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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 755 by mmeineke, Tue Sep 9 20:35:25 2003 UTC vs.
Revision 790 by mmeineke, Mon Sep 29 21:16:11 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 <  
33 >
34    virtual void integrateStep( int calcPot, int calcStress );
35    virtual void preMove( void );
36    virtual void moveA( void );
# 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    
47 +  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48 +
49    void checkConstraints( void );
50    void rotate( int axes1, int axes2, double angle, double j[3],
51           double A[3][3] );
# Line 95 | Line 97 | template<typename T> class NVT : public T { (public)
97   public:
98  
99    NVT ( SimInfo *theInfo, ForceFields* the_ff);
100 <  virtual ~NVT() {}
100 >  virtual ~NVT();
101  
102    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
103    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
104 +  void setChiTolerance(double tol) {chiTolerance = tol;}
105 +  virtual double  getConservedQuantity(void);
106  
107   protected:
108  
# Line 113 | Line 117 | template<typename T> class NVT : public T { (public)
117  
118    double chi;
119  
120 +  //integral of chi(t)dt
121 +  double integralOfChidt;
122 +
123    // targetTemp must be set.  tauThermostat must also be set;
124  
125    double targetTemp;
# Line 120 | Line 127 | template<typename T> class NVT : public T { (public)
127    
128    short int have_tau_thermostat, have_target_temp;
129  
130 +  double *oldVel;
131 +  double *oldJi;
132 +
133 +  double chiTolerance;
134 +  short int have_chi_tolerance;
135 +
136   };
137  
138  
139  
140 < template<typename T> class NPTi : public T{
140 > template<typename T> class NPT : public T{
141  
142   public:
143  
144 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
145 <  virtual ~NPTi() {};
146 <
144 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
145 >  virtual ~NPT();
146 >  
147    virtual void integrateStep( int calcPot, int calcStress ){
148      calcStress = 1;
149      T::integrateStep( calcPot, calcStress );
150    }
151  
152 +  virtual double getConservedQuantity(void) = 0;
153 +
154    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
155    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
156    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
157    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
158 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
159 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
160 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
161  
162   protected:
163  
# Line 150 | Line 168 | template<typename T> class NPTi : public T{ (protected
168  
169    virtual void resetIntegrator( void );
170  
171 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
172 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
173 +  virtual void getPosScale(double pos[3], double COM[3],
174 +                           int index, double sc[3]) = 0;
175 +
176 +  virtual bool chiConverged( void );
177 +  virtual bool etaConverged( void ) = 0;
178 +  
179 +  virtual void evolveChiA( void );
180 +  virtual void evolveEtaA( void ) = 0;
181 +  virtual void evolveChiB( void );
182 +  virtual void evolveEtaB( void ) = 0;
183 +
184 +  virtual void scaleSimBox( void ) = 0;
185 +
186 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
187 +
188    // chi and eta are the propagated degrees of freedom
189  
190 +  double oldChi;
191 +  double prevChi;
192    double chi;
156 –  double eta;
193    double NkBT;
194 +  double fkBT;
195  
196 +  double tt2, tb2;
197 +  double instaTemp, instaPress, instaVol;
198 +  double press[3][3];
199 +
200 +  int Nparticles;
201 +
202 +  double integralOfChidt;
203 +
204    // targetTemp, targetPressure, and tauBarostat must be set.  
205    // One of qmass or tauThermostat must be set;
206  
# Line 167 | Line 212 | template<typename T> class NPTi : public T{ (protected
212    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
213    short int have_target_pressure;
214  
215 < };
215 >  double *oldPos;
216 >  double *oldVel;
217 >  double *oldJi;
218  
219 < template<typename T> class NPTim : public T{
219 >  double chiTolerance;
220 >  short int have_chi_tolerance;
221 >  double posIterTolerance;
222 >  short int have_pos_iter_tolerance;
223 >  double etaTolerance;
224 >  short int have_eta_tolerance;
225  
226 < public:
226 > };
227  
228 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
229 <  virtual ~NPTim() {};
228 > template<typename T> class NPTi : public T{
229 >  
230 > public:
231 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
232 >  ~NPTi();
233  
234 <  virtual void integrateStep( int calcPot, int calcStress ){
235 <    calcStress = 1;
181 <    T::integrateStep( calcPot, calcStress );
182 <  }
234 >  virtual double getConservedQuantity(void);
235 >  virtual void resetIntegrator(void);
236  
184 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
185 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
186 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
187 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
188 –
237   protected:
238  
239 <  virtual void moveA( void );
192 <  virtual void moveB( void );
239 >
240  
241 <  virtual int readyCheck();
241 >  virtual void evolveEtaA(void);
242 >  virtual void evolveEtaB(void);
243  
244 <  virtual void resetIntegrator( void );
244 >  virtual bool etaConverged( void );
245  
246 <  Molecule* myMolecules;
199 <  Atom** myAtoms;
246 >  virtual void scaleSimBox( void );
247  
248 <  // chi and eta are the propagated degrees of freedom
248 >  virtual void getVelScaleA( double sc[3], double vel[3] );
249 >  virtual void getVelScaleB( double sc[3], int index );
250 >  virtual void getPosScale(double pos[3], double COM[3],
251 >                           int index, double sc[3]);
252  
253 <  double chi;
204 <  double eta;
205 <  double NkBT;
206 <
207 <  // targetTemp, targetPressure, and tauBarostat must be set.  
208 <  // One of qmass or tauThermostat must be set;
209 <
210 <  double targetTemp;
211 <  double targetPressure;
212 <  double tauThermostat;
213 <  double tauBarostat;
214 <
215 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
216 <  short int have_target_pressure;
217 <
253 >  double eta, oldEta, prevEta;
254   };
255  
256   template<typename T> class NPTzm : public T{
# Line 271 | Line 307 | template<typename T> class NPTf : public T{ (public)
307   public:
308  
309    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
310 <  virtual ~NPTf() {};
310 >  virtual ~NPTf();
311  
312 <  virtual void integrateStep( int calcPot, int calcStress ){
313 <    calcStress = 1;
278 <    T::integrateStep( calcPot, calcStress );
279 <  }
312 >  virtual double getConservedQuantity(void);
313 >  virtual void resetIntegrator(void);
314  
281 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
282 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
283 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
284 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
285 –
315   protected:
316  
317 <  virtual void  moveA( void );
318 <  virtual void moveB( void );
317 >  virtual void evolveEtaA(void);
318 >  virtual void evolveEtaB(void);
319  
320 <  virtual void resetIntegrator( void );
320 >  virtual bool etaConverged( void );
321  
322 <  virtual int readyCheck();
322 >  virtual void scaleSimBox( void );
323  
324 <  // chi and eta are the propagated degrees of freedom
324 >  virtual void getVelScaleA( double sc[3], double vel[3] );
325 >  virtual void getVelScaleB( double sc[3], int index );
326 >  virtual void getPosScale(double pos[3], double COM[3],
327 >                           int index, double sc[3]);
328  
297 –  double chi;
329    double eta[3][3];
330 <  double NkBT;
331 <
301 <  // targetTemp, targetPressure, and tauBarostat must be set.  
302 <  // One of qmass or tauThermostat must be set;
303 <
304 <  double targetTemp;
305 <  double targetPressure;
306 <  double tauThermostat;
307 <  double tauBarostat;
308 <
309 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
310 <  short int have_target_pressure;
311 <
330 >  double oldEta[3][3];
331 >  double prevEta[3][3];
332   };
333  
334   template<typename T> class NPTxym : public T{
# Line 361 | Line 381 | template<typename T> class NPTxym : public T{ (protect
381  
382   };
383  
364 –
365 – template<typename T> class NPTfm : public T{
366 –
367 – public:
368 –
369 –  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
370 –  virtual ~NPTfm() {};
371 –
372 –  virtual void integrateStep( int calcPot, int calcStress ){
373 –    calcStress = 1;
374 –    T::integrateStep( calcPot, calcStress );
375 –  }
376 –
377 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
378 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
379 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
380 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
381 –
382 – protected:
383 –
384 –  virtual void  moveA( void );
385 –  virtual void moveB( void );
386 –
387 –  virtual void resetIntegrator( void );
388 –
389 –  virtual int readyCheck();
390 –
391 –  Molecule* myMolecules;
392 –  Atom** myAtoms;
393 –
394 –  // chi and eta are the propagated degrees of freedom
395 –
396 –  double chi;
397 –  double eta[3][3];
398 –  double NkBT;
399 –
400 –  // targetTemp, targetPressure, and tauBarostat must be set.  
401 –  // One of qmass or tauThermostat must be set;
402 –
403 –  double targetTemp;
404 –  double targetPressure;
405 –  double tauThermostat;
406 –  double tauBarostat;
407 –
408 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
409 –  short int have_target_pressure;
410 –
411 – };
412 –
413 –
414 – template<typename T> class NPTpr : public T{
415 –
416 – public:
417 –
418 –  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
419 –  virtual ~NPTpr() {};
420 –
421 –  virtual void integrateStep( int calcPot, int calcStress ){
422 –    calcStress = 1;
423 –    T::integrateStep( calcPot, calcStress );
424 –  }
425 –
426 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
427 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
428 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
429 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
430 –
431 – protected:
432 –
433 –  virtual void  moveA( void );
434 –  virtual void moveB( void );
435 –
436 –  virtual int readyCheck();
437 –
438 –  virtual void resetIntegrator( void );
439 –
440 –  // chi and eta are the propagated degrees of freedom
441 –
442 –  double chi;
443 –  double eta[3][3];
444 –  double NkBT;
445 –
446 –  // targetTemp, targetPressure, and tauBarostat must be set.  
447 –  // One of qmass or tauThermostat must be set;
448 –
449 –  double targetTemp;
450 –  double targetPressure;
451 –  double tauThermostat;
452 –  double tauBarostat;
453 –
454 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
455 –  short int have_target_pressure;
456 –
457 – };
458 –
459 –
384   template<typename T> class ZConstraint : public T {
385    
386    public:
# Line 471 | 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 485 | Line 409 | template<typename T> class ZConstraint : public T {
409        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
410      
411      private:
412 <    int totNumOfMovingAtoms;
412 >      int totNumOfMovingAtoms;
413    };
414  
415    class PolicyByMass : public ForceSubtractionPolicy{
# Line 524 | 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 549 | 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
561 –  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 568 | Line 503 | template<typename T> class ZConstraint : public T {
503    double* fz;
504    double* curZPos;
505    
571 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
506  
507 +
508    int whichDirection;                           //constraint direction
509    
510   private:

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