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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 677 by tim, Mon Aug 11 19:41:36 2003 UTC vs.
Revision 755 by mmeineke, Tue Sep 9 20:35:25 2003 UTC

# 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    
47    void checkConstraints( void );
48    void rotate( int axes1, int axes2, double angle, double j[3],
49 <               double A[3][3] );
50 <              
49 >         double A[3][3] );
50 >        
51    ForceFields* myFF;
52  
53    SimInfo *info; // all the info we'll ever need
# Line 56 | Line 58 | template<typename T = BaseIntegrator> class Integrator
58    int nMols;
59  
60    int isConstrained; // boolean to know whether the systems contains
61 <                     // constraints.
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
# Line 105 | Line 107 | template<typename T> class NVT : public T { (protected
107  
108    virtual int readyCheck();
109  
110 +  virtual void resetIntegrator( void );
111 +
112    // chi is a propagated degree of freedom.
113  
114    double chi;
# Line 144 | Line 148 | template<typename T> class NPTi : public T{ (protected
148  
149    virtual int readyCheck();
150  
151 +  virtual void resetIntegrator( void );
152 +
153    // chi and eta are the propagated degrees of freedom
154  
155    double chi;
# Line 187 | Line 193 | template<typename T> class NPTim : public T{ (protecte
193  
194    virtual int readyCheck();
195  
196 +  virtual void resetIntegrator( void );
197 +
198    Molecule* myMolecules;
199    Atom** myAtoms;
200  
# Line 209 | Line 217 | template<typename T> class NPTim : public T{ (protecte
217  
218   };
219  
220 + template<typename T> class NPTzm : public T{
221 +
222 + public:
223 +
224 +  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
225 +  virtual ~NPTzm() {};
226 +
227 +  virtual void integrateStep( int calcPot, int calcStress ){
228 +    calcStress = 1;
229 +    T::integrateStep( calcPot, calcStress );
230 +  }
231 +
232 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
233 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
234 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
235 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
236 +
237 + protected:
238 +
239 +  virtual void moveA( void );
240 +  virtual void moveB( void );
241 +
242 +  virtual int readyCheck();
243 +
244 +  virtual void resetIntegrator( void );
245 +
246 +  Molecule* myMolecules;
247 +  Atom** myAtoms;
248 +
249 +  // chi and eta are the propagated degrees of freedom
250 +
251 +  double chi;
252 +  double eta;
253 +  double etaZ;
254 +  double NkBT;
255 +
256 +  // targetTemp, targetPressure, and tauBarostat must be set.  
257 +  // One of qmass or tauThermostat must be set;
258 +
259 +  double targetTemp;
260 +  double targetPressure;
261 +  double tauThermostat;
262 +  double tauBarostat;
263 +
264 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
265 +  short int have_target_pressure;
266 +
267 + };
268 +
269   template<typename T> class NPTf : public T{
270  
271   public:
# Line 231 | Line 288 | template<typename T> class NPTf : public T{ (protected
288    virtual void  moveA( void );
289    virtual void moveB( void );
290  
291 +  virtual void resetIntegrator( void );
292 +
293    virtual int readyCheck();
294  
295    // chi and eta are the propagated degrees of freedom
296  
297    double chi;
298    double eta[3][3];
299 +  double NkBT;
300 +
301 +  // targetTemp, targetPressure, and tauBarostat must be set.  
302 +  // One of qmass or tauThermostat must be set;
303 +
304 +  double targetTemp;
305 +  double targetPressure;
306 +  double tauThermostat;
307 +  double tauBarostat;
308 +
309 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
310 +  short int have_target_pressure;
311 +
312 + };
313 +
314 + template<typename T> class NPTxym : public T{
315 +
316 + public:
317 +
318 +  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
319 +  virtual ~NPTxym() {};
320 +
321 +  virtual void integrateStep( int calcPot, int calcStress ){
322 +    calcStress = 1;
323 +    T::integrateStep( calcPot, calcStress );
324 +  }
325 +
326 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
327 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
328 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
329 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
330 +
331 + protected:
332 +
333 +  virtual void moveA( void );
334 +  virtual void moveB( void );
335 +
336 +  virtual int readyCheck();
337 +
338 +  virtual void resetIntegrator( void );
339 +
340 +  Molecule* myMolecules;
341 +  Atom** myAtoms;
342 +
343 +  // chi and eta are the propagated degrees of freedom
344 +
345 +  double chi;
346 +  double eta;
347 +  double etaX;
348 +  double etaY;
349    double NkBT;
350  
351    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 252 | Line 361 | template<typename T> class NPTf : public T{ (protected
361  
362   };
363  
364 +
365   template<typename T> class NPTfm : public T{
366  
367   public:
# Line 274 | Line 384 | template<typename T> class NPTfm : public T{ (protecte
384    virtual void  moveA( void );
385    virtual void moveB( void );
386  
387 +  virtual void resetIntegrator( void );
388 +
389    virtual int readyCheck();
390  
391    Molecule* myMolecules;
392    Atom** myAtoms;
393 +
394 +  // chi and eta are the propagated degrees of freedom
395 +
396 +  double chi;
397 +  double eta[3][3];
398 +  double NkBT;
399 +
400 +  // targetTemp, targetPressure, and tauBarostat must be set.  
401 +  // One of qmass or tauThermostat must be set;
402 +
403 +  double targetTemp;
404 +  double targetPressure;
405 +  double tauThermostat;
406 +  double tauBarostat;
407 +
408 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
409 +  short int have_target_pressure;
410  
411 + };
412 +
413 +
414 + template<typename T> class NPTpr : public T{
415 +
416 + public:
417 +
418 +  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
419 +  virtual ~NPTpr() {};
420 +
421 +  virtual void integrateStep( int calcPot, int calcStress ){
422 +    calcStress = 1;
423 +    T::integrateStep( calcPot, calcStress );
424 +  }
425 +
426 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
427 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
428 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
429 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
430 +
431 + protected:
432 +
433 +  virtual void  moveA( void );
434 +  virtual void moveB( void );
435 +
436 +  virtual int readyCheck();
437 +
438 +  virtual void resetIntegrator( void );
439 +
440    // chi and eta are the propagated degrees of freedom
441  
442    double chi;
# Line 298 | Line 456 | template<typename T> class NPTfm : public T{ (protecte
456  
457   };
458  
459 +
460   template<typename T> class ZConstraint : public T {
461 +  
462 +  public:
463 +  class ForceSubtractionPolicy{
464 +    public:
465 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
466  
467 +      virtual void update() = 0;    
468 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
469 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
470 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
471 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
472 +    
473 +   protected:
474 +     ZConstraint<T>* zconsIntegrator;;
475 +  };
476 +
477 +  class PolicyByNumber : public ForceSubtractionPolicy{
478 +
479 +    public:
480 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
481 +      virtual void update();    
482 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
483 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
484 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
485 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
486 +    
487 +    private:
488 +    int totNumOfMovingAtoms;
489 +  };
490 +
491 +  class PolicyByMass : public ForceSubtractionPolicy{
492 +
493 +    public:
494 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
495 +      
496 +      virtual void update();    
497 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
498 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
499 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
500 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
501 +
502 +   private:
503 +     double totMassOfMovingAtoms;
504 +  };
505 +
506   public:
507  
508    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
# Line 308 | Line 511 | template<typename T> class ZConstraint : public T { (p
511    void setZConsTime(double time)                  {this->zconsTime = time;}
512    void getZConsTime()                             {return zconsTime;}
513    
514 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
515 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
514 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
515 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
516    
517 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
517 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
518    string getZConsOutput()                         {return zconsOutput;}
519    
520    virtual void integrate();
521    
522  
523   #ifdef IS_MPI
524 <  virtual void update(); //which is called to indicate the molecules' migration
524 >  virtual void update();                      //which is called to indicate the molecules' migration
525   #endif
526  
527   protected:
528  
529 <  enum ZConsState {zcsMoving, zcsFixed};
327 <
328 <
529 >  enum ZConsState {zcsMoving, zcsFixed};  
530  
531    virtual void calcForce( int calcPot, int calcStress );
532    virtual void thermalize(void);
533    
534    void zeroOutVel();
535    void doZconstraintForce();
536 +  void doHarmonic();
537    bool checkZConsState();
538  
539    bool haveFixedZMols();
# Line 342 | Line 544 | template<typename T> class ZConstraint : public T { (p
544    int isZConstraintMol(Molecule* mol);
545  
546  
547 <  double zconsTime;
548 <  double ztol;
547 >  double zconsTime;                              //sample time
548 >  double zconsTol;                                 //tolerance of z-contratint
549 >  double zForceConst;                           //base force constant term
550 >                                                          //which is estimate by OOPSE
551    
552 <  vector<Molecule*> zconsMols;
553 <  vector<double> massOfZConsMols;
554 <  vector<double> zconsPos;
555 <  vector<double> kz;
556 <  vector<ZConsState> states;
353 <  vector<double> ZPos;
552 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
553 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
554 >  vector<double> kz;                              //force constant array
555 >  vector<ZConsState> states;                 //state of z-constraint molecules
556 >  vector<double> zPos;                          //
557    
558    
559 <  vector<Molecule*> unconsMols;
560 <  vector<double> massOfUnconsMols;
561 <  double totalMassOfUncons;
559 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
560 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
561 >  double totalMassOfUncons;                //total mas of unconstraint molecules
562 >
563 >  vector<ZConsParaItem>* parameters; //
564    
565    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
566  
567    int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
568    double* fz;
569 +  double* curZPos;
570    
571 <  int totNumOfUnconsAtoms;
571 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
572  
573    int whichDirection;                           //constraint direction
574    
575   private:
576    
577 <  string zconsOutput;
578 <  ZConsWriter* fzOut;
577 >  string zconsOutput;                         //filename of zconstraint output
578 >  ZConsWriter* fzOut;                         //z-constraint writer
579  
580 +  double curZconsTime;                      
581  
582 +  double calcMovingMolsCOMVel();
583 +  double calcSysCOMVel();
584 +  double calcTotalForce();
585 +  
586 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
587 +  friend class ForceSubtractionPolicy;
588 +
589   };
590  
591   #endif

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