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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 780 by mmeineke, Mon Sep 22 21:23:25 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 <  
33 >
34    virtual void integrateStep( int calcPot, int calcStress );
35    virtual void preMove( void );
36    virtual void moveA( void );
# Line 38 | Line 38 | template<typename T = BaseIntegrator> class Integrator
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 +  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] );
52 <
46 <
51 >         double A[3][3] );
52 >        
53    ForceFields* myFF;
54  
55    SimInfo *info; // all the info we'll ever need
# Line 54 | Line 60 | template<typename T = BaseIntegrator> class Integrator
60    int nMols;
61  
62    int isConstrained; // boolean to know whether the systems contains
63 <                     // constraints.
63 >         // constraints.
64    int nConstrained;  // counter for number of constraints
65    int *constrainedA; // the i of a constraint pair
66    int *constrainedB; // the j of a constraint pair
# Line 91 | Line 97 | template<typename T> class NVT : public T { (public)
97   public:
98  
99    NVT ( SimInfo *theInfo, ForceFields* the_ff);
100 <  virtual ~NVT() {}
100 >  virtual ~NVT();
101  
102    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
103    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
104 +  void setChiTolerance(double tol) {chiTolerance = tol;}
105 +  virtual double  getConservedQuantity(void);
106  
107   protected:
108  
# Line 103 | Line 111 | template<typename T> class NVT : public T { (public)
111  
112    virtual int readyCheck();
113  
114 +  virtual void resetIntegrator( void );
115 +
116    // chi is a propagated degree of freedom.
117  
118    double chi;
119  
120 +  //integral of chi(t)dt
121 +  double integralOfChidt;
122 +
123    // targetTemp must be set.  tauThermostat must also be set;
124  
125    double targetTemp;
# Line 114 | Line 127 | template<typename T> class NVT : public T { (public)
127    
128    short int have_tau_thermostat, have_target_temp;
129  
130 +  double *oldVel;
131 +  double *oldJi;
132 +
133 +  double chiTolerance;
134 +  short int have_chi_tolerance;
135 +
136   };
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() {};
146 <
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 );
150    }
151  
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;}
156    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
157    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
158 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
159 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
160 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
161  
162   protected:
163  
# Line 142 | Line 166 | template<typename T> class NPTi : public T{ (protected
166  
167    virtual int readyCheck();
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;
148 –  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;
203 +
204    // targetTemp, targetPressure, and tauBarostat must be set.  
205    // One of qmass or tauThermostat must be set;
206  
# Line 159 | Line 212 | template<typename T> class NPTi : public T{ (protected
212    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
213    short int have_target_pressure;
214  
215 +  double *oldPos;
216 +  double *oldVel;
217 +  double *oldJi;
218 +
219 +  double chiTolerance;
220 +  short int have_chi_tolerance;
221 +  double posIterTolerance;
222 +  short int have_pos_iter_tolerance;
223 +  double etaTolerance;
224 +  short int have_eta_tolerance;
225 +
226   };
227  
228 < template<typename T> class NPTim : public T{
228 > template<typename T> class NPTi : public T{
229 >  
230 > public:
231 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
232 >  ~NPTi();
233 >
234 >  virtual double getConservedQuantity(void);
235 >  virtual void resetIntegrator(void);
236  
237 + protected:
238 +
239 +
240 +
241 +  virtual void evolveEtaA(void);
242 +  virtual void evolveEtaB(void);
243 +
244 +  virtual bool etaConverged( void );
245 +
246 +  virtual void scaleSimBox( void );
247 +
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 eta, oldEta, prevEta;
254 + };
255 +
256 + template<typename T> class NPTzm : public T{
257 +
258   public:
259  
260 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
261 <  virtual ~NPTim() {};
260 >  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
261 >  virtual ~NPTzm() {};
262  
263    virtual void integrateStep( int calcPot, int calcStress ){
264      calcStress = 1;
# Line 185 | Line 277 | template<typename T> class NPTim : public T{ (protecte
277  
278    virtual int readyCheck();
279  
280 +  virtual void resetIntegrator( void );
281 +
282    Molecule* myMolecules;
283    Atom** myAtoms;
284  
# Line 192 | Line 286 | template<typename T> class NPTim : public T{ (protecte
286  
287    double chi;
288    double eta;
289 +  double etaZ;
290    double NkBT;
291  
292    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 212 | 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  
312 +  virtual double getConservedQuantity(void);
313 +  virtual void resetIntegrator(void);
314 +
315 + protected:
316 +
317 +  virtual void evolveEtaA(void);
318 +  virtual void evolveEtaB(void);
319 +
320 +  virtual bool etaConverged( void );
321 +
322 +  virtual void scaleSimBox( void );
323 +
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 +
329 +  double eta[3][3];
330 +  double oldEta[3][3];
331 +  double prevEta[3][3];
332 + };
333 +
334 + template<typename T> class NPTxym : public T{
335 +
336 + public:
337 +
338 +  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
339 +  virtual ~NPTxym() {};
340 +
341    virtual void integrateStep( int calcPot, int calcStress ){
342      calcStress = 1;
343      T::integrateStep( calcPot, calcStress );
# Line 226 | Line 350 | template<typename T> class NPTf : public T{ (public)
350  
351   protected:
352  
353 <  virtual void  moveA( void );
353 >  virtual void moveA( void );
354    virtual void moveB( void );
355  
356    virtual int readyCheck();
357  
358 +  virtual void resetIntegrator( void );
359 +
360 +  Molecule* myMolecules;
361 +  Atom** myAtoms;
362 +
363    // chi and eta are the propagated degrees of freedom
364  
365    double chi;
366 <  double eta[3][3];
366 >  double eta;
367 >  double etaX;
368 >  double etaY;
369    double NkBT;
370  
371    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 250 | Line 381 | template<typename T> class NPTfm : public T{
381  
382   };
383  
384 +
385   template<typename T> class NPTfm : public T{
386  
387   public:
# Line 260 | Line 392 | template<typename T> class NPTfm : public T{ (public)
392    virtual void integrateStep( int calcPot, int calcStress ){
393      calcStress = 1;
394      T::integrateStep( calcPot, calcStress );
395 +    accIntegralOfChidt();
396    }
397  
398 +  virtual double getConservedQuantity(void);
399 +  
400    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
401    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
402    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
403    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
404 +  void setChiTolerance(double tol) {chiTolerance = tol;}
405 +  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
406  
407   protected:
408  
409    virtual void  moveA( void );
410    virtual void moveB( void );
411  
412 +  virtual void resetIntegrator( void );
413 +
414    virtual int readyCheck();
415  
416 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
417 +
418    Molecule* myMolecules;
419    Atom** myAtoms;
420  
# Line 282 | Line 423 | template<typename T> class NPTfm : public T{ (public)
423    double chi;
424    double eta[3][3];
425    double NkBT;
426 +  double integralOfChidt;
427  
428    // targetTemp, targetPressure, and tauBarostat must be set.  
429    // One of qmass or tauThermostat must be set;
# Line 293 | Line 435 | template<typename T> class NPTfm : public T{ (public)
435  
436    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
437    short int have_target_pressure;
438 +  double chiTolerance;
439 +  short int have_chi_tolerance;
440 +  double posIterTolerance;
441 +  short int have_pos_iter_tolerance;
442  
443   };
444  
299 – template<typename T> class ZConstraint : public T {
445  
446 + template<typename T> class NPTpr : public T{
447 +
448   public:
449  
450 <  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
451 <  ~ZConstraint();
452 <
453 <  virtual void integrateStep( int calcPot, int calcStress );
450 >  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
451 >  virtual ~NPTpr() {};
452 >
453 >  virtual void integrateStep( int calcPot, int calcStress ){
454 >    calcStress = 1;
455 >    T::integrateStep( calcPot, calcStress );
456 >  }
457 >
458 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
459 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
460 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
461 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
462 >  void setChiTolerance(double tol) {chiTolerance = tol;}
463 >  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
464 >
465 > protected:
466 >
467 >  virtual void  moveA( void );
468 >  virtual void moveB( void );
469 >
470 >  virtual int readyCheck();
471 >
472 >  virtual void resetIntegrator( void );
473 >
474 >  // chi and eta are the propagated degrees of freedom
475 >
476 >  double chi;
477 >  double eta[3][3];
478 >  double NkBT;
479 >
480 >  // targetTemp, targetPressure, and tauBarostat must be set.  
481 >  // One of qmass or tauThermostat must be set;
482 >
483 >  double targetTemp;
484 >  double targetPressure;
485 >  double tauThermostat;
486 >  double tauBarostat;
487 >
488 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
489 >  short int have_target_pressure;
490 >  double chiTolerance;
491 >  short int have_chi_tolerance;
492 >  double posIterTolerance;
493 >  short int have_pos_iter_tolerance;
494 >
495 > };
496 >
497 >
498 > template<typename T> class ZConstraint : public T {
499    
500 <  
500 >  public:
501 >  class ForceSubtractionPolicy{
502 >    public:
503 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
504 >
505 >      virtual void update() = 0;    
506 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
507 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
508 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
509 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
510 >    
511 >   protected:
512 >     ZConstraint<T>* zconsIntegrator;;
513 >  };
514 >
515 >  class PolicyByNumber : public ForceSubtractionPolicy{
516 >
517 >    public:
518 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
519 >      virtual void update();    
520 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
521 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
522 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
523 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
524 >    
525 >    private:
526 >      int totNumOfMovingAtoms;
527 >  };
528 >
529 >  class PolicyByMass : public ForceSubtractionPolicy{
530 >
531 >    public:
532 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
533 >      
534 >      virtual void update();    
535 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
536 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
537 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
538 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
539 >
540 >   private:
541 >     double totMassOfMovingAtoms;
542 >  };
543 >
544 > public:
545 >
546 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
547 >  ~ZConstraint();
548 >    
549    void setZConsTime(double time)                  {this->zconsTime = time;}
550    void getZConsTime()                             {return zconsTime;}
551    
552 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
553 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
552 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
553 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
554    
555 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
555 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
556    string getZConsOutput()                         {return zconsOutput;}
557 +  
558 +  virtual void integrate();
559 +  
560  
561   #ifdef IS_MPI
562 <  virtual void update(); //which is called to indicate the molecules' migration
562 >  virtual void update();                      //which is called to indicate the molecules' migration
563   #endif
564  
565   protected:
566  
567 <  double zconsTime;
567 >  enum ZConsState {zcsMoving, zcsFixed};  
568 >
569 >  virtual void calcForce( int calcPot, int calcStress );
570 >  virtual void thermalize(void);
571    
572 <  void resetZ(void);
572 >  void zeroOutVel();
573 >  void doZconstraintForce();
574 >  void doHarmonic();
575 >  bool checkZConsState();
576 >
577 >  bool haveFixedZMols();
578 >  bool haveMovingZMols();
579 >
580 >  double calcZSys();
581 >
582 >  int isZConstraintMol(Molecule* mol);
583 >
584 >
585 >  double zconsTime;                              //sample time
586 >  double zconsTol;                                 //tolerance of z-contratint
587 >  double zForceConst;                           //base force constant term
588 >                                                          //which is estimate by OOPSE
589    
590 <  vector<Molecule*> zconsMols;
591 <  vector<double> massOfZConsMols;
590 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
591 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
592 >  vector<double> kz;                              //force constant array
593 >  vector<ZConsState> states;                 //state of z-constraint molecules
594 >  vector<double> zPos;                          //
595    
596 <  vector<Molecule*> unconsMols;
597 <  vector<double> massOfUnconsMols;
598 <  double totalMassOfUncons;
596 >  
597 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
598 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
599 >  double totalMassOfUncons;                //total mas of unconstraint molecules
600  
601 <  vector<double> allRefZ;    
336 <  vector<double> refZ;
601 >  vector<ZConsParaItem>* parameters; //
602    
603    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
604 <  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
605 <    
604 >
605 >  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
606    double* fz;
607 +  double* curZPos;
608    
609 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
610 +
611 +  int whichDirection;                           //constraint direction
612 +  
613   private:
614 +  
615 +  string zconsOutput;                         //filename of zconstraint output
616 +  ZConsWriter* fzOut;                         //z-constraint writer
617  
618 <  int isZConstraintMol(Molecule* mol);
619 <  string zconsOutput;
620 <  ZConsWriter* fzOut;
618 >  double curZconsTime;                      
619 >
620 >  double calcMovingMolsCOMVel();
621 >  double calcSysCOMVel();
622 >  double calcTotalForce();
623 >  
624 >  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
625 >  friend class ForceSubtractionPolicy;
626 >
627   };
628  
629   #endif

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