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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 1010 by tim, Tue Feb 3 20:43:08 2004 UTC vs.
Revision 1141 by tim, Wed Apr 28 23:09:32 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 418 | Line 421 | template<typename T> class ZConstraint : public T { (p
421  
422    void zeroOutVel();
423    void doZconstraintForce();
424 <  void doHarmonic();
424 >  void doHarmonic(vector<double>& resPos);
425    bool checkZConsState();
426  
427    bool haveFixedZMols();
# Line 449 | Line 452 | template<typename T> class ZConstraint : public T { (p
452  
453    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
454  
455 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
456 <  double* fz;
457 <  double* curZPos;
455 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
456 >  vector<double> fz;
457 >  vector<double> curZPos;
458  
459 +  bool usingSMD;
460 +  vector<double> prevCantPos;
461 +  vector<double> cantPos;
462 +  vector<double> cantVel;
463  
464 <
464 >  double zconsFixTime;  
465 >  double zconsGap;
466 >  bool hasZConsGap;
467 >  vector<double> endFixTime;
468 >  
469    int whichDirection;                           //constraint direction
470  
471   private:
# Line 467 | Line 478 | template<typename T> class ZConstraint : public T { (p
478    double calcMovingMolsCOMVel();
479    double calcSysCOMVel();
480    double calcTotalForce();
481 <
481 >  void updateZPos();
482 >  void updateCantPos();
483 >  
484    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
485    friend class ForceSubtractionPolicy;
486  
487   };
488  
489 < class OOPSEMinimizerBase : public RealIntegrator {
490 <  public:
489 > /*
490 > template<typename T> class SingleZConstrain : public T{
491  
492 <    OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff );
480 <    virtual ~OOPSEMinimizerBase();
481 <    
482 <    double calcGradient(vector<double>& x, vector<double>& grad);
483 <    void setOptCoor(vector<double>& x);
484 <    void getOptCoor(vector<double>& x);
485 <    void output();
486 <    
492 >
493   };
494 + */
495  
496 < template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
496 > template<typename T> class NonEquMD : public T {
497    public:
498 <    void writeOutput();
498 >    
499 >
500 >
501   };
502 +
503 +
504 + //
505 + template<typename T> class SingleZConstraint : public T{
506 +  public:
507 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
508 +    ~SingleZConstraint();
509 +    
510 +    bool stopIntegrator();
511 +    
512 +  protected:
513 +    
514 + };
515 +
516 + //Steered Molecular Dynamics, curret implement only support one steered molecule
517 + template<typename T> class SMD : public T{
518 +  public:
519 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
520 +    ~SMD();
521    
522 +    virtual void integrate();
523 +    virtual void calcForce( int calcPot, int calcStress );  
524 +    bool stopIntegrator();
525 +  private:
526 +    
527 + };
528 +
529 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
530 + //Driven Molecular Dynamics and ZConstraint Method.
531 + template<typename T> class CoordinateDriver : public T {
532 +  public:
533 +    typedef T ParentIntegrator;
534 +
535 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
536 +    ~CoordinateDriver();
537 +    
538 +    virtual void integrate();
539 +
540 +  private:    
541 +    BaseIntegrator* zconsIntegrator;
542 +    BaseIntegrator* drivenIntegrator;
543 +    
544 + };
545 +
546   #endif

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