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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 1035 by tim, Fri Feb 6 21:37:59 2004 UTC vs.
Revision 1254 by tim, Wed Jun 9 16:16:33 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 12 | 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 20 | Line 22 | const double tol = 1.0e-6;
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
25 <
25 > class RattleFramework;
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 void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
50 >  virtual bool stopIntegrator() {return false;}
51  
52 <  void checkConstraints( void );
52 >  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
53 >
54 >  //void checkConstraints( void );
55    void rotate( int axes1, int axes2, double angle, double j[3],
56           double A[3][3] );
57  
58    ForceFields* myFF;
59  
60    SimInfo *info; // all the info we'll ever need
61 +  vector<StuntDouble*> integrableObjects;
62    int nAtoms;  /* the number of atoms */
63    int oldAtoms;
64    Atom **atoms; /* array of atom pointers */
65    Molecule* molecules;
66    int nMols;
67  
68 <  int isConstrained; // boolean to know whether the systems contains
64 <         // constraints.
65 <  int nConstrained;  // counter for number of constraints
66 <  int *constrainedA; // the i of a constraint pair
67 <  int *constrainedB; // the j of a constraint pair
68 <  double *constrainedDsqr; // the square of the constraint distance
68 >  RattleFramework* rattle;
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 90 | typedef Integrator<BaseIntegrator> RealIntegrator;
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  
98   public:
# Line 418 | Line 427 | template<typename T> class ZConstraint : public T { (p
427  
428    void zeroOutVel();
429    void doZconstraintForce();
430 <  void doHarmonic();
430 >  void doHarmonic(vector<double>& resPos);
431    bool checkZConsState();
432  
433    bool haveFixedZMols();
# Line 449 | Line 458 | template<typename T> class ZConstraint : public T { (p
458  
459    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
460  
461 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
462 <  double* fz;
463 <  double* curZPos;
455 <
461 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
462 >  vector<double> fz;
463 >  vector<double> curZPos;
464  
465 +  bool usingSMD;
466 +  vector<double> prevCantPos;
467 +  vector<double> cantPos;
468 +  vector<double> cantVel;
469  
470 +  double zconsFixTime;  
471 +  double zconsGap;
472 +  bool hasZConsGap;
473 +  vector<double> endFixTime;
474 +  
475    int whichDirection;                           //constraint direction
476  
477   private:
# Line 467 | Line 484 | template<typename T> class ZConstraint : public T { (p
484    double calcMovingMolsCOMVel();
485    double calcSysCOMVel();
486    double calcTotalForce();
487 <
487 >  void updateZPos();
488 >  void updateCantPos();
489 >  
490    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
491    friend class ForceSubtractionPolicy;
492  
493   };
494  
476 – class OOPSEMinimizerBase : public RealIntegrator {
477 –  public:
495  
496 <    OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff );
497 <    virtual ~OOPSEMinimizerBase();
498 <    
499 <    double calcGradient(vector<double>& x, vector<double>& grad);
500 <    void setCoor(vector<double>& x);
501 <    vector<double> getCoor();
502 <    void output(vector<double>& x, int iteration);
503 <    int getDim() {return dim;}
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 >    virtual void moveA();
504 >    virtual void moveB();
505    protected:
506 +    void freeRotor();
507 +    void rotate(int k, double dt);
508      
489 –    int dim;
490 –    void calcDim();
509   };
492 –
493 – //template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
494 – //  public:
495 – //    void writeOutput();
496 – //};
497 –  
510   #endif

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