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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 767 by tim, Tue Sep 16 20:02:11 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 Verlet : public Integrator {
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 <  Verlet( SimInfo &info, ForceFields* the_ff );
28 <  ~Verlet();
27 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
28 >  virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31  
32 < private:
32 > protected:
33    
34 <  void move_a( double dt );
35 <  void move_b( double dt );
34 >  virtual void integrateStep( int calcPot, int calcStress );
35 >  virtual void preMove( void );
36 >  virtual void moveA( void );
37 >  virtual void moveB( void );
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 +        
51    ForceFields* myFF;
52  
53 <  SimInfo *entry_plug; // all the info we'll ever need
54 <  int c_natoms;  /* the number of atoms */
55 <  Atom **c_atoms; /* array of atom pointers */
56 <  SRI **c_sr_interactions; /* array of SRI pointers */
57 <  int c_n_SRI; /* the number of short range interactions */
53 >  SimInfo *info; // all the info we'll ever need
54 >  int nAtoms;  /* the number of atoms */
55 >  int oldAtoms;
56 >  Atom **atoms; /* array of atom pointers */
57 >  Molecule* molecules;
58 >  int nMols;
59  
60 <  int c_is_constrained; /*boolean to know whether the systems contains
61 <                          constraints. */
62 <  int c_n_constrained; /*counter for number of constraints */
63 <  int *c_constrained_i; /* the i of a constraint pair */
64 <  int *c_constrained_j; /* the j of a constraint pair */
65 <  double *c_constrained_dsqr; /* the square of the constraint distance */
66 <  double *c_mass; /* the array of masses */
67 <  short is_first; /*boolean for the first time integrate is called */
68 <  double c_box_x;
69 <  double c_box_y;
70 <  double c_box_z;
60 >  int isConstrained; // boolean to know whether the systems contains
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
65 >  double *constrainedDsqr; // the square of the constraint distance
66 >  
67 >  int* moving; // tells whether we are moving atom i
68 >  int* moved;  // tells whether we have moved atom i
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 >
76 >  Thermo *tStats;
77 >  StatWriter*  statOut;
78 >  DumpWriter*  dumpOut;
79 >  
80   };
81  
82 < class Symplectic : public Integrator {
82 > typedef Integrator<BaseIntegrator> RealIntegrator;
83 >
84 > template<typename T> class NVE : public T {
85 >
86 > public:
87 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
88 >    T( theInfo, the_ff ){}
89 >  virtual ~NVE(){}  
90 > };
91 >
92 >
93 > template<typename T> class NVT : public T {
94 >
95 > public:
96 >
97 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
98 >  virtual ~NVT();
99 >
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 void moveA( void );
108 >  virtual void moveB( void );
109 >
110 >  virtual int readyCheck();
111 >
112 >  virtual void resetIntegrator( void );
113 >
114 >  // chi is a propagated degree of freedom.
115 >
116 >  double chi;
117 >
118 >  //integral of chi(t)dt
119 >  double integralOfChidt;
120 >
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 +  double *oldVel;
129 +  double *oldJi;
130 +
131 +  double chiTolerance;
132 +  short int have_chi_tolerance;
133 +
134 + };
135 +
136 +
137 +
138 + template<typename T> class NPTi : public T{
139 +
140   public:
141 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
142 <  ~Symplectic();
141 >
142 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
143 >  virtual ~NPTi();
144    
145 <  void integrate( void );
145 >  virtual void integrateStep( int calcPot, int calcStress ){
146 >    calcStress = 1;
147 >    T::integrateStep( calcPot, calcStress );
148 >    /* accIntegralOfChidt(); */
149 >  }
150  
151 < private:
151 >  virtual double getConservedQuantity(void);
152  
153 <  void rotate( int axes1, int axes2, double angle, double j[3],
154 <               double A[3][3] );
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 <  SimInfo* entry_plug;
57 <  ForceFields* myFF;
161 > protected:
162  
163 <  int is_constrained; /*boolean to know whether the systems contains
164 <                          constraints. */
61 <  int n_constrained; /*counter for number of constraints */
62 <  int *constrained_i; /* the i of a constraint pair */
63 <  int *constrained_j; /* the j of a constraint pair */
64 <  double *constrained_dsqr; /* the square of the constraint distance */
65 <  double *mass; /* the array of masses */
163 >  virtual void  moveA( void );
164 >  virtual void moveB( void );
165  
166 <  short int isFirst;
166 >  virtual int readyCheck();
167  
168 <  SRI **srInteractions; /* array of SRI pointers */
169 <  int nSRI; /* the number of short range interactions */
168 >  virtual void resetIntegrator( void );
169 >
170 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
171 >
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 >
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;
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 > };
206 >
207 > template<typename T> class NPTim : public T{
208 >
209 > public:
210 >
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 >
220 >  virtual double getConservedQuantity(void);
221 >
222 >  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 >
229 > protected:
230 >
231 >  virtual void moveA( void );
232 >  virtual void moveB( void );
233 >
234 >  virtual int readyCheck();
235 >
236 >  virtual void resetIntegrator( void );
237 >
238 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
239    
240 +  Molecule* myMolecules;
241 +  Atom** myAtoms;
242 +
243 +  // chi and eta are the propagated degrees of freedom
244 +
245 +  double chi;
246 +  double eta;
247 +  double NkBT;
248 +  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   };
266  
267 + 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 +
314 + };
315 +
316 + template<typename T> class NPTf : public T{
317 +
318 + public:
319 +
320 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
321 +  virtual ~NPTf();
322 +
323 +  virtual void integrateStep( int calcPot, int calcStress ){
324 +    calcStress = 1;
325 +    T::integrateStep( calcPot, calcStress );
326 +  }
327 +  
328 +  virtual double getConservedQuantity(void);
329 +
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 +
337 + protected:
338 +
339 +  virtual void  moveA( void );
340 +  virtual void moveB( void );
341 +
342 +  virtual void resetIntegrator( void );
343 +
344 +  virtual int readyCheck();
345 +
346 +
347 +  // chi and eta are the propagated degrees of freedom
348 +
349 +  double chi;
350 +  double eta[3][3];
351 +  double NkBT;
352 +  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 +
428 + };
429 +
430 +
431 + template<typename T> class NPTfm : public T{
432 +
433 + public:
434 +
435 +  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
436 +  virtual ~NPTfm() {};
437 +
438 +  virtual void integrateStep( int calcPot, int calcStress ){
439 +    calcStress = 1;
440 +    T::integrateStep( calcPot, calcStress );
441 +    accIntegralOfChidt();
442 +  }
443 +
444 +  virtual double getConservedQuantity(void);
445 +  
446 +  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;}
452 +
453 + protected:
454 +
455 +  virtual void  moveA( void );
456 +  virtual void moveB( void );
457 +
458 +  virtual void resetIntegrator( void );
459 +
460 +  virtual int readyCheck();
461 +
462 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
463 +
464 +  Molecule* myMolecules;
465 +  Atom** myAtoms;
466 +
467 +  // chi and eta are the propagated degrees of freedom
468 +
469 +  double chi;
470 +  double eta[3][3];
471 +  double NkBT;
472 +  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 +
489 + };
490 +
491 +
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 +
544 + template<typename T> class ZConstraint : public T {
545 +  
546 +  public:
547 +  class ForceSubtractionPolicy{
548 +    public:
549 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
550 +
551 +      virtual void update() = 0;    
552 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
553 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
554 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
555 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
556 +    
557 +   protected:
558 +     ZConstraint<T>* zconsIntegrator;;
559 +  };
560 +
561 +  class PolicyByNumber : public ForceSubtractionPolicy{
562 +
563 +    public:
564 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
565 +      virtual void update();    
566 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
567 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
568 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
569 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
570 +    
571 +    private:
572 +      int totNumOfMovingAtoms;
573 +  };
574 +
575 +  class PolicyByMass : public ForceSubtractionPolicy{
576 +
577 +    public:
578 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
579 +      
580 +      virtual void update();    
581 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
582 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
583 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
584 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
585 +
586 +   private:
587 +     double totMassOfMovingAtoms;
588 +  };
589 +
590 + public:
591 +
592 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
593 +  ~ZConstraint();
594 +    
595 +  void setZConsTime(double time)                  {this->zconsTime = time;}
596 +  void getZConsTime()                             {return zconsTime;}
597 +  
598 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
599 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
600 +  
601 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
602 +  string getZConsOutput()                         {return zconsOutput;}
603 +  
604 +  virtual void integrate();
605 +  
606 +
607 + #ifdef IS_MPI
608 +  virtual void update();                      //which is called to indicate the molecules' migration
609   #endif
610 +
611 + protected:
612 +
613 +  enum ZConsState {zcsMoving, zcsFixed};  
614 +
615 +  virtual void calcForce( int calcPot, int calcStress );
616 +  virtual void thermalize(void);
617 +  
618 +  void zeroOutVel();
619 +  void doZconstraintForce();
620 +  void doHarmonic();
621 +  bool checkZConsState();
622 +
623 +  bool haveFixedZMols();
624 +  bool haveMovingZMols();
625 +
626 +  double calcZSys();
627 +
628 +  int isZConstraintMol(Molecule* mol);
629 +
630 +
631 +  double zconsTime;                              //sample time
632 +  double zconsTol;                                 //tolerance of z-contratint
633 +  double zForceConst;                           //base force constant term
634 +                                                          //which is estimate by OOPSE
635 +  
636 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
637 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
638 +  vector<double> kz;                              //force constant array
639 +  vector<ZConsState> states;                 //state of z-constraint molecules
640 +  vector<double> zPos;                          //
641 +  
642 +  
643 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
644 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
645 +  double totalMassOfUncons;                //total mas of unconstraint molecules
646 +
647 +  vector<ZConsParaItem>* parameters; //
648 +  
649 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
650 +
651 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
652 +  double* fz;
653 +  double* curZPos;
654 +  
655 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
656 +
657 +  int whichDirection;                           //constraint direction
658 +  
659 + private:
660 +  
661 +  string zconsOutput;                         //filename of zconstraint output
662 +  ZConsWriter* fzOut;                         //z-constraint writer
663 +
664 +  double curZconsTime;                      
665 +
666 +  double calcMovingMolsCOMVel();
667 +  double calcSysCOMVel();
668 +  double calcTotalForce();
669 +  
670 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
671 +  friend class ForceSubtractionPolicy;
672 +
673 + };
674 +
675 + #endif

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