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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 857 by mmeineke, Fri Nov 7 17:09:48 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC

# Line 4 | Line 4
4   #include <string>
5   #include <vector>
6   #include "Atom.hpp"
7 + #include "StuntDouble.hpp"
8   #include "Molecule.hpp"
9   #include "SRI.hpp"
10   #include "AbstractClasses.hpp"
# Line 20 | Line 21 | const double tol = 1.0e-6;
21   const int maxIteration = 300;
22   const double tol = 1.0e-6;
23  
23 –
24   template<typename T = BaseIntegrator> class Integrator : public T {
25  
26   public:
# Line 45 | Line 45 | template<typename T = BaseIntegrator> class Integrator
45    virtual void calcForce( int calcPot, int calcStress );
46    virtual void thermalize();
47  
48 <  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48 >  virtual bool stopIntegrator() {return false;}
49  
50 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
51 +
52    void checkConstraints( void );
53    void rotate( int axes1, int axes2, double angle, double j[3],
54           double A[3][3] );
# Line 54 | Line 56 | template<typename T = BaseIntegrator> class Integrator
56    ForceFields* myFF;
57  
58    SimInfo *info; // all the info we'll ever need
59 +  vector<StuntDouble*> integrableObjects;
60    int nAtoms;  /* the number of atoms */
61    int oldAtoms;
62    Atom **atoms; /* array of atom pointers */
# Line 418 | Line 421 | template<typename T> class ZConstraint : public T { (p
421  
422    void zeroOutVel();
423    void doZconstraintForce();
424 <  void doHarmonic();
424 >  void doHarmonic(vector<double>& resPos);
425    bool checkZConsState();
426  
427    bool haveFixedZMols();
# Line 449 | Line 452 | template<typename T> class ZConstraint : public T { (p
452  
453    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
454  
455 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
456 <  double* fz;
457 <  double* curZPos;
455 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
456 >  vector<double> fz;
457 >  vector<double> curZPos;
458  
459 +  bool usingSMD;
460 +  vector<double> cantPos;
461 +  vector<double> cantVel;
462  
463 <
463 >  double zconsFixTime;  
464 >  double zconsGap;
465 >  bool hasZConsGap;
466 >  vector<double> endFixTime;
467 >  
468    int whichDirection;                           //constraint direction
469  
470   private:
# Line 467 | Line 477 | template<typename T> class ZConstraint : public T { (p
477    double calcMovingMolsCOMVel();
478    double calcSysCOMVel();
479    double calcTotalForce();
480 <
480 >  void updateZPos();
481 >  void updateCantPos();
482 >  
483    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
484    friend class ForceSubtractionPolicy;
485  
486   };
487  
488 + /*
489 + template<typename T> class SingleZConstrain : public T{
490 +
491 +
492 + };
493 + */
494 +
495 + template<typename T> class NonEquMD : public T {
496 +  public:
497 +    
498 +
499 +
500 + };
501 +
502 +
503 + //
504 + template<typename T> class SingleZConstraint : public T{
505 +  public:
506 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
507 +    ~SingleZConstraint();
508 +    
509 +    bool stopIntegrator();
510 +    
511 +  protected:
512 +    
513 + };
514 +
515 + //Steered Molecular Dynamics, curret implement only support one steered molecule
516 + template<typename T> class SMD : public T{
517 +  public:
518 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
519 +    ~SMD();
520 +  
521 +    virtual void integrate();
522 +    virtual void calcForce( int calcPot, int calcStress );  
523 +    bool stopIntegrator();
524 +  private:
525 +    
526 + };
527 +
528 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
529 + //Driven Molecular Dynamics and ZConstraint Method.
530 + template<typename T> class CoordinateDriver : public T {
531 +  public:
532 +    typedef T ParentIntegrator;
533 +
534 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
535 +    ~CoordinateDriver();
536 +    
537 +    virtual void integrate();
538 +
539 +  private:    
540 +    BaseIntegrator* zconsIntegrator;
541 +    BaseIntegrator* drivenIntegrator;
542 +    
543 + };
544 +
545   #endif

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