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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 699 by tim, Fri Aug 15 19:24:13 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 169 | Line 175 | template<typename T> class NPTim : public T{ (public)
175  
176    NPTim ( SimInfo *theInfo, ForceFields* the_ff);
177    virtual ~NPTim() {};
178 +
179 +  virtual void integrateStep( int calcPot, int calcStress ){
180 +    calcStress = 1;
181 +    T::integrateStep( calcPot, calcStress );
182 +  }
183 +
184 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
185 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
186 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
187 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
188 +
189 + protected:
190 +
191 +  virtual void moveA( void );
192 +  virtual void moveB( void );
193 +
194 +  virtual int readyCheck();
195 +
196 +  virtual void resetIntegrator( void );
197 +
198 +  Molecule* myMolecules;
199 +  Atom** myAtoms;
200 +
201 +  // chi and eta are the propagated degrees of freedom
202 +
203 +  double chi;
204 +  double eta;
205 +  double NkBT;
206  
207 +  // targetTemp, targetPressure, and tauBarostat must be set.  
208 +  // One of qmass or tauThermostat must be set;
209 +
210 +  double targetTemp;
211 +  double targetPressure;
212 +  double tauThermostat;
213 +  double tauBarostat;
214 +
215 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
216 +  short int have_target_pressure;
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 );
# Line 187 | Line 241 | template<typename T> class NPTim : public T{ (public)
241  
242    virtual int readyCheck();
243  
244 +  virtual void resetIntegrator( void );
245 +
246    Molecule* myMolecules;
247    Atom** myAtoms;
248  
# Line 194 | Line 250 | template<typename T> class NPTim : public T{ (public)
250  
251    double chi;
252    double eta;
253 +  double etaZ;
254    double NkBT;
255  
256    // targetTemp, targetPressure, and tauBarostat must be set.  
# 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 NPTfm : public T{
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;
# Line 298 | Line 410 | template<typename T> class ZConstraint : public T {
410  
411   };
412  
301 – template<typename T> class ZConstraint : public T {
302 –        
303 –  public:      
304 –  class ForceSubstractionPolicy{
305 –    public:
306 –      ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
413  
414 <                virtual void update() = 0;              
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;
443 >  double eta[3][3];
444 >  double NkBT;
445 >
446 >  // targetTemp, targetPressure, and tauBarostat must be set.  
447 >  // One of qmass or tauThermostat must be set;
448 >
449 >  double targetTemp;
450 >  double targetPressure;
451 >  double tauThermostat;
452 >  double tauBarostat;
453 >
454 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
455 >  short int have_target_pressure;
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;;
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 : ForceSubstractionPolicy{
477 >  class PolicyByNumber : public ForceSubtractionPolicy{
478 >
479      public:
480 <                PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}              
481 <                virtual void update();          
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 <                
484 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
485 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
486 >    
487      private:
488 <                int totNumOfMovingAtoms;
488 >    int totNumOfMovingAtoms;
489    };
490  
491 <  class PolicyByMass :ForceSubstractionPolicy{
491 >  class PolicyByMass : public ForceSubtractionPolicy{
492 >
493      public:
494 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}  
495 <                        
496 <                virtual void update();          
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);
499 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
500 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
501  
502 <         private:
503 <           double totMassOfMovingAtoms;
502 >   private:
503 >     double totMassOfMovingAtoms;
504    };
505  
506   public:
# Line 350 | 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};
369 <
370 <
529 >  enum ZConsState {zcsMoving, zcsFixed};  
530  
531    virtual void calcForce( int calcPot, int calcStress );
532    virtual void thermalize(void);
# Line 385 | Line 544 | template<typename T> class ZConstraint : public T { (p
544    int isZConstraintMol(Molecule* mol);
545  
546  
547 <  double zconsTime;
548 <  double zconsTol;
549 <  double zForceConst;
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> kz;
555 <  vector<ZConsState> states;
556 <  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;
563 >  vector<ZConsParaItem>* parameters; //
564    
565    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
566  
# Line 408 | Line 568 | template<typename T> class ZConstraint : public T { (p
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;
580 >  double curZconsTime;                      
581  
582    double calcMovingMolsCOMVel();
583    double calcSysCOMVel();
584    double calcTotalForce();
585 <        
586 <  ForceSubstractionPolicy* forcePolicy;
587 <  friend class ForceSubstractionPolicy;
585 >  
586 >  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
587 >  friend class ForceSubtractionPolicy;
588  
589   };
590  

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