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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 701 by tim, Wed Aug 20 14:34:04 2003 UTC

# Line 38 | Line 38 | template<typename T = BaseIntegrator> class Integrator
38    virtual void constrainA( void );
39    virtual void constrainB( void );
40    virtual int  readyCheck( void ) { return 1; }
41 +
42 +  virtual void calcForce( int calcPot, int calcStress );  
43 +  virtual void thermalize();
44    
45    void checkConstraints( void );
46    void rotate( int axes1, int axes2, double angle, double j[3],
47 <               double A[3][3] );
48 <
46 <
47 >         double A[3][3] );
48 >        
49    ForceFields* myFF;
50  
51    SimInfo *info; // all the info we'll ever need
# Line 54 | 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 297 | Line 299 | template<typename T> class ZConstraint : public T {
299   };
300  
301   template<typename T> class ZConstraint : public T {
302 +  
303 +  public:
304 +  class ForceSubstractionPolicy{
305 +    public:
306 +      ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
307  
308 < public:
309 <
310 <  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
311 <  ~ZConstraint();
308 >      virtual void update() = 0;    
309 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
310 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
311 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
312 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
313 >    
314 >   protected:
315 >     ZConstraint<T>* zconsIntegrator;;
316 >  };
317  
318 <  virtual void integrateStep( int calcPot, int calcStress );
319 <  
320 <  
318 >  class PolicyByNumber : ForceSubstractionPolicy{
319 >    public:
320 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}    
321 >      virtual void update();    
322 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
323 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
324 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
325 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
326 >    
327 >    private:
328 >    int totNumOfMovingAtoms;
329 >  };
330 >
331 >  class PolicyByMass :ForceSubstractionPolicy{
332 >    public:
333 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}  
334 >      
335 >      virtual void update();    
336 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
337 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
338 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
339 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
340 >
341 >   private:
342 >     double totMassOfMovingAtoms;
343 >  };
344 >
345 > public:
346 >
347 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
348 >  ~ZConstraint();
349 >    
350    void setZConsTime(double time)                  {this->zconsTime = time;}
351    void getZConsTime()                             {return zconsTime;}
352    
353 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
354 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
353 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
354 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
355    
356 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
356 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
357    string getZConsOutput()                         {return zconsOutput;}
358 +  
359 +  virtual void integrate();
360 +  
361  
362   #ifdef IS_MPI
363 <  virtual void update(); //which is called to indicate the molecules' migration
363 >  virtual void update();                      //which is called to indicate the molecules' migration
364   #endif
365  
366   protected:
367  
368 <  double zconsTime;
369 <  
370 <  void resetZ(void);
368 >  enum ZConsState {zcsMoving, zcsFixed};  
369 >
370 >  virtual void calcForce( int calcPot, int calcStress );
371 >  virtual void thermalize(void);
372    
373 <  vector<Molecule*> zconsMols;
374 <  vector<double> massOfZConsMols;
373 >  void zeroOutVel();
374 >  void doZconstraintForce();
375 >  void doHarmonic();
376 >  bool checkZConsState();
377 >
378 >  bool haveFixedZMols();
379 >  bool haveMovingZMols();
380 >
381 >  double calcZSys();
382 >
383 >  int isZConstraintMol(Molecule* mol);
384 >
385 >
386 >  double zconsTime;                              //sample time
387 >  double zconsTol;                                 //tolerance of z-contratint
388 >  double zForceConst;                           //base force constant term
389 >                                                          //which is estimate by OOPSE
390    
391 <  vector<Molecule*> unconsMols;
392 <  vector<double> massOfUnconsMols;
393 <  double totalMassOfUncons;
391 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
392 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
393 >  vector<double> kz;                              //force constant array
394 >  vector<ZConsState> states;                 //state of z-constraint molecules
395 >  vector<double> zPos;                          //
396 >  
397 >  
398 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
399 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
400 >  double totalMassOfUncons;                //total mas of unconstraint molecules
401  
402 <  vector<double> allRefZ;    
336 <  vector<double> refZ;
402 >  vector<ZConsParaItem>* parameters; //
403    
404    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
405 <  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
406 <    
405 >
406 >  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
407    double* fz;
408 +  double* curZPos;
409    
410 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
411 +
412 +  int whichDirection;                           //constraint direction
413 +  
414   private:
415 +  
416 +  string zconsOutput;                         //filename of zconstraint output
417 +  ZConsWriter* fzOut;                         //z-constraint writer
418  
419 <  int isZConstraintMol(Molecule* mol);
420 <  string zconsOutput;
421 <  ZConsWriter* fzOut;
419 >  double curZconsTime;                      
420 >
421 >  double calcMovingMolsCOMVel();
422 >  double calcSysCOMVel();
423 >  double calcTotalForce();
424 >  
425 >  ForceSubstractionPolicy* forcePolicy; //force substration policy
426 >  friend class ForceSubstractionPolicy;
427 >
428   };
429  
430   #endif

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