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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 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 179 | Line 185 | template<typename T> class NPT : public T{ (protected)
185    virtual void getPosScale(double pos[3], double COM[3],
186                             int index, double sc[3]) = 0;
187  
188 +  virtual void calcVelScale( void ) = 0;
189 +
190    virtual bool chiConverged( void );
191    virtual bool etaConverged( void ) = 0;
192  
# Line 255 | Line 263 | template<typename T> class NPTi : public T{ (protected
263    virtual void getVelScaleB( double sc[3], int index );
264    virtual void getPosScale(double pos[3], double COM[3],
265                             int index, double sc[3]);
266 +
267 +  virtual void calcVelScale( void );
268  
269    double eta, oldEta, prevEta;
270 +  double vScale;
271   };
272  
273   template<typename T> class NPTf : public T{
# Line 284 | Line 295 | template<typename T> class NPTf : public T{ (protected
295    virtual void getPosScale(double pos[3], double COM[3],
296                             int index, double sc[3]);
297  
298 +  virtual void calcVelScale( void );
299 +
300    double eta[3][3];
301    double oldEta[3][3];
302    double prevEta[3][3];
303 +  double vScale[3][3];
304   };
305  
306   template<typename T> class NPTxyz : public T{
# Line 314 | Line 328 | template<typename T> class NPTxyz : public T{ (protect
328    virtual void getPosScale(double pos[3], double COM[3],
329                             int index, double sc[3]);
330  
331 +  virtual void calcVelScale( void );
332 +
333    double eta[3][3];
334    double oldEta[3][3];
335    double prevEta[3][3];
336 +  double vScale[3][3];
337   };
338  
339  
# Line 407 | 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 438 | 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 456 | 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 + /*
493 + template<typename T> class SingleZConstrain : public T{
494 +
495 +
496 + };
497 + */
498  
499 + template<typename T> class NonEquMD : public T {
500 +  public:
501 +    
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 +    
517 + };
518 +
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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