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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 596 by gezelter, Mon Jul 14 15:04:55 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC

# Line 1 | Line 1
1   #ifndef _INTEGRATOR_H_
2   #define _INTEGRATOR_H_
3  
4 + #include <string>
5 + #include <vector>
6   #include "Atom.hpp"
7 + #include "Molecule.hpp"
8   #include "SRI.hpp"
9   #include "AbstractClasses.hpp"
10   #include "SimInfo.hpp"
11   #include "ForceFields.hpp"
12   #include "Thermo.hpp"
13   #include "ReadWrite.hpp"
14 + #include "ZConsWriter.hpp"
15  
16 + using namespace std;
17   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
18   const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19   const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
20   const int maxIteration = 300;
21   const double tol = 1.0e-6;
22  
18 – class Integrator : public BaseIntegrator {
23  
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31  
25 –
32   protected:
33    
34    virtual void integrateStep( int calcPot, int calcStress );
# Line 32 | Line 38 | class Integrator : public BaseIntegrator { (protected)
38    virtual void constrainA( void );
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    void checkConstraints( void );
48    void rotate( int axes1, int axes2, double angle, double j[3],
49 <               double A[3][3] );
50 <
40 <
49 >         double A[3][3] );
50 >        
51    ForceFields* myFF;
52  
53    SimInfo *info; // all the info we'll ever need
# Line 48 | Line 58 | class Integrator : public BaseIntegrator { (protected)
58    int nMols;
59  
60    int isConstrained; // boolean to know whether the systems contains
61 <                     // constraints.
61 >         // constraints.
62    int nConstrained;  // counter for number of constraints
63    int *constrainedA; // the i of a constraint pair
64    int *constrainedB; // the j of a constraint pair
# Line 63 | Line 73 | class Integrator : public BaseIntegrator { (protected)
73    double dt;
74    double dt2;
75  
66 –  double* pos;
67 –  double* vel;
68 –  double* frc;
69 –  double* trq;
70 –  double* Amat;
71 –
76    Thermo *tStats;
77    StatWriter*  statOut;
78    DumpWriter*  dumpOut;
79    
80   };
81  
82 < class NVE : public Integrator{
82 > typedef Integrator<BaseIntegrator> RealIntegrator;
83  
84 + template<typename T> class NVE : public T {
85 +
86   public:
87    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
88 <    Integrator( theInfo, the_ff ){}
89 <  virtual ~NVE(){}
84 <
85 <  
86 <
88 >    T( theInfo, the_ff ){}
89 >  virtual ~NVE(){}  
90   };
91  
89 – class NVT : public Integrator{
92  
93 + template<typename T> class NVT : public T {
94 +
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 103 | Line 109 | class NVT : public Integrator{ (protected)
109  
110    virtual int readyCheck();
111  
112 +  virtual void resetIntegrator( void );
113 +
114    // chi is a propagated degree of freedom.
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 114 | Line 125 | class NVT : public Integrator{ (protected)
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  
120 – class NPTi : public Integrator{
137  
138 + template<typename T> class NPTi : public T{
139 +
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 <    Integrator::integrateStep( calcPot, calcStress );
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 141 | Line 165 | class NPTi : public Integrator{ (protected)
165  
166    virtual int readyCheck();
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 158 | Line 191 | class NPTi : public Integrator{ (protected)
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 < class NPTim : public Integrator{
209 > template<typename T> class NPTim : public T{
210  
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 <    Integrator::integrateStep( calcPot, calcStress );
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 );
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;
# Line 200 | Line 259 | class NPTim : public Integrator{ (protected)
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 < class NPTf : public Integrator{
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 );
279 +  }
280 +
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 +
286 + protected:
287 +
288 +  virtual void moveA( void );
289 +  virtual void moveB( void );
290 +
291 +  virtual int readyCheck();
292 +
293 +  virtual void resetIntegrator( void );
294 +
295 +  Molecule* myMolecules;
296 +  Atom** myAtoms;
297 +
298 +  // chi and eta are the propagated degrees of freedom
299 +
300 +  double chi;
301 +  double eta;
302 +  double etaZ;
303 +  double NkBT;
304 +
305 +  // targetTemp, targetPressure, and tauBarostat must be set.  
306 +  // One of qmass or tauThermostat must be set;
307 +
308 +  double targetTemp;
309 +  double targetPressure;
310 +  double tauThermostat;
311 +  double tauBarostat;
312 +
313 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
314 +  short int have_target_pressure;
315 +
316 + };
317 +
318 + template<typename T> class NPTf : public T{
319 +
320 + public:
321 +
322    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
323    virtual ~NPTf() {};
324  
325    virtual void integrateStep( int calcPot, int calcStress ){
326      calcStress = 1;
327 <    Integrator::integrateStep( calcPot, calcStress );
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  
342    virtual void  moveA( void );
343    virtual void moveB( void );
344  
345 +  virtual void resetIntegrator( void );
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  
# Line 243 | Line 366 | class NPTf : public Integrator{ (protected)
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 < class NPTfm : public Integrator{
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.  
414 +  // One of qmass or tauThermostat must be set;
415 +
416 +  double targetTemp;
417 +  double targetPressure;
418 +  double tauThermostat;
419 +  double tauBarostat;
420 +
421 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
422 +  short int have_target_pressure;
423 +
424 + };
425 +
426 +
427 + template<typename T> class NPTfm : public T{
428 +
429 + public:
430 +
431    NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
432    virtual ~NPTfm() {};
433  
434    virtual void integrateStep( int calcPot, int calcStress ){
435      calcStress = 1;
436 <    Integrator::integrateStep( calcPot, calcStress );
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  
451    virtual void  moveA( void );
452    virtual void moveB( void );
453  
454 +  virtual void resetIntegrator( void );
455 +
456    virtual int readyCheck();
457  
458 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
459 +
460 +  Molecule* myMolecules;
461 +  Atom** myAtoms;
462 +
463    // chi and eta are the propagated degrees of freedom
464  
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 286 | Line 477 | class NPTfm : public Integrator{ (protected)
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  
487 +
488 + template<typename T> class NPTpr : public T{
489 +
490 + public:
491 +
492 +  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
493 +  virtual ~NPTpr() {};
494 +
495 +  virtual void integrateStep( int calcPot, int calcStress ){
496 +    calcStress = 1;
497 +    T::integrateStep( calcPot, calcStress );
498 +  }
499 +
500 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
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 +
509 +  virtual void  moveA( void );
510 +  virtual void moveB( void );
511 +
512 +  virtual int readyCheck();
513 +
514 +  virtual void resetIntegrator( void );
515 +
516 +  // chi and eta are the propagated degrees of freedom
517 +
518 +  double chi;
519 +  double eta[3][3];
520 +  double NkBT;
521 +
522 +  // targetTemp, targetPressure, and tauBarostat must be set.  
523 +  // One of qmass or tauThermostat must be set;
524 +
525 +  double targetTemp;
526 +  double targetPressure;
527 +  double tauThermostat;
528 +  double tauBarostat;
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 +
539 +
540 + template<typename T> class ZConstraint : public T {
541 +  
542 +  public:
543 +  class ForceSubtractionPolicy{
544 +    public:
545 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
546 +
547 +      virtual void update() = 0;    
548 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
549 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
550 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
551 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
552 +    
553 +   protected:
554 +     ZConstraint<T>* zconsIntegrator;;
555 +  };
556 +
557 +  class PolicyByNumber : public ForceSubtractionPolicy{
558 +
559 +    public:
560 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
561 +      virtual void update();    
562 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
563 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
564 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
565 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
566 +    
567 +    private:
568 +      int totNumOfMovingAtoms;
569 +  };
570 +
571 +  class PolicyByMass : public ForceSubtractionPolicy{
572 +
573 +    public:
574 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
575 +      
576 +      virtual void update();    
577 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
578 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
579 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
580 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
581 +
582 +   private:
583 +     double totMassOfMovingAtoms;
584 +  };
585 +
586 + public:
587 +
588 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
589 +  ~ZConstraint();
590 +    
591 +  void setZConsTime(double time)                  {this->zconsTime = time;}
592 +  void getZConsTime()                             {return zconsTime;}
593 +  
594 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
595 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
596 +  
597 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
598 +  string getZConsOutput()                         {return zconsOutput;}
599 +  
600 +  virtual void integrate();
601 +  
602 +
603 + #ifdef IS_MPI
604 +  virtual void update();                      //which is called to indicate the molecules' migration
605   #endif
606 +
607 + protected:
608 +
609 +  enum ZConsState {zcsMoving, zcsFixed};  
610 +
611 +  virtual void calcForce( int calcPot, int calcStress );
612 +  virtual void thermalize(void);
613 +  
614 +  void zeroOutVel();
615 +  void doZconstraintForce();
616 +  void doHarmonic();
617 +  bool checkZConsState();
618 +
619 +  bool haveFixedZMols();
620 +  bool haveMovingZMols();
621 +
622 +  double calcZSys();
623 +
624 +  int isZConstraintMol(Molecule* mol);
625 +
626 +
627 +  double zconsTime;                              //sample time
628 +  double zconsTol;                                 //tolerance of z-contratint
629 +  double zForceConst;                           //base force constant term
630 +                                                          //which is estimate by OOPSE
631 +  
632 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
633 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
634 +  vector<double> kz;                              //force constant array
635 +  vector<ZConsState> states;                 //state of z-constraint molecules
636 +  vector<double> zPos;                          //
637 +  
638 +  
639 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
640 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
641 +  double totalMassOfUncons;                //total mas of unconstraint molecules
642 +
643 +  vector<ZConsParaItem>* parameters; //
644 +  
645 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
646 +
647 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
648 +  double* fz;
649 +  double* curZPos;
650 +  
651 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
652 +
653 +  int whichDirection;                           //constraint direction
654 +  
655 + private:
656 +  
657 +  string zconsOutput;                         //filename of zconstraint output
658 +  ZConsWriter* fzOut;                         //z-constraint writer
659 +
660 +  double curZconsTime;                      
661 +
662 +  double calcMovingMolsCOMVel();
663 +  double calcSysCOMVel();
664 +  double calcTotalForce();
665 +  
666 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
667 +  friend class ForceSubtractionPolicy;
668 +
669 + };
670 +
671 + #endif

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