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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC vs.
Revision 1323 by gezelter, Wed Jul 14 20:11:29 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 | const double tol = 1.0e-6;
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 45 | Line 47 | template<typename T = BaseIntegrator> class Integrator
47    virtual void calcForce( int calcPot, int calcStress );
48    virtual void thermalize();
49  
50 +  virtual bool stopIntegrator() {return false;}
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 61 | 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
65 <         // constraints.
66 <  int nConstrained;  // counter for number of constraints
67 <  int *constrainedA; // the i of a constraint pair
68 <  int *constrainedB; // the j of a constraint pair
69 <  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 84 | Line 89 | typedef Integrator<BaseIntegrator> RealIntegrator;
89   };
90  
91   typedef Integrator<BaseIntegrator> RealIntegrator;
92 +
93 + // ansi instantiation
94 + // template class Integrator<BaseIntegrator>;
95  
96   template<typename T> class NVE : public T {
97  
# Line 455 | Line 463 | template<typename T> class ZConstraint : public T { (p
463    vector<double> curZPos;
464  
465    bool usingSMD;
466 +  vector<double> prevCantPos;
467    vector<double> cantPos;
468    vector<double> cantVel;
469  
# Line 483 | Line 492 | template<typename T> class ZConstraint : public T { (p
492  
493   };
494  
495 < /*
496 < //Steered Molecular Dynamics
497 < template<typename T> class SMD : public T{
495 >
496 > //Sympletic quaternion Scheme Integrator
497 > //Reference:
498 > // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
499 > //Symplectic quaternion Scheme for biophysical molecular dynamics
500 > //116(20), 8649, J. Chem. Phys. (2002)
501 > template<typename T> class SQSIntegrator : public T{
502    public:
503 <    SMD( SimInfo *theInfo, ForceFields* the_ff);
504 <    ~SMD();
505 <  
506 <   virtual void integrate();
507 <  virtual void calcForce( int calcPot, int calcStress );  
503 >    virtual void moveA();
504 >    virtual void moveB();
505 >  protected:
506 >    void freeRotor();
507 >    void rotate(int k, double dt);
508 >    
509   };
496 – */
510   #endif

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