ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/Integrator.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 987 by tim, Tue Jan 27 19:15:20 2004 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 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],
# 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> cantPos;
461 +  vector<double> cantVel;
462  
463 <
463 >  double zconsFixTime;  
464 >  double zconsGap;
465 >  bool hasZConsGap;
466 >  vector<double> endFixTime;
467 >  
468    int whichDirection;                           //constraint direction
469  
470   private:
# Line 467 | Line 477 | template<typename T> class ZConstraint : public T { (p
477    double calcMovingMolsCOMVel();
478    double calcSysCOMVel();
479    double calcTotalForce();
480 <
480 >  void updateZPos();
481 >  void updateCantPos();
482 >  
483    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
484    friend class ForceSubtractionPolicy;
485  
486   };
487  
488 < class OOPSEMinimizerBase : public RealIntegrator {
489 <  public:
488 > /*
489 > template<typename T> class SingleZConstrain : public T{
490  
491 <    OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff );
480 <    virtual ~OOPSEMinimizerBase();
481 <    
482 <    double calcGradient(const vector<double>& x, vector<double>& grad);
483 <    void setOptCoor(vector<double>& x);
484 <    void getOptCoor(vector<double>& x);
485 <    void output();
486 <    
491 >
492   };
493 + */
494  
495 < template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
495 > template<typename T> class NonEquMD : public T {
496    public:
497 <    void writeOutput();
497 >    
498 >
499 >
500   };
501 +
502 +
503 + //
504 + template<typename T> class SingleZConstraint : public T{
505 +  public:
506 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
507 +    ~SingleZConstraint();
508 +    
509 +    bool stopIntegrator();
510 +    
511 +  protected:
512 +    
513 + };
514 +
515 + //Steered Molecular Dynamics, curret implement only support one steered molecule
516 + template<typename T> class SMD : public T{
517 +  public:
518 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
519 +    ~SMD();
520    
521 +    virtual void integrate();
522 +    virtual void calcForce( int calcPot, int calcStress );  
523 +    bool stopIntegrator();
524 +  private:
525 +    
526 + };
527 +
528 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
529 + //Driven Molecular Dynamics and ZConstraint Method.
530 + template<typename T> class CoordinateDriver : public T {
531 +  public:
532 +    typedef T ParentIntegrator;
533 +
534 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
535 +    ~CoordinateDriver();
536 +    
537 +    virtual void integrate();
538 +
539 +  private:    
540 +    BaseIntegrator* zconsIntegrator;
541 +    BaseIntegrator* drivenIntegrator;
542 +    
543 + };
544 +
545   #endif

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines