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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC vs.
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC

# Line 30 | Line 30 | template<typename T = BaseIntegrator> class Integrator
30    virtual double  getConservedQuantity(void);
31  
32   protected:
33 <  
33 >
34    virtual void integrateStep( int calcPot, int calcStress );
35    virtual void preMove( void );
36    virtual void moveA( void );
# Line 44 | Line 44 | template<typename T = BaseIntegrator> class Integrator
44    virtual void calcForce( int calcPot, int calcStress );  
45    virtual void thermalize();
46    
47 +  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48 +
49    void checkConstraints( void );
50    void rotate( int axes1, int axes2, double angle, double j[3],
51           double A[3][3] );
# Line 135 | Line 137 | template<typename T> class NPTi : public T{
137  
138  
139  
140 < template<typename T> class NPTi : public T{
140 > template<typename T> class NPT : public T{
141  
142   public:
143  
144 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
145 <  virtual ~NPTi();
144 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
145 >  virtual ~NPT();
146    
147    virtual void integrateStep( int calcPot, int calcStress ){
148      calcStress = 1;
149      T::integrateStep( calcPot, calcStress );
148 –    /* accIntegralOfChidt(); */
150    }
151  
152 <  virtual double getConservedQuantity(void);
152 >  virtual double getConservedQuantity(void) = 0;
153  
154    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
155    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
# Line 167 | Line 168 | template<typename T> class NPTi : public T{ (protected
168  
169    virtual void resetIntegrator( void );
170  
171 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
172 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
173 +  virtual void getPosScale(double pos[3], double COM[3],
174 +                           int index, double sc[3]) = 0;
175 +
176 +  virtual bool chiConverged( void );
177 +  virtual bool etaConverged( void ) = 0;
178 +  
179 +  virtual void evolveChiA( void );
180 +  virtual void evolveEtaA( void ) = 0;
181 +  virtual void evolveChiB( void );
182 +  virtual void evolveEtaB( void ) = 0;
183 +
184 +  virtual void scaleSimBox( void ) = 0;
185 +
186    void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
187  
188    // chi and eta are the propagated degrees of freedom
189  
190 +  double oldChi;
191 +  double prevChi;
192    double chi;
175 –  double eta;
193    double NkBT;
194    double fkBT;
195  
196 +  double tt2, tb2;
197 +  double instaTemp, instaPress, instaVol;
198 +  double press[3][3];
199 +
200    int Nparticles;
201  
202    double integralOfChidt;
# Line 202 | Line 223 | template<typename T> class NPTi : public T{ (protected
223    double etaTolerance;
224    short int have_eta_tolerance;
225  
205 –  double volume;
206 –
226   };
227  
228 < template<typename T> class NPTim : public T{
229 <
228 > template<typename T> class NPTi : public T{
229 >  
230   public:
231 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
232 +  ~NPTi();
233  
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 –
234    virtual double getConservedQuantity(void);
235 <
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;}
235 >  virtual void resetIntegrator(void);
236  
237   protected:
238  
239 <  virtual void moveA( void );
234 <  virtual void moveB( void );
239 >
240  
241 <  virtual int readyCheck();
241 >  virtual void evolveEtaA(void);
242 >  virtual void evolveEtaB(void);
243  
244 <  virtual void resetIntegrator( void );
244 >  virtual bool etaConverged( void );
245  
246 <  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
241 <  
242 <  Molecule* myMolecules;
243 <  Atom** myAtoms;
246 >  virtual void scaleSimBox( void );
247  
248 <  // chi and eta are the propagated degrees of freedom
248 >  virtual void getVelScaleA( double sc[3], double vel[3] );
249 >  virtual void getVelScaleB( double sc[3], int index );
250 >  virtual void getPosScale(double pos[3], double COM[3],
251 >                           int index, double sc[3]);
252  
253 <  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 <
253 >  double eta, oldEta, prevEta;
254   };
255  
256 < template<typename T> class NPTzm : public T{
256 > template<typename T> class NPTf : public T{
257  
258   public:
259  
260 <  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
261 <  virtual ~NPTzm() {};
275 <
276 <  virtual void integrateStep( int calcPot, int calcStress ){
277 <    calcStress = 1;
278 <    T::integrateStep( calcPot, calcStress );
279 <  }
260 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
261 >  virtual ~NPTf();
262  
263 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
264 <  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;}
263 >  virtual double getConservedQuantity(void);
264 >  virtual void resetIntegrator(void);
265  
266   protected:
267  
268 <  virtual void moveA( void );
269 <  virtual void moveB( void );
268 >  virtual void evolveEtaA(void);
269 >  virtual void evolveEtaB(void);
270  
271 <  virtual int readyCheck();
271 >  virtual bool etaConverged( void );
272  
273 <  virtual void resetIntegrator( void );
273 >  virtual void scaleSimBox( void );
274  
275 <  Molecule* myMolecules;
276 <  Atom** myAtoms;
275 >  virtual void getVelScaleA( double sc[3], double vel[3] );
276 >  virtual void getVelScaleB( double sc[3], int index );
277 >  virtual void getPosScale(double pos[3], double COM[3],
278 >                           int index, double sc[3]);
279  
280 <  // chi and eta are the propagated degrees of freedom
281 <
282 <  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 <
280 >  double eta[3][3];
281 >  double oldEta[3][3];
282 >  double prevEta[3][3];
283   };
284  
285 < template<typename T> class NPTf : public T{
285 > template<typename T> class NPTxyz : public T{
286  
287   public:
288  
289 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
290 <  virtual ~NPTf() {};
289 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
290 >  virtual ~NPTxyz();
291  
325 –  virtual void integrateStep( int calcPot, int calcStress ){
326 –    calcStress = 1;
327 –    T::integrateStep( calcPot, calcStress );
328 –    accIntegralOfChidt();
329 –  }
330 –  
292    virtual double getConservedQuantity(void);
293 +  virtual void resetIntegrator(void);
294  
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 –
295   protected:
296  
297 <  virtual void  moveA( void );
298 <  virtual void moveB( void );
297 >  virtual void evolveEtaA(void);
298 >  virtual void evolveEtaB(void);
299  
300 <  virtual void resetIntegrator( void );
300 >  virtual bool etaConverged( void );
301  
302 <  virtual int readyCheck();
302 >  virtual void scaleSimBox( void );
303  
304 <  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
304 >  virtual void getVelScaleA( double sc[3], double vel[3] );
305 >  virtual void getVelScaleB( double sc[3], int index );
306 >  virtual void getPosScale(double pos[3], double COM[3],
307 >                           int index, double sc[3]);
308  
351 –  // chi and eta are the propagated degrees of freedom
352 –
353 –  double chi;
309    double eta[3][3];
310 <  double NkBT;
311 <
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 <
310 >  double oldEta[3][3];
311 >  double prevEta[3][3];
312   };
313  
376 – template<typename T> class NPTxym : public T{
314  
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 –
315   template<typename T> class ZConstraint : public T {
316    
317    public:
# Line 551 | Line 326 | template<typename T> class ZConstraint : public T {
326        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
327      
328     protected:
329 <     ZConstraint<T>* zconsIntegrator;;
329 >     ZConstraint<T>* zconsIntegrator;
330    };
331  
332    class PolicyByNumber : public ForceSubtractionPolicy{
# Line 604 | Line 379 | template<typename T> class ZConstraint : public T {
379    virtual void update();                      //which is called to indicate the molecules' migration
380   #endif
381  
382 +  enum ZConsState {zcsMoving, zcsFixed};  
383 +
384 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
385 +  vector<ZConsState> states;                 //state of z-constraint molecules
386 +
387 +
388 +
389 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
390 +  double totalMassOfUncons;                //total mas of unconstraint molecules
391 +
392 +
393   protected:
394  
395 <  enum ZConsState {zcsMoving, zcsFixed};  
395 >
396  
397    virtual void calcForce( int calcPot, int calcStress );
398    virtual void thermalize(void);
# Line 629 | Line 415 | template<typename T> class ZConstraint : public T {
415    double zForceConst;                           //base force constant term
416                                                            //which is estimate by OOPSE
417    
418 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
418 >
419    vector<double> massOfZConsMols;       //mass of z-constraint molecule
420    vector<double> kz;                              //force constant array
421 <  vector<ZConsState> states;                 //state of z-constraint molecules
421 >
422    vector<double> zPos;                          //
423    
424    
425    vector<Molecule*> unconsMols;           //unconstraint molecules array
426    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
641 –  double totalMassOfUncons;                //total mas of unconstraint molecules
427  
428 +
429    vector<ZConsParaItem>* parameters; //
430    
431    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
# Line 648 | Line 434 | template<typename T> class ZConstraint : public T {
434    double* fz;
435    double* curZPos;
436    
651 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
437  
438 +
439    int whichDirection;                           //constraint direction
440    
441   private:

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