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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 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC

# Line 251 | Line 251 | template<typename T> class NPTi : public T{ (protected
251                             int index, double sc[3]);
252  
253    double eta, oldEta, prevEta;
254 – };
255 –
256 – template<typename T> class NPTzm : public T{
257 –
258 – public:
259 –
260 –  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
261 –  virtual ~NPTzm() {};
262 –
263 –  virtual void integrateStep( int calcPot, int calcStress ){
264 –    calcStress = 1;
265 –    T::integrateStep( calcPot, calcStress );
266 –  }
267 –
268 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
269 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
270 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
271 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
272 –
273 – protected:
274 –
275 –  virtual void moveA( void );
276 –  virtual void moveB( void );
277 –
278 –  virtual int readyCheck();
279 –
280 –  virtual void resetIntegrator( void );
281 –
282 –  Molecule* myMolecules;
283 –  Atom** myAtoms;
284 –
285 –  // chi and eta are the propagated degrees of freedom
286 –
287 –  double chi;
288 –  double eta;
289 –  double etaZ;
290 –  double NkBT;
291 –
292 –  // targetTemp, targetPressure, and tauBarostat must be set.  
293 –  // One of qmass or tauThermostat must be set;
294 –
295 –  double targetTemp;
296 –  double targetPressure;
297 –  double tauThermostat;
298 –  double tauBarostat;
299 –
300 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
301 –  short int have_target_pressure;
302 –
254   };
255  
256   template<typename T> class NPTf : public T{
# Line 331 | Line 282 | template<typename T> class NPTxym : public T{
282    double prevEta[3][3];
283   };
284  
285 < template<typename T> class NPTxym : public T{
285 > template<typename T> class NPTxyz : public T{
286  
287   public:
288  
289 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
290 <  virtual ~NPTxym() {};
289 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
290 >  virtual ~NPTxyz();
291  
292 <  virtual void integrateStep( int calcPot, int calcStress ){
293 <    calcStress = 1;
343 <    T::integrateStep( calcPot, calcStress );
344 <  }
345 <
346 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
347 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
348 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
349 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
292 >  virtual double getConservedQuantity(void);
293 >  virtual void resetIntegrator(void);
294  
295   protected:
296  
297 <  virtual void moveA( void );
298 <  virtual void moveB( void );
297 >  virtual void evolveEtaA(void);
298 >  virtual void evolveEtaB(void);
299  
300 <  virtual int readyCheck();
300 >  virtual bool etaConverged( void );
301  
302 <  virtual void resetIntegrator( void );
302 >  virtual void scaleSimBox( void );
303  
304 <  Molecule* myMolecules;
305 <  Atom** myAtoms;
304 >  virtual void getVelScaleA( double sc[3], double vel[3] );
305 >  virtual void getVelScaleB( double sc[3], int index );
306 >  virtual void getPosScale(double pos[3], double COM[3],
307 >                           int index, double sc[3]);
308  
309 <  // chi and eta are the propagated degrees of freedom
310 <
311 <  double chi;
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];
425 <  double NkBT;
426 <  double integralOfChidt;
427 <
428 <  // targetTemp, targetPressure, and tauBarostat must be set.  
429 <  // One of qmass or tauThermostat must be set;
430 <
431 <  double targetTemp;
432 <  double targetPressure;
433 <  double tauThermostat;
434 <  double tauBarostat;
435 <
436 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
437 <  short int have_target_pressure;
438 <  double chiTolerance;
439 <  short int have_chi_tolerance;
440 <  double posIterTolerance;
441 <  short int have_pos_iter_tolerance;
442 <
309 >  double eta[3][3];
310 >  double oldEta[3][3];
311 >  double prevEta[3][3];
312   };
313  
314  
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 –
315   template<typename T> class ZConstraint : public T {
316    
317    public:
# Line 509 | Line 326 | template<typename T> class ZConstraint : public T {
326        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
327      
328     protected:
329 <     ZConstraint<T>* zconsIntegrator;;
329 >     ZConstraint<T>* zconsIntegrator;
330    };
331  
332    class PolicyByNumber : public ForceSubtractionPolicy{
# Line 562 | Line 379 | template<typename T> class ZConstraint : public T {
379    virtual void update();                      //which is called to indicate the molecules' migration
380   #endif
381  
382 +  enum ZConsState {zcsMoving, zcsFixed};  
383 +
384 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
385 +  vector<ZConsState> states;                 //state of z-constraint molecules
386 +
387 +
388 +
389 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
390 +  double totalMassOfUncons;                //total mas of unconstraint molecules
391 +
392 +
393   protected:
394  
395 <  enum ZConsState {zcsMoving, zcsFixed};  
395 >
396  
397    virtual void calcForce( int calcPot, int calcStress );
398    virtual void thermalize(void);
# Line 587 | Line 415 | template<typename T> class ZConstraint : public T {
415    double zForceConst;                           //base force constant term
416                                                            //which is estimate by OOPSE
417    
418 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
418 >
419    vector<double> massOfZConsMols;       //mass of z-constraint molecule
420    vector<double> kz;                              //force constant array
421 <  vector<ZConsState> states;                 //state of z-constraint molecules
421 >
422    vector<double> zPos;                          //
423    
424    
425    vector<Molecule*> unconsMols;           //unconstraint molecules array
426    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
599 –  double totalMassOfUncons;                //total mas of unconstraint molecules
427  
428 +
429    vector<ZConsParaItem>* parameters; //
430    
431    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
# Line 606 | Line 434 | template<typename T> class ZConstraint : public T {
434    double* fz;
435    double* curZPos;
436    
609 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
437  
438 +
439    int whichDirection;                           //constraint direction
440    
441   private:

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