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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 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 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> cantPos;
461 +  vector<double> cantVel;
462  
463 +  double zconsFixTime;  
464 +  double zconsGap;
465 +  bool hasZConsGap;
466 +  vector<double> endFixTime;
467 +  
468    int whichDirection;                           //constraint direction
469  
470   private:
# Line 456 | 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 + /*
489 + template<typename T> class SingleZConstrain : public T{
490 +
491 +
492 + };
493 + */
494 +
495 + template<typename T> class NonEquMD : public T {
496 +  public:
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

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