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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC

# Line 1 | Line 1
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 < class Integrator : public BaseIntegrator {
16 > using namespace std;
17 > const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-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 amu*fs^-2*Ang^-1 -> atm
20 > const int maxIteration = 300;
21 > const double tol = 1.0e-6;
22  
23 +
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27 <  Integrator( SimInfo &theInfo, ForceFields* the_ff );
27 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31  
19 –
32   protected:
33    
34    virtual void integrateStep( int calcPot, int calcStress );
# Line 26 | Line 38 | class Integrator : public BaseIntegrator { (protected)
38    virtual void constrainA( void );
39    virtual void constrainB( void );
40    virtual int  readyCheck( void ) { return 1; }
41 +
42 +  virtual void resetIntegrator( void ) { }
43 +
44 +  virtual void calcForce( int calcPot, int calcStress );  
45 +  virtual void thermalize();
46    
47    void checkConstraints( void );
48    void rotate( int axes1, int axes2, double angle, double j[3],
49 <               double A[3][3] );
50 <
34 <
49 >         double A[3][3] );
50 >        
51    ForceFields* myFF;
52  
53    SimInfo *info; // all the info we'll ever need
# Line 42 | Line 58 | class Integrator : public BaseIntegrator { (protected)
58    int nMols;
59  
60    int isConstrained; // boolean to know whether the systems contains
61 <                     // constraints.
61 >         // constraints.
62    int nConstrained;  // counter for number of constraints
63    int *constrainedA; // the i of a constraint pair
64    int *constrainedB; // the j of a constraint pair
# Line 50 | Line 66 | class Integrator : public BaseIntegrator { (protected)
66    
67    int* moving; // tells whether we are moving atom i
68    int* moved;  // tells whether we have moved atom i
69 <  double* prePos; // pre constrained positions
69 >  double* oldPos; // pre constrained positions
70  
71    short isFirst; /*boolean for the first time integrate is called */
72    
73    double dt;
74    double dt2;
75  
60 –  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
61 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
62 –  const int maxIteration = 300;
63 –  const double tol = 1.0e-6;
64 –  
65 –  double* pos;
66 –  double* vel;
67 –  double* frc;
68 –  double* trq;
69 –  double* Amat;
70 –
76    Thermo *tStats;
77    StatWriter*  statOut;
78    DumpWriter*  dumpOut;
79    
80   };
81  
82 < class NVE : public Integrator{
82 > typedef Integrator<BaseIntegrator> RealIntegrator;
83  
84 <  NVE ( void ):
80 <    Integrator( theInfo, the_ff ){}
81 <  virtual ~NVE(){}
84 > template<typename T> class NVE : public T {
85  
86 <  
87 <
86 > public:
87 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
88 >    T( theInfo, the_ff ){}
89 >  virtual ~NVE(){}  
90   };
91  
87 – class NVT : public Integrator{
92  
93 + template<typename T> class NVT : public T {
94 +
95   public:
96  
97 <  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
92 <    Integrator( theInfo, the_ff );
97 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
98    virtual ~NVT();
99  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
100    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
101    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
102 +  void setChiTolerance(double tol) {chiTolerance = tol;}
103 +  virtual double  getConservedQuantity(void);
104  
105   protected:
106  
107 <  virtual moveA( void );
108 <  virtual moveB( void );
107 >  virtual void moveA( void );
108 >  virtual void moveB( void );
109  
110 <  int readyCheck();
110 >  virtual int readyCheck();
111  
112 <  Atom** atoms;
112 >  virtual void resetIntegrator( void );
113  
114 <  // zeta is a propagated degree of freedom.
114 >  // chi is a propagated degree of freedom.
115  
116 <  double zeta;
116 >  double chi;
117  
118 <  // targetTemp must be set.  One of qmass or tauThermostat must be set;
118 >  //integral of chi(t)dt
119 >  double integralOfChidt;
120  
121 <  double qmass;
121 >  // targetTemp must be set.  tauThermostat must also be set;
122 >
123    double targetTemp;
124    double tauThermostat;
125 +  
126 +  short int have_tau_thermostat, have_target_temp;
127  
128 <  short int have_tau_thermostat, have_target_temp, have_qmass;
128 >  double *oldVel;
129 >  double *oldJi;
130  
131 +  double chiTolerance;
132 +  short int have_chi_tolerance;
133 +
134   };
135  
136  
123 – class NPT : public Integrator{
137  
138 + template<typename T> class NPTi : public T{
139 +
140   public:
141  
142 <  NPT ( SimInfo &theInfo, ForceFields* the_ff) :
143 <    Integrator( theInfo, the_ff );
144 <  virtual ~NPT();
142 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
143 >  virtual ~NPTi();
144 >  
145 >  virtual void integrateStep( int calcPot, int calcStress ){
146 >    calcStress = 1;
147 >    T::integrateStep( calcPot, calcStress );
148 >    /* accIntegralOfChidt(); */
149 >  }
150  
151 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
151 >  virtual double getConservedQuantity(void);
152 >
153    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
154    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
155    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
156    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
157 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
158 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
159 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
160  
161   protected:
162  
163 <  virtual moveA( void );
164 <  virtual moveB( void );
163 >  virtual void  moveA( void );
164 >  virtual void moveB( void );
165  
166 <  int readyCheck();
166 >  virtual int readyCheck();
167  
168 <  Atom** atoms;
168 >  virtual void resetIntegrator( void );
169  
170 <  // zeta and epsilonDot are the propagated degrees of freedom.
170 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
171  
172 <  double zeta;
149 <  double epsilonDot;
172 >  // chi and eta are the propagated degrees of freedom
173  
174 +  double chi;
175 +  double eta;
176 +  double NkBT;
177 +  double fkBT;
178 +
179 +  int Nparticles;
180 +
181 +  double integralOfChidt;
182 +
183    // targetTemp, targetPressure, and tauBarostat must be set.  
184    // One of qmass or tauThermostat must be set;
185  
154 –  double qmass;
186    double targetTemp;
187    double targetPressure;
188    double tauThermostat;
189    double tauBarostat;
190  
191    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
192 <  short int have_target_pressure, have_qmass;
192 >  short int have_target_pressure;
193 >
194 >  double *oldPos;
195 >  double *oldVel;
196 >  double *oldJi;
197 >
198 >  double chiTolerance;
199 >  short int have_chi_tolerance;
200 >  double posIterTolerance;
201 >  short int have_pos_iter_tolerance;
202 >  double etaTolerance;
203 >  short int have_eta_tolerance;
204 >
205 >  double volume;
206 >
207 > };
208 >
209 > template<typename T> class NPTim : public T{
210 >
211 > public:
212 >
213 >  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
214 >  virtual ~NPTim() {}
215 >
216 >  virtual void integrateStep( int calcPot, int calcStress ){
217 >    calcStress = 1;
218 >    T::integrateStep( calcPot, calcStress );
219 >    accIntegralOfChidt();  
220 >  }
221 >
222 >  virtual double getConservedQuantity(void);
223 >
224 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
225 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
226 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
227 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
228 >  void setChiTolerance(double tol) {chiTolerance = tol;}
229 >  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
230 >
231 > protected:
232 >
233 >  virtual void moveA( void );
234 >  virtual void moveB( void );
235 >
236 >  virtual int readyCheck();
237 >
238 >  virtual void resetIntegrator( void );
239 >
240 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
241 >  
242 >  Molecule* myMolecules;
243 >  Atom** myAtoms;
244 >
245 >  // chi and eta are the propagated degrees of freedom
246 >
247 >  double chi;
248 >  double eta;
249 >  double NkBT;
250 >  double integralOfChidt;
251 >
252 >  // targetTemp, targetPressure, and tauBarostat must be set.  
253 >  // One of qmass or tauThermostat must be set;
254 >
255 >  double targetTemp;
256 >  double targetPressure;
257 >  double tauThermostat;
258 >  double tauBarostat;
259 >
260 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
261 >  short int have_target_pressure;
262 >  double chiTolerance;
263 >  short int have_chi_tolerance;
264 >  double posIterTolerance;
265 >  short int have_pos_iter_tolerance;
266 >
267 > };
268 >
269 > template<typename T> class NPTzm : public T{
270 >
271 > public:
272 >
273 >  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
274 >  virtual ~NPTzm() {};
275 >
276 >  virtual void integrateStep( int calcPot, int calcStress ){
277 >    calcStress = 1;
278 >    T::integrateStep( calcPot, calcStress );
279 >  }
280 >
281 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
282 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
283 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
284 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
285 >
286 > protected:
287 >
288 >  virtual void moveA( void );
289 >  virtual void moveB( void );
290 >
291 >  virtual int readyCheck();
292 >
293 >  virtual void resetIntegrator( void );
294 >
295 >  Molecule* myMolecules;
296 >  Atom** myAtoms;
297 >
298 >  // chi and eta are the propagated degrees of freedom
299 >
300 >  double chi;
301 >  double eta;
302 >  double etaZ;
303 >  double NkBT;
304 >
305 >  // targetTemp, targetPressure, and tauBarostat must be set.  
306 >  // One of qmass or tauThermostat must be set;
307 >
308 >  double targetTemp;
309 >  double targetPressure;
310 >  double tauThermostat;
311 >  double tauBarostat;
312 >
313 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
314 >  short int have_target_pressure;
315 >
316 > };
317 >
318 > template<typename T> class NPTf : public T{
319 >
320 > public:
321 >
322 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
323 >  virtual ~NPTf() {};
324 >
325 >  virtual void integrateStep( int calcPot, int calcStress ){
326 >    calcStress = 1;
327 >    T::integrateStep( calcPot, calcStress );
328 >    accIntegralOfChidt();
329 >  }
330 >  
331 >  virtual double getConservedQuantity(void);
332 >
333 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
334 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
335 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
336 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
337 >  void setChiTolerance(double tol) {chiTolerance = tol;}
338 >  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
339 >
340 > protected:
341 >
342 >  virtual void  moveA( void );
343 >  virtual void moveB( void );
344 >
345 >  virtual void resetIntegrator( void );
346 >
347 >  virtual int readyCheck();
348 >
349 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
350 >
351 >  // chi and eta are the propagated degrees of freedom
352 >
353 >  double chi;
354 >  double eta[3][3];
355 >  double NkBT;
356 >
357 >  double integralOfChidt;
358 >  
359 >  // targetTemp, targetPressure, and tauBarostat must be set.  
360 >  // One of qmass or tauThermostat must be set;
361 >
362 >  double targetTemp;
363 >  double targetPressure;
364 >  double tauThermostat;
365 >  double tauBarostat;
366  
367 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
368 +  short int have_target_pressure;
369 +  double chiTolerance;
370 +  short int have_chi_tolerance;
371 +  double posIterTolerance;
372 +  short int have_pos_iter_tolerance;
373 +
374   };
375  
376 + template<typename T> class NPTxym : public T{
377 +
378 + public:
379 +
380 +  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
381 +  virtual ~NPTxym() {};
382 +
383 +  virtual void integrateStep( int calcPot, int calcStress ){
384 +    calcStress = 1;
385 +    T::integrateStep( calcPot, calcStress );
386 +  }
387 +
388 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
389 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
390 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
391 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
392 +
393 + protected:
394 +
395 +  virtual void moveA( void );
396 +  virtual void moveB( void );
397 +
398 +  virtual int readyCheck();
399 +
400 +  virtual void resetIntegrator( void );
401 +
402 +  Molecule* myMolecules;
403 +  Atom** myAtoms;
404 +
405 +  // chi and eta are the propagated degrees of freedom
406 +
407 +  double chi;
408 +  double eta;
409 +  double etaX;
410 +  double etaY;
411 +  double NkBT;
412 +
413 +  // targetTemp, targetPressure, and tauBarostat must be set.  
414 +  // One of qmass or tauThermostat must be set;
415 +
416 +  double targetTemp;
417 +  double targetPressure;
418 +  double tauThermostat;
419 +  double tauBarostat;
420 +
421 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
422 +  short int have_target_pressure;
423 +
424 + };
425 +
426 +
427 + template<typename T> class NPTfm : public T{
428 +
429 + public:
430 +
431 +  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
432 +  virtual ~NPTfm() {};
433 +
434 +  virtual void integrateStep( int calcPot, int calcStress ){
435 +    calcStress = 1;
436 +    T::integrateStep( calcPot, calcStress );
437 +    accIntegralOfChidt();
438 +  }
439 +
440 +  virtual double getConservedQuantity(void);
441 +  
442 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
443 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
444 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
445 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
446 +  void setChiTolerance(double tol) {chiTolerance = tol;}
447 +  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
448 +
449 + protected:
450 +
451 +  virtual void  moveA( void );
452 +  virtual void moveB( void );
453 +
454 +  virtual void resetIntegrator( void );
455 +
456 +  virtual int readyCheck();
457 +
458 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
459 +
460 +  Molecule* myMolecules;
461 +  Atom** myAtoms;
462 +
463 +  // chi and eta are the propagated degrees of freedom
464 +
465 +  double chi;
466 +  double eta[3][3];
467 +  double NkBT;
468 +  double integralOfChidt;
469 +
470 +  // targetTemp, targetPressure, and tauBarostat must be set.  
471 +  // One of qmass or tauThermostat must be set;
472 +
473 +  double targetTemp;
474 +  double targetPressure;
475 +  double tauThermostat;
476 +  double tauBarostat;
477 +
478 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
479 +  short int have_target_pressure;
480 +  double chiTolerance;
481 +  short int have_chi_tolerance;
482 +  double posIterTolerance;
483 +  short int have_pos_iter_tolerance;
484 +
485 + };
486 +
487 +
488 + template<typename T> class NPTpr : public T{
489 +
490 + public:
491 +
492 +  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
493 +  virtual ~NPTpr() {};
494 +
495 +  virtual void integrateStep( int calcPot, int calcStress ){
496 +    calcStress = 1;
497 +    T::integrateStep( calcPot, calcStress );
498 +  }
499 +
500 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
501 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
502 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
503 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
504 +  void setChiTolerance(double tol) {chiTolerance = tol;}
505 +  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
506 +
507 + protected:
508 +
509 +  virtual void  moveA( void );
510 +  virtual void moveB( void );
511 +
512 +  virtual int readyCheck();
513 +
514 +  virtual void resetIntegrator( void );
515 +
516 +  // chi and eta are the propagated degrees of freedom
517 +
518 +  double chi;
519 +  double eta[3][3];
520 +  double NkBT;
521 +
522 +  // targetTemp, targetPressure, and tauBarostat must be set.  
523 +  // One of qmass or tauThermostat must be set;
524 +
525 +  double targetTemp;
526 +  double targetPressure;
527 +  double tauThermostat;
528 +  double tauBarostat;
529 +
530 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
531 +  short int have_target_pressure;
532 +  double chiTolerance;
533 +  short int have_chi_tolerance;
534 +  double posIterTolerance;
535 +  short int have_pos_iter_tolerance;
536 +
537 + };
538 +
539 +
540 + template<typename T> class ZConstraint : public T {
541 +  
542 +  public:
543 +  class ForceSubtractionPolicy{
544 +    public:
545 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
546 +
547 +      virtual void update() = 0;    
548 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
549 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
550 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
551 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
552 +    
553 +   protected:
554 +     ZConstraint<T>* zconsIntegrator;;
555 +  };
556 +
557 +  class PolicyByNumber : public ForceSubtractionPolicy{
558 +
559 +    public:
560 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
561 +      virtual void update();    
562 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
563 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
564 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
565 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
566 +    
567 +    private:
568 +      int totNumOfMovingAtoms;
569 +  };
570 +
571 +  class PolicyByMass : public ForceSubtractionPolicy{
572 +
573 +    public:
574 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
575 +      
576 +      virtual void update();    
577 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
578 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
579 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
580 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
581 +
582 +   private:
583 +     double totMassOfMovingAtoms;
584 +  };
585 +
586 + public:
587 +
588 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
589 +  ~ZConstraint();
590 +    
591 +  void setZConsTime(double time)                  {this->zconsTime = time;}
592 +  void getZConsTime()                             {return zconsTime;}
593 +  
594 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
595 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
596 +  
597 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
598 +  string getZConsOutput()                         {return zconsOutput;}
599 +  
600 +  virtual void integrate();
601 +  
602 +
603 + #ifdef IS_MPI
604 +  virtual void update();                      //which is called to indicate the molecules' migration
605   #endif
606 +
607 + protected:
608 +
609 +  enum ZConsState {zcsMoving, zcsFixed};  
610 +
611 +  virtual void calcForce( int calcPot, int calcStress );
612 +  virtual void thermalize(void);
613 +  
614 +  void zeroOutVel();
615 +  void doZconstraintForce();
616 +  void doHarmonic();
617 +  bool checkZConsState();
618 +
619 +  bool haveFixedZMols();
620 +  bool haveMovingZMols();
621 +
622 +  double calcZSys();
623 +
624 +  int isZConstraintMol(Molecule* mol);
625 +
626 +
627 +  double zconsTime;                              //sample time
628 +  double zconsTol;                                 //tolerance of z-contratint
629 +  double zForceConst;                           //base force constant term
630 +                                                          //which is estimate by OOPSE
631 +  
632 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
633 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
634 +  vector<double> kz;                              //force constant array
635 +  vector<ZConsState> states;                 //state of z-constraint molecules
636 +  vector<double> zPos;                          //
637 +  
638 +  
639 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
640 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
641 +  double totalMassOfUncons;                //total mas of unconstraint molecules
642 +
643 +  vector<ZConsParaItem>* parameters; //
644 +  
645 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
646 +
647 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
648 +  double* fz;
649 +  double* curZPos;
650 +  
651 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
652 +
653 +  int whichDirection;                           //constraint direction
654 +  
655 + private:
656 +  
657 +  string zconsOutput;                         //filename of zconstraint output
658 +  ZConsWriter* fzOut;                         //z-constraint writer
659 +
660 +  double curZconsTime;                      
661 +
662 +  double calcMovingMolsCOMVel();
663 +  double calcSysCOMVel();
664 +  double calcTotalForce();
665 +  
666 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
667 +  friend class ForceSubtractionPolicy;
668 +
669 + };
670 +
671 + #endif

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