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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 747 by gezelter, Fri Sep 5 21:28:52 2003 UTC

# Line 38 | Line 38 | template<typename T = BaseIntegrator> class Integrator
38    virtual void constrainA( void );
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 <
46 <
49 >         double A[3][3] );
50 >        
51    ForceFields* myFF;
52  
53    SimInfo *info; // all the info we'll ever need
# Line 54 | 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 102 | Line 106 | template<typename T> class NVT : public T { (protected
106    virtual void moveB( void );
107  
108    virtual int readyCheck();
109 +
110 +  virtual void resetIntegrator( void );
111  
112    // chi is a propagated degree of freedom.
113  
# Line 142 | 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 185 | 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 229 | 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 272 | 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 296 | Line 310 | template<typename T> class ZConstraint : public T {
310  
311   };
312  
299 – template<typename T> class ZConstraint : public T {
313  
314 + template<typename T> class NPTpr : public T{
315 +
316   public:
317  
318 <  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
319 <  ~ZConstraint();
318 >  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
319 >  virtual ~NPTpr() {};
320  
321 <  virtual void integrateStep( int calcPot, int calcStress );
322 <  
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);
409 +  ~ZConstraint();
410 +    
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 <  double zconsTime;
429 >  enum ZConsState {zcsMoving, zcsFixed};  
430 >
431 >  virtual void calcForce( int calcPot, int calcStress );
432 >  virtual void thermalize(void);
433    
434 <  void resetZ(void);
434 >  void zeroOutVel();
435 >  void doZconstraintForce();
436 >  void doHarmonic();
437 >  bool checkZConsState();
438 >
439 >  bool haveFixedZMols();
440 >  bool haveMovingZMols();
441 >
442 >  double calcZSys();
443 >
444 >  int isZConstraintMol(Molecule* mol);
445 >
446 >
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;
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 <  vector<Molecule*> unconsMols;
459 <  vector<double> massOfUnconsMols;
460 <  double totalMassOfUncons;
458 >  
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<double> allRefZ;    
336 <  vector<double> refZ;
463 >  vector<ZConsParaItem>* parameters; //
464    
465    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
466 <  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
467 <    
466 >
467 >  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
468    double* fz;
469 +  double* curZPos;
470    
471 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
472 +
473 +  int whichDirection;                           //constraint direction
474 +  
475   private:
476 +  
477 +  string zconsOutput;                         //filename of zconstraint output
478 +  ZConsWriter* fzOut;                         //z-constraint writer
479  
480 <  int isZConstraintMol(Molecule* mol);
481 <  string zconsOutput;
482 <  ZConsWriter* fzOut;
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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