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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 1161 by tim, Tue May 11 21:44:05 2004 UTC vs.
Revision 1330 by gezelter, Fri Jul 16 16:29:44 2004 UTC

# Line 13 | Line 13
13   #include "Thermo.hpp"
14   #include "ReadWrite.hpp"
15   #include "ZConsWriter.hpp"
16 + #include "Restraints.hpp"
17  
18   using namespace std;
19   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
# Line 21 | Line 22 | template<typename T = BaseIntegrator> class Integrator
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
25 + class VelVerletConsFramework;
26   template<typename T = BaseIntegrator> class Integrator : public T {
27  
28   public:
# Line 33 | Line 35 | template<typename T = BaseIntegrator> class Integrator
35   protected:
36  
37    virtual void integrateStep( int calcPot, int calcStress );
38 <  virtual void preMove( void );
38 >  //virtual void preMove( void );
39    virtual void moveA( void );
40    virtual void moveB( void );
41 <  virtual void constrainA( void );
42 <  virtual void constrainB( void );
41 >  //virtual void constrainA( void );
42 >  //virtual void constrainB( void );
43    virtual int  readyCheck( void ) { return 1; }
44  
45    virtual void resetIntegrator( void ) { }
# Line 49 | Line 51 | template<typename T = BaseIntegrator> class Integrator
51  
52    virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
53  
54 <  void checkConstraints( void );
54 >  //void checkConstraints( void );
55    void rotate( int axes1, int axes2, double angle, double j[3],
56           double A[3][3] );
57  
# Line 63 | Line 65 | template<typename T = BaseIntegrator> class Integrator
65    Molecule* molecules;
66    int nMols;
67  
68 <  int isConstrained; // boolean to know whether the systems contains
67 <         // constraints.
68 <  int nConstrained;  // counter for number of constraints
69 <  int *constrainedA; // the i of a constraint pair
70 <  int *constrainedB; // the j of a constraint pair
71 <  double *constrainedDsqr; // the square of the constraint distance
68 >  VelVerletConsFramework* consFramework;
69  
70 <  int* moving; // tells whether we are moving atom i
71 <  int* moved;  // tells whether we have moved atom i
72 <  double* oldPos; // pre constrained positions
70 >  //int isConstrained; // boolean to know whether the systems contains constraints.
71 >  //int nConstrained;  // counter for number of constraints
72 >  //int *constrainedA; // the i of a constraint pair
73 >  //int *constrainedB; // the j of a constraint pair
74 >  //double *constrainedDsqr; // the square of the constraint distance
75  
76 +  //int* moving; // tells whether we are moving atom i
77 +  //int* moved;  // tells whether we have moved atom i
78 +  //double* oldPos; // pre constrained positions
79 +
80    short isFirst; /*boolean for the first time integrate is called */
81  
82    double dt;
# Line 88 | Line 91 | template class Integrator<BaseIntegrator>;
91   typedef Integrator<BaseIntegrator> RealIntegrator;
92  
93   // ansi instantiation
94 < template class Integrator<BaseIntegrator>;
94 > // template class Integrator<BaseIntegrator>;
95  
96 +
97   template<typename T> class NVE : public T {
98  
99   public:
# Line 489 | Line 493 | template<typename T> class ZConstraint : public T { (p
493  
494   };
495  
492 – /*
493 – template<typename T> class SingleZConstrain : public T{
496  
497 <
498 < };
499 < */
500 <
501 < template<typename T> class NonEquMD : public T {
502 <  public:
501 <    
502 <
503 <
504 < };
505 <
506 <
507 < //
508 < template<typename T> class SingleZConstraint : public T{
497 > //Sympletic quaternion Scheme Integrator
498 > //Reference:
499 > // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
500 > //Symplectic quaternion Scheme for biophysical molecular dynamics
501 > //116(20), 8649, J. Chem. Phys. (2002)
502 > template<typename T> class SQSIntegrator : public T{
503    public:
504 <    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
505 <    ~SingleZConstraint();
512 <    
513 <    bool stopIntegrator();
514 <    
504 >    virtual void moveA();
505 >    virtual void moveB();
506    protected:
507 +    void freeRotor();
508 +    void rotate(int k, double dt);
509      
510   };
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 );  
527 –    bool stopIntegrator();
528 –  private:
529 –    
530 – };
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 –
511   #endif

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