ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/Integrator.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 597 by mmeineke, Mon Jul 14 21:28:54 2003 UTC vs.
Revision 755 by mmeineke, Tue Sep 9 20:35:25 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"
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();
# 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[9] );
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);
# Line 103 | Line 107 | class NVT : public Integrator{ (protected)
107  
108    virtual int readyCheck();
109  
110 +  virtual void resetIntegrator( void );
111 +
112    // chi is a propagated degree of freedom.
113  
114    double chi;
# Line 117 | Line 123 | class NPTi : public Integrator{
123   };
124  
125  
120 – class NPTi : public Integrator{
126  
127 + template<typename T> class NPTi : public T{
128 +
129   public:
130  
131    NPTi ( SimInfo *theInfo, ForceFields* the_ff);
# Line 126 | Line 133 | class NPTi : public Integrator{ (public)
133  
134    virtual void integrateStep( int calcPot, int calcStress ){
135      calcStress = 1;
136 <    Integrator::integrateStep( calcPot, calcStress );
136 >    T::integrateStep( calcPot, calcStress );
137    }
138  
139    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 141 | Line 148 | class NPTi : public Integrator{ (public)
148  
149    virtual int readyCheck();
150  
151 +  virtual void resetIntegrator( void );
152 +
153    // chi and eta are the propagated degrees of freedom
154  
155    double chi;
# Line 160 | Line 169 | class NPTim : public Integrator{
169  
170   };
171  
172 < class NPTim : public Integrator{
172 > template<typename T> class NPTim : public T{
173  
174   public:
175  
# Line 169 | Line 178 | class NPTim : public Integrator{ (public)
178  
179    virtual void integrateStep( int calcPot, int calcStress ){
180      calcStress = 1;
181 <    Integrator::integrateStep( calcPot, calcStress );
181 >    T::integrateStep( calcPot, calcStress );
182    }
183  
184    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 179 | Line 188 | class NPTim : public Integrator{ (public)
188  
189   protected:
190  
191 <  virtual void  moveA( void );
191 >  virtual void moveA( void );
192    virtual void moveB( void );
193  
194    virtual int readyCheck();
195  
196 +  virtual void resetIntegrator( void );
197 +
198 +  Molecule* myMolecules;
199 +  Atom** myAtoms;
200 +
201    // chi and eta are the propagated degrees of freedom
202  
203    double chi;
# Line 203 | Line 217 | class NPTf : public Integrator{
217  
218   };
219  
220 < class NPTf : public Integrator{
220 > template<typename T> class NPTzm : public T{
221 >
222 > public:
223 >
224 >  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
225 >  virtual ~NPTzm() {};
226 >
227 >  virtual void integrateStep( int calcPot, int calcStress ){
228 >    calcStress = 1;
229 >    T::integrateStep( calcPot, calcStress );
230 >  }
231 >
232 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
233 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
234 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
235 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
236 >
237 > protected:
238 >
239 >  virtual void moveA( void );
240 >  virtual void moveB( void );
241 >
242 >  virtual int readyCheck();
243 >
244 >  virtual void resetIntegrator( void );
245 >
246 >  Molecule* myMolecules;
247 >  Atom** myAtoms;
248  
249 +  // chi and eta are the propagated degrees of freedom
250 +
251 +  double chi;
252 +  double eta;
253 +  double etaZ;
254 +  double NkBT;
255 +
256 +  // targetTemp, targetPressure, and tauBarostat must be set.  
257 +  // One of qmass or tauThermostat must be set;
258 +
259 +  double targetTemp;
260 +  double targetPressure;
261 +  double tauThermostat;
262 +  double tauBarostat;
263 +
264 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
265 +  short int have_target_pressure;
266 +
267 + };
268 +
269 + template<typename T> class NPTf : public T{
270 +
271   public:
272  
273    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
# Line 212 | Line 275 | class NPTf : public Integrator{ (public)
275  
276    virtual void integrateStep( int calcPot, int calcStress ){
277      calcStress = 1;
278 <    Integrator::integrateStep( calcPot, calcStress );
278 >    T::integrateStep( calcPot, calcStress );
279    }
280  
281    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 225 | Line 288 | class NPTf : public Integrator{ (public)
288    virtual void  moveA( void );
289    virtual void moveB( void );
290  
291 +  virtual void resetIntegrator( void );
292 +
293    virtual int readyCheck();
294  
295    // chi and eta are the propagated degrees of freedom
# Line 246 | Line 311 | class NPTfm : public Integrator{
311  
312   };
313  
314 < class NPTfm : public Integrator{
314 > template<typename T> class NPTxym : public T{
315  
316   public:
317  
318 +  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
319 +  virtual ~NPTxym() {};
320 +
321 +  virtual void integrateStep( int calcPot, int calcStress ){
322 +    calcStress = 1;
323 +    T::integrateStep( calcPot, calcStress );
324 +  }
325 +
326 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
327 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
328 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
329 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
330 +
331 + protected:
332 +
333 +  virtual void moveA( void );
334 +  virtual void moveB( void );
335 +
336 +  virtual int readyCheck();
337 +
338 +  virtual void resetIntegrator( void );
339 +
340 +  Molecule* myMolecules;
341 +  Atom** myAtoms;
342 +
343 +  // chi and eta are the propagated degrees of freedom
344 +
345 +  double chi;
346 +  double eta;
347 +  double etaX;
348 +  double etaY;
349 +  double NkBT;
350 +
351 +  // targetTemp, targetPressure, and tauBarostat must be set.  
352 +  // One of qmass or tauThermostat must be set;
353 +
354 +  double targetTemp;
355 +  double targetPressure;
356 +  double tauThermostat;
357 +  double tauBarostat;
358 +
359 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
360 +  short int have_target_pressure;
361 +
362 + };
363 +
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 <    Integrator::integrateStep( calcPot, calcStress );
374 >    T::integrateStep( calcPot, calcStress );
375    }
376  
377    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 268 | Line 384 | class NPTfm : public Integrator{ (protected)
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;
# Line 289 | Line 410 | class NPTfm : public Integrator{ (protected)
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 +
460 + template<typename T> class ZConstraint : public T {
461 +  
462 +  public:
463 +  class ForceSubtractionPolicy{
464 +    public:
465 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
466 +
467 +      virtual void update() = 0;    
468 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
469 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
470 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
471 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
472 +    
473 +   protected:
474 +     ZConstraint<T>* zconsIntegrator;;
475 +  };
476 +
477 +  class PolicyByNumber : public ForceSubtractionPolicy{
478 +
479 +    public:
480 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
481 +      virtual void update();    
482 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
483 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
484 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
485 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
486 +    
487 +    private:
488 +    int totNumOfMovingAtoms;
489 +  };
490 +
491 +  class PolicyByMass : public ForceSubtractionPolicy{
492 +
493 +    public:
494 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
495 +      
496 +      virtual void update();    
497 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
498 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
499 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
500 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
501 +
502 +   private:
503 +     double totMassOfMovingAtoms;
504 +  };
505 +
506 + public:
507 +
508 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
509 +  ~ZConstraint();
510 +    
511 +  void setZConsTime(double time)                  {this->zconsTime = time;}
512 +  void getZConsTime()                             {return zconsTime;}
513 +  
514 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
515 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
516 +  
517 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
518 +  string getZConsOutput()                         {return zconsOutput;}
519 +  
520 +  virtual void integrate();
521 +  
522 +
523 + #ifdef IS_MPI
524 +  virtual void update();                      //which is called to indicate the molecules' migration
525   #endif
526 +
527 + protected:
528 +
529 +  enum ZConsState {zcsMoving, zcsFixed};  
530 +
531 +  virtual void calcForce( int calcPot, int calcStress );
532 +  virtual void thermalize(void);
533 +  
534 +  void zeroOutVel();
535 +  void doZconstraintForce();
536 +  void doHarmonic();
537 +  bool checkZConsState();
538 +
539 +  bool haveFixedZMols();
540 +  bool haveMovingZMols();
541 +
542 +  double calcZSys();
543 +
544 +  int isZConstraintMol(Molecule* mol);
545 +
546 +
547 +  double zconsTime;                              //sample time
548 +  double zconsTol;                                 //tolerance of z-contratint
549 +  double zForceConst;                           //base force constant term
550 +                                                          //which is estimate by OOPSE
551 +  
552 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
553 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
554 +  vector<double> kz;                              //force constant array
555 +  vector<ZConsState> states;                 //state of z-constraint molecules
556 +  vector<double> zPos;                          //
557 +  
558 +  
559 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
560 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
561 +  double totalMassOfUncons;                //total mas of unconstraint molecules
562 +
563 +  vector<ZConsParaItem>* parameters; //
564 +  
565 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
566 +
567 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
568 +  double* fz;
569 +  double* curZPos;
570 +  
571 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
572 +
573 +  int whichDirection;                           //constraint direction
574 +  
575 + private:
576 +  
577 +  string zconsOutput;                         //filename of zconstraint output
578 +  ZConsWriter* fzOut;                         //z-constraint writer
579 +
580 +  double curZconsTime;                      
581 +
582 +  double calcMovingMolsCOMVel();
583 +  double calcSysCOMVel();
584 +  double calcTotalForce();
585 +  
586 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
587 +  friend class ForceSubtractionPolicy;
588 +
589 + };
590 +
591 + #endif

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines