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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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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 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 143 | Line 147 | template<typename T> class NPTi : public T{ (protected
147    virtual void moveB( void );
148  
149    virtual int readyCheck();
150 +
151 +  virtual void resetIntegrator( void );
152  
153    // chi and eta are the propagated degrees of freedom
154  
# 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 298 | Line 310 | template<typename T> class ZConstraint : public T {
310  
311   };
312  
313 < template<typename T> class ZConstraint : public T {
314 <        
303 <  public:      
304 <  class ForceSubstractionPolicy{
305 <    public:
306 <      ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
313 >
314 > template<typename T> class NPTpr : public T{
315  
316 <                virtual void update() = 0;              
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;;
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 : ForceSubstractionPolicy{
377 >  class PolicyByNumber : public ForceSubtractionPolicy{
378 >
379      public:
380 <                PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}              
381 <                virtual void update();          
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 <                
384 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
385 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
386 >    
387      private:
388 <                int totNumOfMovingAtoms;
388 >    int totNumOfMovingAtoms;
389    };
390  
391 <  class PolicyByMass :ForceSubstractionPolicy{
391 >  class PolicyByMass : public ForceSubtractionPolicy{
392 >
393      public:
394 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}  
395 <                        
396 <                virtual void update();          
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);
399 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
400 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
401  
402 <         private:
403 <           double totMassOfMovingAtoms;
402 >   private:
403 >     double totMassOfMovingAtoms;
404    };
405  
406   public:
# Line 350 | 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};
369 <
370 <
429 >  enum ZConsState {zcsMoving, zcsFixed};  
430  
431    virtual void calcForce( int calcPot, int calcStress );
432    virtual void thermalize(void);
# Line 385 | 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  
# Line 408 | Line 468 | template<typename T> class ZConstraint : public T { (p
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 curZconsTime;
480 >  double curZconsTime;                      
481  
482    double calcMovingMolsCOMVel();
483    double calcSysCOMVel();
484    double calcTotalForce();
485 <        
486 <  ForceSubstractionPolicy* forcePolicy;
487 <  friend class ForceSubstractionPolicy;
485 >  
486 >  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
487 >  friend class ForceSubtractionPolicy;
488  
489   };
490  

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