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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 1452 by tim, Mon Aug 23 15:11:36 2004 UTC

# Line 13 | Line 13
13   #include "Thermo.hpp"
14   #include "ReadWrite.hpp"
15   #include "ZConsWriter.hpp"
16 + #include "Restraints.hpp"
17 + #include "Quaternion.hpp"
18 + #include "Mat4x4d.hpp"
19  
20   using namespace std;
21   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
# Line 21 | Line 24 | const double tol = 1.0e-6;
24   const int maxIteration = 300;
25   const double tol = 1.0e-6;
26  
27 + class VelVerletConsFramework;
28   template<typename T = BaseIntegrator> class Integrator : public T {
29  
30   public:
# Line 33 | Line 37 | template<typename T = BaseIntegrator> class Integrator
37   protected:
38  
39    virtual void integrateStep( int calcPot, int calcStress );
40 <  virtual void preMove( void );
40 >  //virtual void preMove( void );
41    virtual void moveA( void );
42    virtual void moveB( void );
43 <  virtual void constrainA( void );
44 <  virtual void constrainB( void );
43 >  //virtual void constrainA( void );
44 >  //virtual void constrainB( void );
45    virtual int  readyCheck( void ) { return 1; }
46  
47    virtual void resetIntegrator( void ) { }
# Line 45 | Line 49 | template<typename T = BaseIntegrator> class Integrator
49    virtual void calcForce( int calcPot, int calcStress );
50    virtual void thermalize();
51  
52 +  virtual bool stopIntegrator() {return false;}
53 +
54    virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
55  
56 <  void checkConstraints( void );
56 >  //void checkConstraints( void );
57    void rotate( int axes1, int axes2, double angle, double j[3],
58           double A[3][3] );
59  
60 +  void printQuaternion(StuntDouble* sd);
61 +  Mat4x4d getS(const Quaternion& q);
62 +
63    ForceFields* myFF;
64  
65    SimInfo *info; // all the info we'll ever need
# Line 61 | Line 70 | template<typename T = BaseIntegrator> class Integrator
70    Molecule* molecules;
71    int nMols;
72  
73 <  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
73 >  VelVerletConsFramework* consFramework;
74  
75 <  int* moving; // tells whether we are moving atom i
76 <  int* moved;  // tells whether we have moved atom i
77 <  double* oldPos; // pre constrained positions
75 >  //int isConstrained; // boolean to know whether the systems contains constraints.
76 >  //int nConstrained;  // counter for number of constraints
77 >  //int *constrainedA; // the i of a constraint pair
78 >  //int *constrainedB; // the j of a constraint pair
79 >  //double *constrainedDsqr; // the square of the constraint distance
80  
81 +  //int* moving; // tells whether we are moving atom i
82 +  //int* moved;  // tells whether we have moved atom i
83 +  //double* oldPos; // pre constrained positions
84 +
85    short isFirst; /*boolean for the first time integrate is called */
86  
87    double dt;
# Line 84 | Line 94 | typedef Integrator<BaseIntegrator> RealIntegrator;
94   };
95  
96   typedef Integrator<BaseIntegrator> RealIntegrator;
97 +
98 + // ansi instantiation
99 + // template class Integrator<BaseIntegrator>;
100 +
101  
102   template<typename T> class NVE : public T {
103  
# Line 455 | Line 469 | template<typename T> class ZConstraint : public T { (p
469    vector<double> curZPos;
470  
471    bool usingSMD;
472 +  vector<double> prevCantPos;
473    vector<double> cantPos;
474    vector<double> cantVel;
475  
# Line 483 | Line 498 | template<typename T> class ZConstraint : public T { (p
498  
499   };
500  
501 < /*
502 < //Steered Molecular Dynamics
503 < template<typename T> class SMD : public T{
501 >
502 > //Sympletic quaternion Scheme Integrator
503 > //Reference:
504 > // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
505 > //Symplectic quaternion Scheme for biophysical molecular dynamics
506 > //116(20), 8649, J. Chem. Phys. (2002)
507 > template<typename T> class SQSIntegrator : public T{
508    public:
509 <    SMD( SimInfo *theInfo, ForceFields* the_ff);
510 <    ~SMD();
511 <  
512 <   virtual void integrate();
513 <  virtual void calcForce( int calcPot, int calcStress );  
509 >    SQSIntegrator( SimInfo *theInfo, ForceFields* the_ff );
510 >    virtual void moveA();
511 >    virtual void moveB();
512 >  protected:
513 >    void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I);
514 >    void rotate(int k, double dt,  Quaternion& q,  Vector4d& qdot, double Ik);
515 >  private:
516 >    Quaternion getPk(int i, const Vector4d& q);
517 >    Mat4x4d getS(const Quaternion& q);
518 >    vector<Quaternion> q;
519 >    vector<Vector4d> p_qua;
520 >    vector<double> I0;
521 >
522 >                Vector4d p2j(const Vector4d& p, Mat4x4d& m);    
523 >                Vector4d j2p(const Vector4d& j, Mat4x4d& m);
524   };
496 – */
525   #endif

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