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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 677 by tim, Mon Aug 11 19:41:36 2003 UTC vs.
Revision 718 by gezelter, Mon Aug 25 21:51:30 2003 UTC

# Line 44 | Line 44 | template<typename T = BaseIntegrator> class Integrator
44    
45    void checkConstraints( void );
46    void rotate( int axes1, int axes2, double angle, double j[3],
47 <               double A[3][3] );
48 <              
47 >         double A[3][3] );
48 >        
49    ForceFields* myFF;
50  
51    SimInfo *info; // all the info we'll ever need
# Line 56 | Line 56 | template<typename T = BaseIntegrator> class Integrator
56    int nMols;
57  
58    int isConstrained; // boolean to know whether the systems contains
59 <                     // constraints.
59 >         // constraints.
60    int nConstrained;  // counter for number of constraints
61    int *constrainedA; // the i of a constraint pair
62    int *constrainedB; // the j of a constraint pair
# Line 278 | Line 278 | template<typename T> class NPTfm : public T{ (protecte
278  
279    Molecule* myMolecules;
280    Atom** myAtoms;
281 +
282 +  // chi and eta are the propagated degrees of freedom
283 +
284 +  double chi;
285 +  double eta[3][3];
286 +  double NkBT;
287 +
288 +  // targetTemp, targetPressure, and tauBarostat must be set.  
289 +  // One of qmass or tauThermostat must be set;
290 +
291 +  double targetTemp;
292 +  double targetPressure;
293 +  double tauThermostat;
294 +  double tauBarostat;
295 +
296 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
297 +  short int have_target_pressure;
298 +
299 + };
300 +
301 +
302 + template<typename T> class NPTpr : public T{
303 +
304 + public:
305 +
306 +  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
307 +  virtual ~NPTpr() {};
308 +
309 +  virtual void integrateStep( int calcPot, int calcStress ){
310 +    calcStress = 1;
311 +    T::integrateStep( calcPot, calcStress );
312 +  }
313 +
314 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
315 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
316 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
317 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
318  
319 + protected:
320 +
321 +  virtual void  moveA( void );
322 +  virtual void moveB( void );
323 +
324 +  virtual int readyCheck();
325 +
326    // chi and eta are the propagated degrees of freedom
327  
328    double chi;
# Line 298 | Line 342 | template<typename T> class NPTfm : public T{ (protecte
342  
343   };
344  
345 +
346   template<typename T> class ZConstraint : public T {
347 +  
348 +  public:
349 +  class ForceSubstractionPolicy{
350 +    public:
351 +      ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
352 +
353 +      virtual void update() = 0;    
354 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
355 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
356 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
357 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
358 +    
359 +   protected:
360 +     ZConstraint<T>* zconsIntegrator;;
361 +  };
362 +
363 +  class PolicyByNumber : ForceSubstractionPolicy{
364 +    public:
365 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}    
366 +      virtual void update();    
367 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
368 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
369 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
370 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
371 +    
372 +    private:
373 +    int totNumOfMovingAtoms;
374 +  };
375  
376 +  class PolicyByMass :ForceSubstractionPolicy{
377 +    public:
378 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}  
379 +      
380 +      virtual void update();    
381 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
382 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
383 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
384 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
385 +
386 +   private:
387 +     double totMassOfMovingAtoms;
388 +  };
389 +
390   public:
391  
392    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
# Line 308 | Line 395 | template<typename T> class ZConstraint : public T { (p
395    void setZConsTime(double time)                  {this->zconsTime = time;}
396    void getZConsTime()                             {return zconsTime;}
397    
398 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
399 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
398 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
399 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
400    
401 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
401 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
402    string getZConsOutput()                         {return zconsOutput;}
403    
404    virtual void integrate();
405    
406  
407   #ifdef IS_MPI
408 <  virtual void update(); //which is called to indicate the molecules' migration
408 >  virtual void update();                      //which is called to indicate the molecules' migration
409   #endif
410  
411   protected:
412  
413 <  enum ZConsState {zcsMoving, zcsFixed};
327 <
328 <
413 >  enum ZConsState {zcsMoving, zcsFixed};  
414  
415    virtual void calcForce( int calcPot, int calcStress );
416    virtual void thermalize(void);
417    
418    void zeroOutVel();
419    void doZconstraintForce();
420 +  void doHarmonic();
421    bool checkZConsState();
422  
423    bool haveFixedZMols();
# Line 342 | Line 428 | template<typename T> class ZConstraint : public T { (p
428    int isZConstraintMol(Molecule* mol);
429  
430  
431 <  double zconsTime;
432 <  double ztol;
431 >  double zconsTime;                              //sample time
432 >  double zconsTol;                                 //tolerance of z-contratint
433 >  double zForceConst;                           //base force constant term
434 >                                                          //which is estimate by OOPSE
435    
436 <  vector<Molecule*> zconsMols;
437 <  vector<double> massOfZConsMols;
438 <  vector<double> zconsPos;
439 <  vector<double> kz;
440 <  vector<ZConsState> states;
353 <  vector<double> ZPos;
436 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
437 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
438 >  vector<double> kz;                              //force constant array
439 >  vector<ZConsState> states;                 //state of z-constraint molecules
440 >  vector<double> zPos;                          //
441    
442    
443 <  vector<Molecule*> unconsMols;
444 <  vector<double> massOfUnconsMols;
445 <  double totalMassOfUncons;
443 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
444 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
445 >  double totalMassOfUncons;                //total mas of unconstraint molecules
446 >
447 >  vector<ZConsParaItem>* parameters; //
448    
449    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
450  
451    int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
452    double* fz;
453 +  double* curZPos;
454    
455 <  int totNumOfUnconsAtoms;
455 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
456  
457    int whichDirection;                           //constraint direction
458    
459   private:
460    
461 <  string zconsOutput;
462 <  ZConsWriter* fzOut;
461 >  string zconsOutput;                         //filename of zconstraint output
462 >  ZConsWriter* fzOut;                         //z-constraint writer
463  
464 +  double curZconsTime;                      
465  
466 +  double calcMovingMolsCOMVel();
467 +  double calcSysCOMVel();
468 +  double calcTotalForce();
469 +  
470 +  ForceSubstractionPolicy* forcePolicy; //force substration policy
471 +  friend class ForceSubstractionPolicy;
472 +
473   };
474  
475   #endif

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