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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC vs.
Revision 780 by mmeineke, Mon Sep 22 21:23:25 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"
# Line 9 | Line 11
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  
19 – 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  
26 –
32   protected:
33 <  
33 >
34    virtual void integrateStep( int calcPot, int calcStress );
35    virtual void preMove( void );
36    virtual void moveA( void );
# Line 33 | 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 +  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 <
41 <
51 >         double A[3][3] );
52 >        
53    ForceFields* myFF;
54  
55    SimInfo *info; // all the info we'll ever need
# Line 49 | Line 60 | class Integrator : public BaseIntegrator { (protected)
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 70 | Line 81 | class NVE : public Integrator{
81    
82   };
83  
84 < class NVE : public Integrator{
84 > typedef Integrator<BaseIntegrator> RealIntegrator;
85  
86 + template<typename T> class NVE : public T {
87 +
88   public:
89    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
90 <    Integrator( theInfo, the_ff ){}
91 <  virtual ~NVE(){}
79 <
80 <  
81 <
90 >    T( theInfo, the_ff ){}
91 >  virtual ~NVE(){}  
92   };
93  
84 – class NVT : public Integrator{
94  
95 + template<typename T> class NVT : public T {
96 +
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 98 | Line 111 | class NVT : public Integrator{ (protected)
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 109 | Line 127 | class NVT : public Integrator{ (protected)
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  
115 – class NPTi : public Integrator{
139  
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 <    Integrator::integrateStep( calcPot, calcStress );
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 136 | Line 166 | class NPTi : public Integrator{ (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;
142 –  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 153 | Line 212 | class NPTi : public Integrator{ (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 < class NPTim : public Integrator{
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;
265 <    Integrator::integrateStep( calcPot, calcStress );
265 >    T::integrateStep( calcPot, calcStress );
266    }
267  
268    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 179 | Line 277 | class NPTim : public Integrator{ (protected)
277  
278    virtual int readyCheck();
279  
280 +  virtual void resetIntegrator( void );
281 +
282    Molecule* myMolecules;
283    Atom** myAtoms;
284  
# Line 186 | Line 286 | class NPTim : public Integrator{ (protected)
286  
287    double chi;
288    double eta;
289 +  double etaZ;
290    double NkBT;
291  
292    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 201 | Line 302 | class NPTf : public Integrator{
302  
303   };
304  
305 < class NPTf : public Integrator{
305 > template<typename T> class NPTf : public T{
306  
307   public:
308  
309    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
310 <  virtual ~NPTf() {};
310 >  virtual ~NPTf();
311  
312 +  virtual double getConservedQuantity(void);
313 +  virtual void resetIntegrator(void);
314 +
315 + protected:
316 +
317 +  virtual void evolveEtaA(void);
318 +  virtual void evolveEtaB(void);
319 +
320 +  virtual bool etaConverged( void );
321 +
322 +  virtual void scaleSimBox( void );
323 +
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 +  double eta[3][3];
330 +  double oldEta[3][3];
331 +  double prevEta[3][3];
332 + };
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 <    Integrator::integrateStep( calcPot, calcStress );
343 >    T::integrateStep( calcPot, calcStress );
344    }
345  
346    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 220 | Line 350 | class NPTf : public Integrator{ (protected)
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 244 | Line 381 | class NPTfm : public Integrator{
381  
382   };
383  
247 – class NPTfm : public Integrator{
384  
385 + template<typename T> class NPTfm : public T{
386 +
387   public:
388  
389    NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
# Line 253 | Line 391 | class NPTfm : public Integrator{ (public)
391  
392    virtual void integrateStep( int calcPot, int calcStress ){
393      calcStress = 1;
394 <    Integrator::integrateStep( calcPot, calcStress );
394 >    T::integrateStep( calcPot, calcStress );
395 >    accIntegralOfChidt();
396    }
397  
398 +  virtual double getConservedQuantity(void);
399 +  
400    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
401    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
402    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
403    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
404 +  void setChiTolerance(double tol) {chiTolerance = tol;}
405 +  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
406  
407   protected:
408  
409    virtual void  moveA( void );
410    virtual void moveB( void );
411  
412 +  virtual void resetIntegrator( void );
413 +
414    virtual int readyCheck();
415  
416 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
417 +
418 +  Molecule* myMolecules;
419 +  Atom** myAtoms;
420 +
421    // chi and eta are the propagated degrees of freedom
422  
423    double chi;
424    double eta[3][3];
425    double NkBT;
426 +  double integralOfChidt;
427  
428    // targetTemp, targetPressure, and tauBarostat must be set.  
429    // One of qmass or tauThermostat must be set;
# Line 284 | Line 435 | class NPTfm : public Integrator{ (public)
435  
436    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
437    short int have_target_pressure;
438 +  double chiTolerance;
439 +  short int have_chi_tolerance;
440 +  double posIterTolerance;
441 +  short int have_pos_iter_tolerance;
442  
443   };
444  
445 +
446 + template<typename T> class NPTpr : public T{
447 +
448 + public:
449 +
450 +  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
451 +  virtual ~NPTpr() {};
452 +
453 +  virtual void integrateStep( int calcPot, int calcStress ){
454 +    calcStress = 1;
455 +    T::integrateStep( calcPot, calcStress );
456 +  }
457 +
458 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
459 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
460 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
461 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
462 +  void setChiTolerance(double tol) {chiTolerance = tol;}
463 +  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
464 +
465 + protected:
466 +
467 +  virtual void  moveA( void );
468 +  virtual void moveB( void );
469 +
470 +  virtual int readyCheck();
471 +
472 +  virtual void resetIntegrator( void );
473 +
474 +  // chi and eta are the propagated degrees of freedom
475 +
476 +  double chi;
477 +  double eta[3][3];
478 +  double NkBT;
479 +
480 +  // targetTemp, targetPressure, and tauBarostat must be set.  
481 +  // One of qmass or tauThermostat must be set;
482 +
483 +  double targetTemp;
484 +  double targetPressure;
485 +  double tauThermostat;
486 +  double tauBarostat;
487 +
488 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
489 +  short int have_target_pressure;
490 +  double chiTolerance;
491 +  short int have_chi_tolerance;
492 +  double posIterTolerance;
493 +  short int have_pos_iter_tolerance;
494 +
495 + };
496 +
497 +
498 + template<typename T> class ZConstraint : public T {
499 +  
500 +  public:
501 +  class ForceSubtractionPolicy{
502 +    public:
503 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
504 +
505 +      virtual void update() = 0;    
506 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
507 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
508 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
509 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
510 +    
511 +   protected:
512 +     ZConstraint<T>* zconsIntegrator;;
513 +  };
514 +
515 +  class PolicyByNumber : public ForceSubtractionPolicy{
516 +
517 +    public:
518 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
519 +      virtual void update();    
520 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
521 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
522 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
523 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
524 +    
525 +    private:
526 +      int totNumOfMovingAtoms;
527 +  };
528 +
529 +  class PolicyByMass : public ForceSubtractionPolicy{
530 +
531 +    public:
532 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
533 +      
534 +      virtual void update();    
535 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
536 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
537 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
538 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
539 +
540 +   private:
541 +     double totMassOfMovingAtoms;
542 +  };
543 +
544 + public:
545 +
546 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
547 +  ~ZConstraint();
548 +    
549 +  void setZConsTime(double time)                  {this->zconsTime = time;}
550 +  void getZConsTime()                             {return zconsTime;}
551 +  
552 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
553 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
554 +  
555 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
556 +  string getZConsOutput()                         {return zconsOutput;}
557 +  
558 +  virtual void integrate();
559 +  
560 +
561 + #ifdef IS_MPI
562 +  virtual void update();                      //which is called to indicate the molecules' migration
563   #endif
564 +
565 + protected:
566 +
567 +  enum ZConsState {zcsMoving, zcsFixed};  
568 +
569 +  virtual void calcForce( int calcPot, int calcStress );
570 +  virtual void thermalize(void);
571 +  
572 +  void zeroOutVel();
573 +  void doZconstraintForce();
574 +  void doHarmonic();
575 +  bool checkZConsState();
576 +
577 +  bool haveFixedZMols();
578 +  bool haveMovingZMols();
579 +
580 +  double calcZSys();
581 +
582 +  int isZConstraintMol(Molecule* mol);
583 +
584 +
585 +  double zconsTime;                              //sample time
586 +  double zconsTol;                                 //tolerance of z-contratint
587 +  double zForceConst;                           //base force constant term
588 +                                                          //which is estimate by OOPSE
589 +  
590 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
591 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
592 +  vector<double> kz;                              //force constant array
593 +  vector<ZConsState> states;                 //state of z-constraint molecules
594 +  vector<double> zPos;                          //
595 +  
596 +  
597 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
598 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
599 +  double totalMassOfUncons;                //total mas of unconstraint molecules
600 +
601 +  vector<ZConsParaItem>* parameters; //
602 +  
603 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
604 +
605 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
606 +  double* fz;
607 +  double* curZPos;
608 +  
609 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
610 +
611 +  int whichDirection;                           //constraint direction
612 +  
613 + private:
614 +  
615 +  string zconsOutput;                         //filename of zconstraint output
616 +  ZConsWriter* fzOut;                         //z-constraint writer
617 +
618 +  double curZconsTime;                      
619 +
620 +  double calcMovingMolsCOMVel();
621 +  double calcSysCOMVel();
622 +  double calcTotalForce();
623 +  
624 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
625 +  friend class ForceSubtractionPolicy;
626 +
627 + };
628 +
629 + #endif

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