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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 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 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;
292    Atom** myAtoms;
293 +
294 +  // chi and eta are the propagated degrees of freedom
295 +
296 +  double chi;
297 +  double eta[3][3];
298 +  double NkBT;
299 +
300 +  // targetTemp, targetPressure, and tauBarostat must be set.  
301 +  // One of qmass or tauThermostat must be set;
302 +
303 +  double targetTemp;
304 +  double targetPressure;
305 +  double tauThermostat;
306 +  double tauBarostat;
307 +
308 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
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;
# Line 298 | Line 356 | template<typename T> class ZConstraint : public T {
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 +    public:
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 +    
386 +    private:
387 +    int totNumOfMovingAtoms;
388 +  };
389 +
390 +  class PolicyByMass : public ForceSubtractionPolicy{
391 +    public:
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);
399 +
400 +   private:
401 +     double totMassOfMovingAtoms;
402 +  };
403 +
404   public:
405  
406    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
# Line 308 | 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};
327 <
328 <
427 >  enum ZConsState {zcsMoving, zcsFixed};  
428  
429    virtual void calcForce( int calcPot, int calcStress );
430    virtual void thermalize(void);
# Line 343 | 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  
465    int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
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 calcCOMVel();
378 <  double calcCOMVel2();
478 >  double curZconsTime;                      
479  
480 +  double calcMovingMolsCOMVel();
481 +  double calcSysCOMVel();
482 +  double calcTotalForce();
483 +  
484 +  ForceSubtractionPolicy* forcePolicy; //force substration policy
485 +  friend class ForceSubtractionPolicy;
486 +
487   };
488  
489   #endif

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