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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 843 by mmeineke, Wed Oct 29 20:41:39 2003 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],
# 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 179 | Line 182 | template<typename T> class NPT : public T{ (protected)
182    virtual void getPosScale(double pos[3], double COM[3],
183                             int index, double sc[3]) = 0;
184  
185 +  virtual void calcVelScale( void ) = 0;
186 +
187    virtual bool chiConverged( void );
188    virtual bool etaConverged( void ) = 0;
189  
# Line 256 | Line 261 | template<typename T> class NPTi : public T{ (protected
261    virtual void getPosScale(double pos[3], double COM[3],
262                             int index, double sc[3]);
263  
264 +  virtual void calcVelScale( void );
265 +
266    double eta, oldEta, prevEta;
267 +  double vScale;
268   };
269  
270   template<typename T> class NPTf : public T{
# Line 284 | Line 292 | template<typename T> class NPTf : public T{ (protected
292    virtual void getPosScale(double pos[3], double COM[3],
293                             int index, double sc[3]);
294  
295 +  virtual void calcVelScale( void );
296 +
297    double eta[3][3];
298    double oldEta[3][3];
299    double prevEta[3][3];
300 +  double vScale[3][3];
301   };
302  
303   template<typename T> class NPTxyz : public T{
# Line 314 | Line 325 | template<typename T> class NPTxyz : public T{ (protect
325    virtual void getPosScale(double pos[3], double COM[3],
326                             int index, double sc[3]);
327  
328 +  virtual void calcVelScale( void );
329 +
330    double eta[3][3];
331    double oldEta[3][3];
332    double prevEta[3][3];
333 +  double vScale[3][3];
334   };
335  
336  
# Line 407 | 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 437 | Line 451 | template<typename T> class ZConstraint : public T { (p
451    vector<ZConsParaItem>* parameters; //
452  
453    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
440 –
441 –  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
442 –  double* fz;
443 –  double* curZPos;
454  
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 +  double zconsFixTime;  
465 +  double zconsGap;
466 +  bool hasZConsGap;
467 +  vector<double> endFixTime;
468 +  
469    int whichDirection;                           //constraint direction
470  
471   private:
# Line 456 | 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 + /*
490 + template<typename T> class SingleZConstrain : public T{
491 +
492 +
493 + };
494 + */
495 +
496 + template<typename T> class NonEquMD : public T {
497 +  public:
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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