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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 746 by mmeineke, Thu Sep 4 21:48:35 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      public:
379 <                PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}              
380 <                virtual void update();          
379 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
380 >      virtual void update();    
381        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
382        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
383 <           virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
384 <                virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
385 <                
383 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
384 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
385 >    
386      private:
387 <                int totNumOfMovingAtoms;
387 >    int totNumOfMovingAtoms;
388    };
389  
390 <  class PolicyByMass :ForceSubstractionPolicy{
390 >  class PolicyByMass : public ForceSubtractionPolicy{
391      public:
392 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}  
393 <                        
394 <                virtual void update();          
392 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
393 >      
394 >      virtual void update();    
395        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
396        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
397 <           virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
398 <                virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
397 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
398 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
399  
400 <         private:
401 <           double totMassOfMovingAtoms;
400 >   private:
401 >     double totMassOfMovingAtoms;
402    };
403  
404   public:
# Line 350 | Line 409 | template<typename T> class ZConstraint : public T { (p
409    void setZConsTime(double time)                  {this->zconsTime = time;}
410    void getZConsTime()                             {return zconsTime;}
411    
412 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
413 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
412 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
413 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
414    
415 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
415 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
416    string getZConsOutput()                         {return zconsOutput;}
417    
418    virtual void integrate();
419    
420  
421   #ifdef IS_MPI
422 <  virtual void update(); //which is called to indicate the molecules' migration
422 >  virtual void update();                      //which is called to indicate the molecules' migration
423   #endif
424  
425   protected:
426  
427 <  enum ZConsState {zcsMoving, zcsFixed};
369 <
370 <
427 >  enum ZConsState {zcsMoving, zcsFixed};  
428  
429    virtual void calcForce( int calcPot, int calcStress );
430    virtual void thermalize(void);
# Line 385 | Line 442 | template<typename T> class ZConstraint : public T { (p
442    int isZConstraintMol(Molecule* mol);
443  
444  
445 <  double zconsTime;
446 <  double zconsTol;
447 <  double zForceConst;
445 >  double zconsTime;                              //sample time
446 >  double zconsTol;                                 //tolerance of z-contratint
447 >  double zForceConst;                           //base force constant term
448 >                                                          //which is estimate by OOPSE
449    
450 <  vector<Molecule*> zconsMols;
451 <  vector<double> massOfZConsMols;
452 <  vector<double> kz;
453 <  vector<ZConsState> states;
454 <  vector<double> zPos;
450 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
451 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
452 >  vector<double> kz;                              //force constant array
453 >  vector<ZConsState> states;                 //state of z-constraint molecules
454 >  vector<double> zPos;                          //
455    
456    
457 <  vector<Molecule*> unconsMols;
458 <  vector<double> massOfUnconsMols;
459 <  double totalMassOfUncons;
457 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
458 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
459 >  double totalMassOfUncons;                //total mas of unconstraint molecules
460  
461 <  vector<ZConsParaItem>* parameters;
461 >  vector<ZConsParaItem>* parameters; //
462    
463    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
464  
# Line 408 | Line 466 | template<typename T> class ZConstraint : public T { (p
466    double* fz;
467    double* curZPos;
468    
469 <  int totNumOfUnconsAtoms;
469 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
470  
471    int whichDirection;                           //constraint direction
472    
473   private:
474    
475 <  string zconsOutput;
476 <  ZConsWriter* fzOut;
475 >  string zconsOutput;                         //filename of zconstraint output
476 >  ZConsWriter* fzOut;                         //z-constraint writer
477  
478 <  double curZconsTime;
478 >  double curZconsTime;                      
479  
480    double calcMovingMolsCOMVel();
481    double calcSysCOMVel();
482    double calcTotalForce();
483 <        
484 <  ForceSubstractionPolicy* forcePolicy;
485 <  friend class ForceSubstractionPolicy;
483 >  
484 >  ForceSubtractionPolicy* forcePolicy; //force substration policy
485 >  friend class ForceSubtractionPolicy;
486  
487   };
488  

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