] );
288 >  virtual void getVelScaleB( double sc[3], int index );
289 >  virtual void getPosScale(double pos[3], double COM[3],
290 >                           int index, double sc[3]);
291  
292 <  // chi and eta are the propagated degrees of freedom
292 >  virtual void calcVelScale( void );
293  
294 <  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 <
294 >  double eta[3][3];
295 >  double oldEta[3][3];
296 >  double prevEta[3][3];
297 >  double vScale[3][3];
298   };
299  
300 < template<typename T> class NPTzm : public T{
300 > template<typename T> class NPTxyz : public T{
301  
302   public:
303  
304 <  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
305 <  virtual ~NPTzm() {};
304 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
305 >  virtual ~NPTxyz();
306  
307 <  virtual void integrateStep( int calcPot, int calcStress ){
308 <    calcStress = 1;
309 <    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;}
307 >  virtual double getConservedQuantity(void);
308 >  virtual string getAdditionalParameters(void);
309 >  virtual void resetIntegrator(void);
310  
311   protected:
312  
313 <  virtual void moveA( void );
314 <  virtual void moveB( void );
313 >  virtual void evolveEtaA(void);
314 >  virtual void evolveEtaB(void);
315  
316 <  virtual int readyCheck();
316 >  virtual bool etaConverged( void );
317  
318 <  virtual void resetIntegrator( void );
318 >  virtual void scaleSimBox( void );
319  
320 <  Molecule* myMolecules;
321 <  Atom** myAtoms;
322 <
323 <  // 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 <  
377 <  virtual double getConservedQuantity(void);
378 <
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 <
386 < protected:
387 <
388 <  virtual void  moveA( void );
389 <  virtual void moveB( void );
390 <
391 <  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 );
454 <
455 <  Molecule* myMolecules;
456 <  Atom** myAtoms;
320 >  virtual void getVelScaleA( double sc[3], double vel[3] );
321 >  virtual void getVelScaleB( double sc[3], int index );
322 >  virtual void getPosScale(double pos[3], double COM[3],
323 >                           int index, double sc[3]);
324  
325 <  // chi and eta are the propagated degrees of freedom
325 >  virtual void calcVelScale( void );
326  
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;
327    double eta[3][3];
328 <  double NkBT;
329 <  double integralOfChidt;
330 <
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 <
328 >  double oldEta[3][3];
329 >  double prevEta[3][3];
330 >  double vScale[3][3];
331   };
332  
333  
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 –
334   template<typename T> class ZConstraint : public T {
335 <  
336 <  public:
335 >
336 >  public:
337    class ForceSubtractionPolicy{
338      public:
339        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
340  
341 <      virtual void update() = 0;    
341 >      virtual void update() = 0;
342        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
343        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
344        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
345        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
346 <    
346 >
347     protected:
348 <     ZConstraint<T>* zconsIntegrator;;
348 >     ZConstraint<T>* zconsIntegrator;
349    };
350  
351    class PolicyByNumber : public ForceSubtractionPolicy{
352  
353      public:
354 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
355 <      virtual void update();    
354 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
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);
359        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
360 <    
360 >
361      private:
362        int totNumOfMovingAtoms;
363    };
# Line 624 | Line 365 | template<typename T> class ZConstraint : public T {
365    class PolicyByMass : public ForceSubtractionPolicy{
366  
367      public:
368 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
369 <      
370 <      virtual void update();    
368 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
369 >
370 >      virtual void update();
371        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
372        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
373        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 640 | Line 381 | template<typename T> class ZConstraint : public T {
381  
382    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
383    ~ZConstraint();
384 <    
384 >
385    void setZConsTime(double time)                  {this->zconsTime = time;}
386    void getZConsTime()                             {return zconsTime;}
387 <  
387 >
388    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
389    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
390 <  
390 >
391    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
392    string getZConsOutput()                         {return zconsOutput;}
393 <  
393 >
394    virtual void integrate();
654 –  
395  
396 +
397   #ifdef IS_MPI
398    virtual void update();                      //which is called to indicate the molecules' migration
399   #endif
400  
401 +  enum ZConsState {zcsMoving, zcsFixed};
402 +
403 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
404 +  vector<ZConsState> states;                 //state of z-constraint molecules
405 +
406 +
407 +
408 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
409 +  double totalMassOfUncons;                //total mas of unconstraint molecules
410 +
411 +
412   protected:
413  
414 <  enum ZConsState {zcsMoving, zcsFixed};  
415 <
416 <  virtual void calcForce( int calcPot, int calcStress );
414 >
415 >
416 >  virtual void calcForce( int calcPot, int calcStress );
417    virtual void thermalize(void);
418 <  
418 >
419    void zeroOutVel();
420    void doZconstraintForce();
421    void doHarmonic();
# Line 681 | Line 433 | template<typename T> class ZConstraint : public T {
433    double zconsTol;                                 //tolerance of z-contratint
434    double zForceConst;                           //base force constant term
435                                                            //which is estimate by OOPSE
436 <  
437 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
438 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
436 >
437 >
438 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
439    vector<double> kz;                              //force constant array
440 <  vector<ZConsState> states;                 //state of z-constraint molecules
440 >
441    vector<double> zPos;                          //
442 <  
443 <  
442 >
443 >
444    vector<Molecule*> unconsMols;           //unconstraint molecules array
445    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
694 –  double totalMassOfUncons;                //total mas of unconstraint molecules
446  
447 +
448    vector<ZConsParaItem>* parameters; //
449 <  
449 >
450    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
451  
452 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
452 >  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
453    double* fz;
454    double* curZPos;
703 –  
704 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
455  
456 <  int whichDirection;                           //constraint direction
457 <  
456 >
457 >
458 >  int whichDirection;                           //constraint direction
459 >
460   private:
461 <  
461 >
462    string zconsOutput;                         //filename of zconstraint output
463    ZConsWriter* fzOut;                         //z-constraint writer
464  
465 <  double curZconsTime;                      
465 >  double curZconsTime;
466  
467    double calcMovingMolsCOMVel();
468    double calcSysCOMVel();
469    double calcTotalForce();
470 <  
470 >
471    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
472    friend class ForceSubtractionPolicy;
473  
474   };
475  
476 + class OOPSEMinimizerBase : public RealIntegrator {
477 +  public:
478 +
479 +    OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff );
480 +    virtual ~OOPSEMinimizerBase();
481 +    
482 +    double calcGradient(const vector<double>& x, vector<double>& grad);
483 +    void setOptCoor(vector<double>& x);
484 +    void getOptCoor(vector<double>& x);
485 +    void output();
486 +    
487 + };
488 +
489 + template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
490 +  public:
491 +    
492 + };
493 +  
494   #endif

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