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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 747 by gezelter, Fri Sep 5 21:28:52 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC

# Line 27 | Line 27 | template<typename T = BaseIntegrator> class Integrator
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31  
31 –
32   protected:
33    
34    virtual void integrateStep( int calcPot, int calcStress );
# Line 40 | Line 40 | template<typename T = BaseIntegrator> class Integrator
40    virtual int  readyCheck( void ) { return 1; }
41  
42    virtual void resetIntegrator( void ) { }
43 <
43 >
44    virtual void calcForce( int calcPot, int calcStress );  
45    virtual void thermalize();
46    
# Line 95 | Line 95 | template<typename T> class NVT : public T { (public)
95   public:
96  
97    NVT ( SimInfo *theInfo, ForceFields* the_ff);
98 <  virtual ~NVT() {}
98 >  virtual ~NVT();
99  
100    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
101    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
102 +  void setChiTolerance(double tol) {chiTolerance = tol;}
103 +  virtual double  getConservedQuantity(void);
104  
105   protected:
106  
# Line 113 | Line 115 | template<typename T> class NVT : public T { (public)
115  
116    double chi;
117  
118 +  //integral of chi(t)dt
119 +  double integralOfChidt;
120 +
121    // targetTemp must be set.  tauThermostat must also be set;
122  
123    double targetTemp;
# Line 120 | Line 125 | template<typename T> class NVT : public T { (public)
125    
126    short int have_tau_thermostat, have_target_temp;
127  
128 +  double *oldVel;
129 +  double *oldJi;
130 +
131 +  double chiTolerance;
132 +  short int have_chi_tolerance;
133 +
134   };
135  
136  
# Line 129 | Line 140 | template<typename T> class NPTi : public T{ (public)
140   public:
141  
142    NPTi ( SimInfo *theInfo, ForceFields* the_ff);
143 <  virtual ~NPTi() {};
144 <
143 >  virtual ~NPTi();
144 >  
145    virtual void integrateStep( int calcPot, int calcStress ){
146      calcStress = 1;
147      T::integrateStep( calcPot, calcStress );
148 +    /* accIntegralOfChidt(); */
149    }
150  
151 +  virtual double getConservedQuantity(void);
152 +
153    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
154    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
155    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
156    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
157 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
158 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
159 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
160  
161   protected:
162  
# Line 150 | Line 167 | template<typename T> class NPTi : public T{ (public)
167  
168    virtual void resetIntegrator( void );
169  
170 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
171 +
172    // chi and eta are the propagated degrees of freedom
173  
174    double chi;
175    double eta;
176    double NkBT;
177 +  double fkBT;
178  
179 +  int Nparticles;
180 +
181 +  double integralOfChidt;
182 +
183    // targetTemp, targetPressure, and tauBarostat must be set.  
184    // One of qmass or tauThermostat must be set;
185  
# Line 167 | Line 191 | template<typename T> class NPTi : public T{ (public)
191    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
192    short int have_target_pressure;
193  
194 +  double *oldPos;
195 +  double *oldVel;
196 +  double *oldJi;
197 +
198 +  double chiTolerance;
199 +  short int have_chi_tolerance;
200 +  double posIterTolerance;
201 +  short int have_pos_iter_tolerance;
202 +  double etaTolerance;
203 +  short int have_eta_tolerance;
204 +
205 +  double volume;
206 +
207   };
208  
209   template<typename T> class NPTim : public T{
# Line 174 | Line 211 | template<typename T> class NPTim : public T{ (public)
211   public:
212  
213    NPTim ( SimInfo *theInfo, ForceFields* the_ff);
214 <  virtual ~NPTim() {};
214 >  virtual ~NPTim() {}
215 >
216 >  virtual void integrateStep( int calcPot, int calcStress ){
217 >    calcStress = 1;
218 >    T::integrateStep( calcPot, calcStress );
219 >    accIntegralOfChidt();  
220 >  }
221 >
222 >  virtual double getConservedQuantity(void);
223 >
224 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
225 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
226 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
227 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
228 >  void setChiTolerance(double tol) {chiTolerance = tol;}
229 >  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
230 >
231 > protected:
232 >
233 >  virtual void moveA( void );
234 >  virtual void moveB( void );
235 >
236 >  virtual int readyCheck();
237 >
238 >  virtual void resetIntegrator( void );
239 >
240 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
241 >  
242 >  Molecule* myMolecules;
243 >  Atom** myAtoms;
244 >
245 >  // chi and eta are the propagated degrees of freedom
246 >
247 >  double chi;
248 >  double eta;
249 >  double NkBT;
250 >  double integralOfChidt;
251 >
252 >  // targetTemp, targetPressure, and tauBarostat must be set.  
253 >  // One of qmass or tauThermostat must be set;
254 >
255 >  double targetTemp;
256 >  double targetPressure;
257 >  double tauThermostat;
258 >  double tauBarostat;
259 >
260 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
261 >  short int have_target_pressure;
262 >  double chiTolerance;
263 >  short int have_chi_tolerance;
264 >  double posIterTolerance;
265 >  short int have_pos_iter_tolerance;
266  
267 + };
268 +
269 + template<typename T> class NPTzm : public T{
270 +
271 + public:
272 +
273 +  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
274 +  virtual ~NPTzm() {};
275 +
276    virtual void integrateStep( int calcPot, int calcStress ){
277      calcStress = 1;
278      T::integrateStep( calcPot, calcStress );
# Line 202 | Line 299 | template<typename T> class NPTim : public T{ (public)
299  
300    double chi;
301    double eta;
302 +  double etaZ;
303    double NkBT;
304  
305    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 227 | Line 325 | template<typename T> class NPTf : public T{ (public)
325    virtual void integrateStep( int calcPot, int calcStress ){
326      calcStress = 1;
327      T::integrateStep( calcPot, calcStress );
328 +    accIntegralOfChidt();
329    }
330 +  
331 +  virtual double getConservedQuantity(void);
332  
333    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
334    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
335    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
336    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
337 +  void setChiTolerance(double tol) {chiTolerance = tol;}
338 +  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
339  
340   protected:
341  
# Line 243 | Line 346 | template<typename T> class NPTf : public T{ (public)
346  
347    virtual int readyCheck();
348  
349 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
350 +
351    // chi and eta are the propagated degrees of freedom
352  
353    double chi;
354    double eta[3][3];
355 +  double NkBT;
356 +
357 +  double integralOfChidt;
358 +  
359 +  // targetTemp, targetPressure, and tauBarostat must be set.  
360 +  // One of qmass or tauThermostat must be set;
361 +
362 +  double targetTemp;
363 +  double targetPressure;
364 +  double tauThermostat;
365 +  double tauBarostat;
366 +
367 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
368 +  short int have_target_pressure;
369 +  double chiTolerance;
370 +  short int have_chi_tolerance;
371 +  double posIterTolerance;
372 +  short int have_pos_iter_tolerance;
373 +
374 + };
375 +
376 + template<typename T> class NPTxym : public T{
377 +
378 + public:
379 +
380 +  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
381 +  virtual ~NPTxym() {};
382 +
383 +  virtual void integrateStep( int calcPot, int calcStress ){
384 +    calcStress = 1;
385 +    T::integrateStep( calcPot, calcStress );
386 +  }
387 +
388 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
389 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
390 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
391 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
392 +
393 + protected:
394 +
395 +  virtual void moveA( void );
396 +  virtual void moveB( void );
397 +
398 +  virtual int readyCheck();
399 +
400 +  virtual void resetIntegrator( void );
401 +
402 +  Molecule* myMolecules;
403 +  Atom** myAtoms;
404 +
405 +  // chi and eta are the propagated degrees of freedom
406 +
407 +  double chi;
408 +  double eta;
409 +  double etaX;
410 +  double etaY;
411    double NkBT;
412  
413    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 262 | Line 423 | template<typename T> class NPTfm : public T{
423  
424   };
425  
426 +
427   template<typename T> class NPTfm : public T{
428  
429   public:
# Line 272 | Line 434 | template<typename T> class NPTfm : public T{ (public)
434    virtual void integrateStep( int calcPot, int calcStress ){
435      calcStress = 1;
436      T::integrateStep( calcPot, calcStress );
437 +    accIntegralOfChidt();
438    }
439  
440 +  virtual double getConservedQuantity(void);
441 +  
442    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
443    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
444    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
445    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
446 +  void setChiTolerance(double tol) {chiTolerance = tol;}
447 +  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
448  
449   protected:
450  
# Line 288 | Line 455 | template<typename T> class NPTfm : public T{ (public)
455  
456    virtual int readyCheck();
457  
458 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
459 +
460    Molecule* myMolecules;
461    Atom** myAtoms;
462  
# Line 296 | Line 465 | template<typename T> class NPTfm : public T{ (public)
465    double chi;
466    double eta[3][3];
467    double NkBT;
468 +  double integralOfChidt;
469  
470    // targetTemp, targetPressure, and tauBarostat must be set.  
471    // One of qmass or tauThermostat must be set;
# Line 307 | Line 477 | template<typename T> class NPTfm : public T{ (public)
477  
478    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
479    short int have_target_pressure;
480 +  double chiTolerance;
481 +  short int have_chi_tolerance;
482 +  double posIterTolerance;
483 +  short int have_pos_iter_tolerance;
484  
485   };
486  
# Line 327 | Line 501 | template<typename T> class NPTpr : public T{ (public)
501    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
502    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
503    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
504 +  void setChiTolerance(double tol) {chiTolerance = tol;}
505 +  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
506  
507   protected:
508  
# Line 353 | Line 529 | template<typename T> class NPTpr : public T{ (public)
529  
530    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
531    short int have_target_pressure;
532 +  double chiTolerance;
533 +  short int have_chi_tolerance;
534 +  double posIterTolerance;
535 +  short int have_pos_iter_tolerance;
536  
537   };
538  
# Line 385 | Line 565 | template<typename T> class ZConstraint : public T {
565        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
566      
567      private:
568 <    int totNumOfMovingAtoms;
568 >      int totNumOfMovingAtoms;
569    };
570  
571    class PolicyByMass : public ForceSubtractionPolicy{

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