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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 701 by tim, Wed Aug 20 14:34:04 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC

# Line 27 | Line 27 | template<typename T = BaseIntegrator> class Integrator
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31  
31 –
32   protected:
33    
34    virtual void integrateStep( int calcPot, int calcStress );
# Line 39 | Line 39 | template<typename T = BaseIntegrator> class Integrator
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    
# Line 93 | Line 95 | template<typename T> class NVT : public T { (public)
95   public:
96  
97    NVT ( SimInfo *theInfo, ForceFields* the_ff);
98 <  virtual ~NVT() {}
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  
# Line 105 | Line 109 | template<typename T> class NVT : public T { (public)
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;
# Line 116 | Line 125 | template<typename T> class NVT : public T { (public)
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  
# Line 125 | Line 140 | template<typename T> class NPTi : public T{ (public)
140   public:
141  
142    NPTi ( SimInfo *theInfo, ForceFields* the_ff);
143 <  virtual ~NPTi() {};
144 <
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 +  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  
# Line 144 | Line 165 | template<typename T> class NPTi : public T{ (public)
165  
166    virtual int readyCheck();
167  
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  
# Line 161 | Line 191 | template<typename T> class NPTi : public T{ (public)
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{
# Line 168 | Line 211 | template<typename T> class NPTim : public T{ (public)
211   public:
212  
213    NPTim ( SimInfo *theInfo, ForceFields* the_ff);
214 <  virtual ~NPTim() {};
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  
# Line 187 | Line 235 | template<typename T> class NPTim : public T{ (public)
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  
# Line 195 | Line 247 | template<typename T> class NPTim : public T{ (public)
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;
# Line 206 | Line 259 | template<typename T> class NPTim : public T{ (public)
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:
# Line 219 | Line 325 | template<typename T> class NPTf : public T{ (public)
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  
# Line 249 | Line 366 | template<typename T> class NPTf : public T{ (public)
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:
# Line 262 | Line 434 | template<typename T> class NPTfm : public T{ (public)
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  
# Line 284 | Line 465 | template<typename T> class NPTfm : public T{ (public)
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;
# Line 295 | Line 477 | template<typename T> class NPTfm : public T{ (public)
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 ForceSubstractionPolicy{
543 >  class ForceSubtractionPolicy{
544      public:
545 <      ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
545 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
546  
547        virtual void update() = 0;    
548        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
# Line 315 | Line 554 | template<typename T> class ZConstraint : public T {
554       ZConstraint<T>* zconsIntegrator;;
555    };
556  
557 <  class PolicyByNumber : ForceSubstractionPolicy{
557 >  class PolicyByNumber : public ForceSubtractionPolicy{
558 >
559      public:
560 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}    
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) ;
# Line 325 | Line 565 | template<typename T> class ZConstraint : public T {
565        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
566      
567      private:
568 <    int totNumOfMovingAtoms;
568 >      int totNumOfMovingAtoms;
569    };
570  
571 <  class PolicyByMass :ForceSubstractionPolicy{
571 >  class PolicyByMass : public ForceSubtractionPolicy{
572 >
573      public:
574 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}  
574 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
575        
576        virtual void update();    
577        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
# Line 422 | Line 663 | template<typename T> class ZConstraint : public T {
663    double calcSysCOMVel();
664    double calcTotalForce();
665    
666 <  ForceSubstractionPolicy* forcePolicy; //force substration policy
667 <  friend class ForceSubstractionPolicy;
666 >  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
667 >  friend class ForceSubtractionPolicy;
668  
669   };
670  

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