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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC vs.
Revision 747 by gezelter, Fri Sep 5 21:28:52 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 231 | Line 239 | template<typename T> class NPTf : public T{ (protected
239    virtual void  moveA( void );
240    virtual void moveB( void );
241  
242 +  virtual void resetIntegrator( void );
243 +
244    virtual int readyCheck();
245  
246    // chi and eta are the propagated degrees of freedom
# Line 274 | Line 284 | template<typename T> class NPTfm : public T{ (protecte
284    virtual void  moveA( void );
285    virtual void moveB( void );
286  
287 +  virtual void resetIntegrator( void );
288 +
289    virtual int readyCheck();
290  
291    Molecule* myMolecules;
# Line 297 | Line 309 | template<typename T> class NPTfm : public T{ (protecte
309    short int have_target_pressure;
310  
311   };
312 +
313 +
314 + template<typename T> class NPTpr : public T{
315 +
316 + public:
317  
318 +  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
319 +  virtual ~NPTpr() {};
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 +  // chi and eta are the propagated degrees of freedom
341 +
342 +  double chi;
343 +  double eta[3][3];
344 +  double NkBT;
345 +
346 +  // targetTemp, targetPressure, and tauBarostat must be set.  
347 +  // One of qmass or tauThermostat must be set;
348 +
349 +  double targetTemp;
350 +  double targetPressure;
351 +  double tauThermostat;
352 +  double tauBarostat;
353 +
354 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
355 +  short int have_target_pressure;
356 +
357 + };
358 +
359 +
360   template<typename T> class ZConstraint : public T {
361 +  
362 +  public:
363 +  class ForceSubtractionPolicy{
364 +    public:
365 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
366  
367 +      virtual void update() = 0;    
368 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
369 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
370 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
371 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
372 +    
373 +   protected:
374 +     ZConstraint<T>* zconsIntegrator;;
375 +  };
376 +
377 +  class PolicyByNumber : public ForceSubtractionPolicy{
378 +
379 +    public:
380 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
381 +      virtual void update();    
382 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
383 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
384 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
385 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
386 +    
387 +    private:
388 +    int totNumOfMovingAtoms;
389 +  };
390 +
391 +  class PolicyByMass : public ForceSubtractionPolicy{
392 +
393 +    public:
394 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
395 +      
396 +      virtual void update();    
397 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
398 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
399 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
400 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
401 +
402 +   private:
403 +     double totMassOfMovingAtoms;
404 +  };
405 +
406   public:
407  
408    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
# Line 308 | Line 411 | template<typename T> class ZConstraint : public T { (p
411    void setZConsTime(double time)                  {this->zconsTime = time;}
412    void getZConsTime()                             {return zconsTime;}
413    
414 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
415 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
414 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
415 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
416    
417 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
417 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
418    string getZConsOutput()                         {return zconsOutput;}
419    
420    virtual void integrate();
421    
422  
423   #ifdef IS_MPI
424 <  virtual void update(); //which is called to indicate the molecules' migration
424 >  virtual void update();                      //which is called to indicate the molecules' migration
425   #endif
426  
427   protected:
428  
429 <  enum ZConsState {zcsMoving, zcsFixed};
327 <
328 <
429 >  enum ZConsState {zcsMoving, zcsFixed};  
430  
431    virtual void calcForce( int calcPot, int calcStress );
432    virtual void thermalize(void);
# Line 343 | Line 444 | template<typename T> class ZConstraint : public T { (p
444    int isZConstraintMol(Molecule* mol);
445  
446  
447 <  double zconsTime;
448 <  double zconsTol;
449 <  double zForceConst;
447 >  double zconsTime;                              //sample time
448 >  double zconsTol;                                 //tolerance of z-contratint
449 >  double zForceConst;                           //base force constant term
450 >                                                          //which is estimate by OOPSE
451    
452 <  vector<Molecule*> zconsMols;
453 <  vector<double> massOfZConsMols;
454 <  vector<double> kz;
455 <  vector<ZConsState> states;
456 <  vector<double> zPos;
452 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
453 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
454 >  vector<double> kz;                              //force constant array
455 >  vector<ZConsState> states;                 //state of z-constraint molecules
456 >  vector<double> zPos;                          //
457    
458    
459 <  vector<Molecule*> unconsMols;
460 <  vector<double> massOfUnconsMols;
461 <  double totalMassOfUncons;
459 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
460 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
461 >  double totalMassOfUncons;                //total mas of unconstraint molecules
462  
463 <  vector<ZConsParaItem>* parameters;
463 >  vector<ZConsParaItem>* parameters; //
464    
465    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
466  
467    int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
468    double* fz;
469 +  double* curZPos;
470    
471 <  int totNumOfUnconsAtoms;
471 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
472  
473    int whichDirection;                           //constraint direction
474    
475   private:
476    
477 <  string zconsOutput;
478 <  ZConsWriter* fzOut;
477 >  string zconsOutput;                         //filename of zconstraint output
478 >  ZConsWriter* fzOut;                         //z-constraint writer
479  
480 <  double calcCOMVel();
378 <  double calcCOMVel2();
480 >  double curZconsTime;                      
481  
482 +  double calcMovingMolsCOMVel();
483 +  double calcSysCOMVel();
484 +  double calcTotalForce();
485 +  
486 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
487 +  friend class ForceSubtractionPolicy;
488 +
489   };
490  
491   #endif

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