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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 780 by mmeineke, Mon Sep 22 21:23:25 2003 UTC vs.
Revision 790 by mmeineke, Mon Sep 29 21:16:11 2003 UTC

# Line 366 | Line 366 | template<typename T> class NPTxym : public T{ (protect
366    double eta;
367    double etaX;
368    double etaY;
369 –  double NkBT;
370 –
371 –  // targetTemp, targetPressure, and tauBarostat must be set.  
372 –  // One of qmass or tauThermostat must be set;
373 –
374 –  double targetTemp;
375 –  double targetPressure;
376 –  double tauThermostat;
377 –  double tauBarostat;
378 –
379 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
380 –  short int have_target_pressure;
381 –
382 – };
383 –
384 –
385 – template<typename T> class NPTfm : public T{
386 –
387 – public:
388 –
389 –  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
390 –  virtual ~NPTfm() {};
391 –
392 –  virtual void integrateStep( int calcPot, int calcStress ){
393 –    calcStress = 1;
394 –    T::integrateStep( calcPot, calcStress );
395 –    accIntegralOfChidt();
396 –  }
397 –
398 –  virtual double getConservedQuantity(void);
399 –  
400 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
401 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
402 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
403 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
404 –  void setChiTolerance(double tol) {chiTolerance = tol;}
405 –  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
406 –
407 – protected:
408 –
409 –  virtual void  moveA( void );
410 –  virtual void moveB( void );
411 –
412 –  virtual void resetIntegrator( void );
413 –
414 –  virtual int readyCheck();
415 –
416 –  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
417 –
418 –  Molecule* myMolecules;
419 –  Atom** myAtoms;
420 –
421 –  // chi and eta are the propagated degrees of freedom
422 –
423 –  double chi;
424 –  double eta[3][3];
369    double NkBT;
426 –  double integralOfChidt;
370  
371    // targetTemp, targetPressure, and tauBarostat must be set.  
372    // One of qmass or tauThermostat must be set;
# Line 435 | Line 378 | template<typename T> class NPTfm : public T{ (protecte
378  
379    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
380    short int have_target_pressure;
438 –  double chiTolerance;
439 –  short int have_chi_tolerance;
440 –  double posIterTolerance;
441 –  short int have_pos_iter_tolerance;
381  
382   };
383  
445 –
446 – template<typename T> class NPTpr : public T{
447 –
448 – public:
449 –
450 –  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
451 –  virtual ~NPTpr() {};
452 –
453 –  virtual void integrateStep( int calcPot, int calcStress ){
454 –    calcStress = 1;
455 –    T::integrateStep( calcPot, calcStress );
456 –  }
457 –
458 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
459 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
460 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
461 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
462 –  void setChiTolerance(double tol) {chiTolerance = tol;}
463 –  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
464 –
465 – protected:
466 –
467 –  virtual void  moveA( void );
468 –  virtual void moveB( void );
469 –
470 –  virtual int readyCheck();
471 –
472 –  virtual void resetIntegrator( void );
473 –
474 –  // chi and eta are the propagated degrees of freedom
475 –
476 –  double chi;
477 –  double eta[3][3];
478 –  double NkBT;
479 –
480 –  // targetTemp, targetPressure, and tauBarostat must be set.  
481 –  // One of qmass or tauThermostat must be set;
482 –
483 –  double targetTemp;
484 –  double targetPressure;
485 –  double tauThermostat;
486 –  double tauBarostat;
487 –
488 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
489 –  short int have_target_pressure;
490 –  double chiTolerance;
491 –  short int have_chi_tolerance;
492 –  double posIterTolerance;
493 –  short int have_pos_iter_tolerance;
494 –
495 – };
496 –
497 –
384   template<typename T> class ZConstraint : public T {
385    
386    public:
# Line 509 | Line 395 | template<typename T> class ZConstraint : public T {
395        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
396      
397     protected:
398 <     ZConstraint<T>* zconsIntegrator;;
398 >     ZConstraint<T>* zconsIntegrator;
399    };
400  
401    class PolicyByNumber : public ForceSubtractionPolicy{
# Line 562 | Line 448 | template<typename T> class ZConstraint : public T {
448    virtual void update();                      //which is called to indicate the molecules' migration
449   #endif
450  
451 +  enum ZConsState {zcsMoving, zcsFixed};  
452 +
453 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
454 +  vector<ZConsState> states;                 //state of z-constraint molecules
455 +
456 +
457 +
458 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
459 +  double totalMassOfUncons;                //total mas of unconstraint molecules
460 +
461 +
462   protected:
463  
464 <  enum ZConsState {zcsMoving, zcsFixed};  
464 >
465  
466    virtual void calcForce( int calcPot, int calcStress );
467    virtual void thermalize(void);
# Line 587 | Line 484 | template<typename T> class ZConstraint : public T {
484    double zForceConst;                           //base force constant term
485                                                            //which is estimate by OOPSE
486    
487 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
487 >
488    vector<double> massOfZConsMols;       //mass of z-constraint molecule
489    vector<double> kz;                              //force constant array
490 <  vector<ZConsState> states;                 //state of z-constraint molecules
490 >
491    vector<double> zPos;                          //
492    
493    
494    vector<Molecule*> unconsMols;           //unconstraint molecules array
495    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
599 –  double totalMassOfUncons;                //total mas of unconstraint molecules
496  
497 +
498    vector<ZConsParaItem>* parameters; //
499    
500    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
# Line 606 | Line 503 | template<typename T> class ZConstraint : public T {
503    double* fz;
504    double* curZPos;
505    
609 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
506  
507 +
508    int whichDirection;                           //constraint direction
509    
510   private:

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