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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 782 by mmeineke, Tue Sep 23 20:34:31 2003 UTC vs.
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC

# Line 253 | Line 253 | template<typename T> class NPTi : public T{ (protected
253    double eta, oldEta, prevEta;
254   };
255  
256 < template<typename T> class NPTzm : public T{
256 > template<typename T> class NPTf : 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 <  }
260 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
261 >  virtual ~NPTf();
262  
263 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
264 <  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;}
263 >  virtual double getConservedQuantity(void);
264 >  virtual void resetIntegrator(void);
265  
266   protected:
267  
268 <  virtual void moveA( void );
269 <  virtual void moveB( void );
268 >  virtual void evolveEtaA(void);
269 >  virtual void evolveEtaB(void);
270  
271 <  virtual int readyCheck();
271 >  virtual bool etaConverged( void );
272  
273 <  virtual void resetIntegrator( void );
273 >  virtual void scaleSimBox( void );
274  
275 <  Molecule* myMolecules;
276 <  Atom** myAtoms;
275 >  virtual void getVelScaleA( double sc[3], double vel[3] );
276 >  virtual void getVelScaleB( double sc[3], int index );
277 >  virtual void getPosScale(double pos[3], double COM[3],
278 >                           int index, double sc[3]);
279  
280 <  // chi and eta are the propagated degrees of freedom
281 <
282 <  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 <
280 >  double eta[3][3];
281 >  double oldEta[3][3];
282 >  double prevEta[3][3];
283   };
284  
285 < template<typename T> class NPTf : public T{
285 > template<typename T> class NPTxyz : public T{
286  
287   public:
288  
289 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
290 <  virtual ~NPTf();
289 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
290 >  virtual ~NPTxyz();
291  
292    virtual double getConservedQuantity(void);
293    virtual void resetIntegrator(void);
# Line 330 | Line 310 | template<typename T> class NPTf : public T{ (protected
310    double oldEta[3][3];
311    double prevEta[3][3];
312   };
333 –
334 – template<typename T> class NPTxym : public T{
335 –
336 – public:
337 –
338 –  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
339 –  virtual ~NPTxym() {};
340 –
341 –  virtual void integrateStep( int calcPot, int calcStress ){
342 –    calcStress = 1;
343 –    T::integrateStep( calcPot, calcStress );
344 –  }
313  
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;}
314  
351 – protected:
352 –
353 –  virtual void moveA( void );
354 –  virtual void moveB( void );
355 –
356 –  virtual int readyCheck();
357 –
358 –  virtual void resetIntegrator( void );
359 –
360 –  Molecule* myMolecules;
361 –  Atom** myAtoms;
362 –
363 –  // chi and eta are the propagated degrees of freedom
364 –
365 –  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 –
315   template<typename T> class ZConstraint : public T {
316    
317    public:
# Line 395 | 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 448 | 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 473 | 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
485 –  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 492 | Line 434 | template<typename T> class ZConstraint : public T {
434    double* fz;
435    double* curZPos;
436    
495 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
437  
438 +
439    int whichDirection;                           //constraint direction
440    
441   private:

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