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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 696 by tim, Thu Aug 14 16:16:39 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 39 | Line 39 | template<typename T = BaseIntegrator> class Integrator
39    virtual void constrainB( void );
40    virtual int  readyCheck( void ) { return 1; }
41  
42 +  virtual void resetIntegrator( void ) { }
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] );
52 <              
51 >         double A[3][3] );
52 >        
53    ForceFields* myFF;
54  
55    SimInfo *info; // all the info we'll ever need
# Line 56 | Line 60 | template<typename T = BaseIntegrator> class Integrator
60    int nMols;
61  
62    int isConstrained; // boolean to know whether the systems contains
63 <                     // constraints.
63 >         // constraints.
64    int nConstrained;  // counter for number of constraints
65    int *constrainedA; // the i of a constraint pair
66    int *constrainedB; // the j of a constraint pair
# Line 93 | 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 105 | Line 111 | template<typename T> class NVT : public T { (public)
111  
112    virtual int readyCheck();
113  
114 +  virtual void resetIntegrator( void );
115 +
116    // chi is a propagated degree of freedom.
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 116 | 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 144 | Line 166 | template<typename T> class NPTi : public T{ (protected
166  
167    virtual int readyCheck();
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;
150 –  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 161 | 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 +  double *oldPos;
216 +  double *oldVel;
217 +  double *oldJi;
218 +
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   };
227  
228 < template<typename T> class NPTim : public T{
228 > template<typename T> class NPTi : public T{
229 >  
230 > public:
231 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
232 >  ~NPTi();
233  
234 +  virtual double getConservedQuantity(void);
235 +  virtual void resetIntegrator(void);
236 +
237 + protected:
238 +
239 +
240 +
241 +  virtual void evolveEtaA(void);
242 +  virtual void evolveEtaB(void);
243 +
244 +  virtual bool etaConverged( void );
245 +
246 +  virtual void scaleSimBox( void );
247 +
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 eta, oldEta, prevEta;
254 + };
255 +
256 + template<typename T> class NPTzm : public T{
257 +
258   public:
259  
260 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
261 <  virtual ~NPTim() {};
260 >  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
261 >  virtual ~NPTzm() {};
262  
263    virtual void integrateStep( int calcPot, int calcStress ){
264      calcStress = 1;
# Line 187 | Line 277 | template<typename T> class NPTim : public T{ (protecte
277  
278    virtual int readyCheck();
279  
280 +  virtual void resetIntegrator( void );
281 +
282    Molecule* myMolecules;
283    Atom** myAtoms;
284  
# Line 194 | Line 286 | template<typename T> class NPTim : public T{ (protecte
286  
287    double chi;
288    double eta;
289 +  double etaZ;
290    double NkBT;
291  
292    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 214 | 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;
221 <    T::integrateStep( calcPot, calcStress );
222 <  }
312 >  virtual double getConservedQuantity(void);
313 >  virtual void resetIntegrator(void);
314  
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 –
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 int readyCheck();
320 >  virtual bool etaConverged( void );
321  
322 <  // chi and eta are the propagated degrees of freedom
322 >  virtual void scaleSimBox( void );
323  
324 <  double chi;
325 <  double eta[3][3];
326 <  double NkBT;
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  
329 <  // targetTemp, targetPressure, and tauBarostat must be set.  
330 <  // One of qmass or tauThermostat must be set;
331 <
245 <  double targetTemp;
246 <  double targetPressure;
247 <  double tauThermostat;
248 <  double tauBarostat;
249 <
250 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
251 <  short int have_target_pressure;
252 <
329 >  double eta[3][3];
330 >  double oldEta[3][3];
331 >  double prevEta[3][3];
332   };
333  
334 < template<typename T> class NPTfm : public T{
334 > template<typename T> class NPTxym : public T{
335  
336   public:
337  
338 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
339 <  virtual ~NPTfm() {};
338 >  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
339 >  virtual ~NPTxym() {};
340  
341    virtual void integrateStep( int calcPot, int calcStress ){
342      calcStress = 1;
# Line 271 | Line 350 | template<typename T> class NPTfm : public T{ (protecte
350  
351   protected:
352  
353 <  virtual void  moveA( void );
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[3][3];
366 >  double eta;
367 >  double etaX;
368 >  double etaY;
369    double NkBT;
370  
371    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 299 | Line 382 | template<typename T> class ZConstraint : public T {
382   };
383  
384   template<typename T> class ZConstraint : public T {
385 +  
386 +  public:
387 +  class ForceSubtractionPolicy{
388 +    public:
389 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
390  
391 +      virtual void update() = 0;    
392 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
393 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
394 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
395 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
396 +    
397 +   protected:
398 +     ZConstraint<T>* zconsIntegrator;
399 +  };
400 +
401 +  class PolicyByNumber : public ForceSubtractionPolicy{
402 +
403 +    public:
404 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
405 +      virtual void update();    
406 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
407 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
408 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
409 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
410 +    
411 +    private:
412 +      int totNumOfMovingAtoms;
413 +  };
414 +
415 +  class PolicyByMass : public ForceSubtractionPolicy{
416 +
417 +    public:
418 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
419 +      
420 +      virtual void update();    
421 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
422 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
423 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
424 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
425 +
426 +   private:
427 +     double totMassOfMovingAtoms;
428 +  };
429 +
430   public:
431  
432    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
# Line 308 | Line 435 | template<typename T> class ZConstraint : public T {
435    void setZConsTime(double time)                  {this->zconsTime = time;}
436    void getZConsTime()                             {return zconsTime;}
437    
438 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
439 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
438 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
439 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
440    
441 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
441 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
442    string getZConsOutput()                         {return zconsOutput;}
443    
444    virtual void integrate();
445    
446  
447   #ifdef IS_MPI
448 <  virtual void update(); //which is called to indicate the molecules' migration
448 >  virtual void update();                      //which is called to indicate the molecules' migration
449   #endif
450  
451 < protected:
451 >  enum ZConsState {zcsMoving, zcsFixed};  
452  
453 <  enum ZConsState {zcsMoving, zcsFixed};
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 +
465  
466    virtual void calcForce( int calcPot, int calcStress );
467    virtual void thermalize(void);
# Line 343 | Line 479 | template<typename T> class ZConstraint : public T {
479    int isZConstraintMol(Molecule* mol);
480  
481  
482 <  double zconsTime;
483 <  double zconsTol;
484 <  double zForceConst;
482 >  double zconsTime;                              //sample time
483 >  double zconsTol;                                 //tolerance of z-contratint
484 >  double zForceConst;                           //base force constant term
485 >                                                          //which is estimate by OOPSE
486    
487 <  vector<Molecule*> zconsMols;
488 <  vector<double> massOfZConsMols;
489 <  vector<double> kz;
490 <  vector<ZConsState> states;
491 <  vector<double> zPos;
487 >
488 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
489 >  vector<double> kz;                              //force constant array
490 >
491 >  vector<double> zPos;                          //
492    
493    
494 <  vector<Molecule*> unconsMols;
495 <  vector<double> massOfUnconsMols;
359 <  double totalMassOfUncons;
494 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
495 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
496  
497 <  vector<ZConsParaItem>* parameters;
497 >
498 >  vector<ZConsParaItem>* parameters; //
499    
500    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
501  
502    int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
503    double* fz;
504 +  double* curZPos;
505    
368 –  int totNumOfUnconsAtoms;
506  
507 +
508    int whichDirection;                           //constraint direction
509    
510   private:
511    
512 <  string zconsOutput;
513 <  ZConsWriter* fzOut;
512 >  string zconsOutput;                         //filename of zconstraint output
513 >  ZConsWriter* fzOut;                         //z-constraint writer
514  
515 +  double curZconsTime;                      
516 +
517    double calcMovingMolsCOMVel();
518    double calcSysCOMVel();
519    double calcTotalForce();
520 +  
521 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
522 +  friend class ForceSubtractionPolicy;
523  
524   };
525  

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