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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 1091 by tim, Tue Mar 16 19:22:56 2004 UTC vs.
Revision 1161 by tim, Tue May 11 21:44:05 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 84 | Line 87 | template<typename T> class NVE : public T {
87  
88   typedef Integrator<BaseIntegrator> RealIntegrator;
89  
90 + // ansi instantiation
91 + template class Integrator<BaseIntegrator>;
92 +
93   template<typename T> class NVE : public T {
94  
95   public:
# Line 418 | Line 424 | template<typename T> class ZConstraint : public T { (p
424  
425    void zeroOutVel();
426    void doZconstraintForce();
427 <  void doHarmonic();
427 >  void doHarmonic(vector<double>& resPos);
428    bool checkZConsState();
429  
430    bool haveFixedZMols();
# Line 449 | Line 455 | template<typename T> class ZConstraint : public T { (p
455  
456    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
457  
458 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
459 <  double* fz;
460 <  double* curZPos;
458 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
459 >  vector<double> fz;
460 >  vector<double> curZPos;
461  
462 +  bool usingSMD;
463 +  vector<double> prevCantPos;
464 +  vector<double> cantPos;
465 +  vector<double> cantVel;
466 +
467    double zconsFixTime;  
468    double zconsGap;
469    bool hasZConsGap;
# Line 471 | Line 482 | template<typename T> class ZConstraint : public T { (p
482    double calcSysCOMVel();
483    double calcTotalForce();
484    void updateZPos();
485 <
485 >  void updateCantPos();
486 >  
487    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
488    friend class ForceSubtractionPolicy;
489  
490   };
491  
492   /*
493 < //Steered Molecular Dynamics
493 > template<typename T> class SingleZConstrain : public T{
494 >
495 >
496 > };
497 > */
498 >
499 > template<typename T> class NonEquMD : public T {
500 >  public:
501 >    
502 >
503 >
504 > };
505 >
506 >
507 > //
508 > template<typename T> class SingleZConstraint : public T{
509 >  public:
510 >    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
511 >    ~SingleZConstraint();
512 >    
513 >    bool stopIntegrator();
514 >    
515 >  protected:
516 >    
517 > };
518 >
519 > //Steered Molecular Dynamics, curret implement only support one steered molecule
520   template<typename T> class SMD : public T{
521    public:
522      SMD( SimInfo *theInfo, ForceFields* the_ff);
523      ~SMD();
524    
525 <   virtual void integrate();
526 <  virtual void calcForce( int calcPot, int calcStress );  
525 >    virtual void integrate();
526 >    virtual void calcForce( int calcPot, int calcStress );  
527 >    bool stopIntegrator();
528 >  private:
529 >    
530   };
531 < */
531 >
532 > //By using state pattern, Coordinate Drive is responsible for switching back and forth between
533 > //Driven Molecular Dynamics and ZConstraint Method.
534 > template<typename T> class CoordinateDriver : public T {
535 >  public:
536 >    typedef T ParentIntegrator;
537 >
538 >    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
539 >    ~CoordinateDriver();
540 >    
541 >    virtual void integrate();
542 >
543 >  private:    
544 >    BaseIntegrator* zconsIntegrator;
545 >    BaseIntegrator* drivenIntegrator;
546 >    
547 > };
548 >
549   #endif

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