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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 790 by mmeineke, Mon Sep 29 21:16:11 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 +  virtual void resetIntegrator(void);
236  
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 –
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{
# Line 320 | Line 307 | template<typename T> class NPTf : public T{ (public)
307   public:
308  
309    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
310 <  virtual ~NPTf() {};
310 >  virtual ~NPTf();
311  
325 –  virtual void integrateStep( int calcPot, int calcStress ){
326 –    calcStress = 1;
327 –    T::integrateStep( calcPot, calcStress );
328 –    accIntegralOfChidt();
329 –  }
330 –  
312    virtual double getConservedQuantity(void);
313 +  virtual void resetIntegrator(void);
314  
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 –
315   protected:
316  
317 <  virtual void  moveA( void );
318 <  virtual void moveB( void );
317 >  virtual void evolveEtaA(void);
318 >  virtual void evolveEtaB(void);
319  
320 <  virtual void resetIntegrator( void );
320 >  virtual bool etaConverged( void );
321  
322 <  virtual int readyCheck();
322 >  virtual void scaleSimBox( void );
323  
324 <  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
324 >  virtual void getVelScaleA( double sc[3], double vel[3] );
325 >  virtual void getVelScaleB( double sc[3], int index );
326 >  virtual void getPosScale(double pos[3], double COM[3],
327 >                           int index, double sc[3]);
328  
351 –  // chi and eta are the propagated degrees of freedom
352 –
353 –  double chi;
329    double eta[3][3];
330 <  double NkBT;
331 <
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 <
330 >  double oldEta[3][3];
331 >  double prevEta[3][3];
332   };
333  
334   template<typename T> class NPTxym : public T{
# Line 423 | Line 381 | template<typename T> class NPTxym : public T{ (protect
381  
382   };
383  
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 –
384   template<typename T> class ZConstraint : public T {
385    
386    public:
# Line 551 | Line 395 | template<typename T> class ZConstraint : public T {
395        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
396      
397     protected:
398 <     ZConstraint<T>* zconsIntegrator;;
398 >     ZConstraint<T>* zconsIntegrator;
399    };
400  
401    class PolicyByNumber : public ForceSubtractionPolicy{
# Line 604 | Line 448 | template<typename T> class ZConstraint : public T {
448    virtual void update();                      //which is called to indicate the molecules' migration
449   #endif
450  
451 +  enum ZConsState {zcsMoving, zcsFixed};  
452 +
453 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
454 +  vector<ZConsState> states;                 //state of z-constraint molecules
455 +
456 +
457 +
458 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
459 +  double totalMassOfUncons;                //total mas of unconstraint molecules
460 +
461 +
462   protected:
463  
464 <  enum ZConsState {zcsMoving, zcsFixed};  
464 >
465  
466    virtual void calcForce( int calcPot, int calcStress );
467    virtual void thermalize(void);
# Line 629 | Line 484 | template<typename T> class ZConstraint : public T {
484    double zForceConst;                           //base force constant term
485                                                            //which is estimate by OOPSE
486    
487 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
487 >
488    vector<double> massOfZConsMols;       //mass of z-constraint molecule
489    vector<double> kz;                              //force constant array
490 <  vector<ZConsState> states;                 //state of z-constraint molecules
490 >
491    vector<double> zPos;                          //
492    
493    
494    vector<Molecule*> unconsMols;           //unconstraint molecules array
495    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
641 –  double totalMassOfUncons;                //total mas of unconstraint molecules
496  
497 +
498    vector<ZConsParaItem>* parameters; //
499    
500    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
# Line 648 | Line 503 | template<typename T> class ZConstraint : public T {
503    double* fz;
504    double* curZPos;
505    
651 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
506  
507 +
508    int whichDirection;                           //constraint direction
509    
510   private:

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