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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 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 <
467 >  double zconsFixTime;  
468 >  double zconsGap;
469 >  bool hasZConsGap;
470 >  vector<double> endFixTime;
471 >  
472    int whichDirection;                           //constraint direction
473  
474   private:
# Line 467 | Line 481 | template<typename T> class ZConstraint : public T { (p
481    double calcMovingMolsCOMVel();
482    double calcSysCOMVel();
483    double calcTotalForce();
484 <
484 >  void updateZPos();
485 >  void updateCantPos();
486 >  
487    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
488    friend class ForceSubtractionPolicy;
489  
490   };
491  
492 < class OOPSEMinimizerBase : public RealIntegrator {
493 <  public:
492 > /*
493 > template<typename T> class SingleZConstrain : public T{
494  
495 <    OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff );
496 <    virtual ~OOPSEMinimizerBase();
495 >
496 > };
497 > */
498 >
499 > template<typename T> class NonEquMD : public T {
500 >  public:
501      
502 <    double calcGradient(vector<double>& x, vector<double>& grad);
503 <    void setCoor(vector<double>& x);
504 <    vector<double> getCoor();
505 <    void output(vector<double>& x, int iteration);
506 <    int getDim() {return dim;}
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      
489 –    int dim;
490 –    void calcDim();
517   };
518  
519 < //template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
520 < //  public:
521 < //    void writeOutput();
522 < //};
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 +
549   #endif

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