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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Integrator.hpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Integrator.hpp (file contents), 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 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 >  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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