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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 812 by mmeineke, Wed Oct 22 21:17:32 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 28 | Line 28 | template<typename T = BaseIntegrator> class Integrator
28    virtual ~Integrator();
29    void integrate( void );
30    virtual double  getConservedQuantity(void);
31 +  virtual string getAdditionalParameters(void);
32  
33   protected:
34  
# Line 40 | Line 41 | template<typename T = BaseIntegrator> class Integrator
41    virtual int  readyCheck( void ) { return 1; }
42  
43    virtual void resetIntegrator( void ) { }
44 <
45 <  virtual void calcForce( int calcPot, int calcStress );  
44 >
45 >  virtual void calcForce( int calcPot, int calcStress );
46    virtual void thermalize();
46 –  
47 –  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
47  
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],
53 >  void rotate( int axes1, int axes2, double angle, double j[3],
54           double A[3][3] );
55 <        
55 >
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 61 | Line 65 | template<typename T = BaseIntegrator> class Integrator
65  
66    int isConstrained; // boolean to know whether the systems contains
67           // constraints.
68 <  int nConstrained;  // counter for number of constraints
69 <  int *constrainedA; // the i of a constraint pair
70 <  int *constrainedB; // the j of a constraint pair
71 <  double *constrainedDsqr; // the square of the constraint distance
72 <  
68 >  int nConstrained;  // counter for number of constraints
69 >  int *constrainedA; // the i of a constraint pair
70 >  int *constrainedB; // the j of a constraint pair
71 >  double *constrainedDsqr; // the square of the constraint distance
72 >
73    int* moving; // tells whether we are moving atom i
74    int* moved;  // tells whether we have moved atom i
75 <  double* oldPos; // pre constrained positions
75 >  double* oldPos; // pre constrained positions
76  
77    short isFirst; /*boolean for the first time integrate is called */
78 <  
78 >
79    double dt;
80    double dt2;
81  
82    Thermo *tStats;
83    StatWriter*  statOut;
84    DumpWriter*  dumpOut;
85 <  
85 >
86   };
87  
88   typedef Integrator<BaseIntegrator> RealIntegrator;
# Line 88 | Line 92 | template<typename T> class NVE : public T { (public)
92   public:
93    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
94      T( theInfo, the_ff ){}
95 <  virtual ~NVE(){}  
95 >  virtual ~NVE(){}
96   };
97  
98  
# Line 103 | Line 107 | template<typename T> class NVT : public T { (public)
107    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
108    void setChiTolerance(double tol) {chiTolerance = tol;}
109    virtual double  getConservedQuantity(void);
110 +  virtual string getAdditionalParameters(void);
111  
112   protected:
113  
# Line 124 | Line 129 | template<typename T> class NVT : public T { (public)
129  
130    double targetTemp;
131    double tauThermostat;
132 <  
132 >
133    short int have_tau_thermostat, have_target_temp;
134  
135    double *oldVel;
# Line 143 | Line 148 | template<typename T> class NPT : public T{ (public)
148  
149    NPT ( SimInfo *theInfo, ForceFields* the_ff);
150    virtual ~NPT();
151 <  
151 >
152    virtual void integrateStep( int calcPot, int calcStress ){
153      calcStress = 1;
154      T::integrateStep( calcPot, calcStress );
155    }
156  
157    virtual double getConservedQuantity(void) = 0;
158 +  virtual string getAdditionalParameters(void) = 0;
159 +  
160 +  double myTauThermo( void ) { return tauThermostat; }
161 +  double myTauBaro( void ) { return tauBarostat; }
162  
163    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
164    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
# Line 170 | Line 179 | template<typename T> class NPT : public T{ (public)
179  
180    virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
181    virtual void getVelScaleB( double sc[3], int index ) = 0;
182 <  virtual void getPosScale(double pos[3], double COM[3],
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 <  
189 >
190    virtual void evolveChiA( void );
191    virtual void evolveEtaA( void ) = 0;
192    virtual void evolveChiB( void );
# Line 201 | Line 212 | template<typename T> class NPT : public T{ (public)
212  
213    double integralOfChidt;
214  
215 <  // targetTemp, targetPressure, and tauBarostat must be set.  
215 >  // targetTemp, targetPressure, and tauBarostat must be set.
216    // One of qmass or tauThermostat must be set;
217  
218    double targetTemp;
# Line 226 | Line 237 | template<typename T> class NPTi : public T{
237   };
238  
239   template<typename T> class NPTi : public T{
240 <  
240 >
241   public:
242    NPTi( SimInfo *theInfo, ForceFields* the_ff);
243    ~NPTi();
244  
245    virtual double getConservedQuantity(void);
246    virtual void resetIntegrator(void);
247 <
247 >  virtual string getAdditionalParameters(void);
248   protected:
249  
239 –
250  
251 +
252    virtual void evolveEtaA(void);
253    virtual void evolveEtaB(void);
254  
# Line 247 | Line 258 | template<typename T> class NPTi : public T{ (protected
258  
259    virtual void getVelScaleA( double sc[3], double vel[3] );
260    virtual void getVelScaleB( double sc[3], int index );
261 <  virtual void getPosScale(double pos[3], double COM[3],
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 261 | Line 275 | template<typename T> class NPTf : public T{ (public)
275    virtual ~NPTf();
276  
277    virtual double getConservedQuantity(void);
278 +  virtual string getAdditionalParameters(void);
279    virtual void resetIntegrator(void);
280  
281   protected:
# Line 274 | Line 289 | template<typename T> class NPTf : public T{ (public)
289  
290    virtual void getVelScaleA( double sc[3], double vel[3] );
291    virtual void getVelScaleB( double sc[3], int index );
292 <  virtual void getPosScale(double pos[3], double COM[3],
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 290 | Line 308 | template<typename T> class NPTxyz : public T{ (public)
308    virtual ~NPTxyz();
309  
310    virtual double getConservedQuantity(void);
311 +  virtual string getAdditionalParameters(void);
312    virtual void resetIntegrator(void);
313  
314   protected:
# Line 303 | Line 322 | template<typename T> class NPTxyz : public T{ (public)
322  
323    virtual void getVelScaleA( double sc[3], double vel[3] );
324    virtual void getVelScaleB( double sc[3], int index );
325 <  virtual void getPosScale(double pos[3], double COM[3],
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  
337   template<typename T> class ZConstraint : public T {
338 <  
339 <  public:
338 >
339 >  public:
340    class ForceSubtractionPolicy{
341      public:
342        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
343  
344 <      virtual void update() = 0;    
344 >      virtual void update() = 0;
345        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
347        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
348        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
349 <    
349 >
350     protected:
351       ZConstraint<T>* zconsIntegrator;
352    };
# Line 332 | Line 354 | template<typename T> class ZConstraint : public T {
354    class PolicyByNumber : public ForceSubtractionPolicy{
355  
356      public:
357 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
358 <      virtual void update();    
357 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358 >      virtual void update();
359        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
360        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
361        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
362        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
363 <    
363 >
364      private:
365        int totNumOfMovingAtoms;
366    };
# Line 346 | Line 368 | template<typename T> class ZConstraint : public T {
368    class PolicyByMass : public ForceSubtractionPolicy{
369  
370      public:
371 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
372 <      
373 <      virtual void update();    
371 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
372 >
373 >      virtual void update();
374        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
375        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
376        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 362 | Line 384 | template<typename T> class ZConstraint : public T {
384  
385    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
386    ~ZConstraint();
387 <    
387 >
388    void setZConsTime(double time)                  {this->zconsTime = time;}
389    void getZConsTime()                             {return zconsTime;}
390 <  
390 >
391    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
392    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
393 <  
393 >
394    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
395    string getZConsOutput()                         {return zconsOutput;}
396 <  
396 >
397    virtual void integrate();
376 –  
398  
399 +
400   #ifdef IS_MPI
401    virtual void update();                      //which is called to indicate the molecules' migration
402   #endif
403  
404 <  enum ZConsState {zcsMoving, zcsFixed};  
404 >  enum ZConsState {zcsMoving, zcsFixed};
405  
406    vector<Molecule*> zconsMols;              //z-constraint molecules array
407    vector<ZConsState> states;                 //state of z-constraint molecules
408  
387 –
409  
410 +
411    int totNumOfUnconsAtoms;              //total number of uncontraint atoms
412    double totalMassOfUncons;                //total mas of unconstraint molecules
413  
# Line 393 | Line 415 | template<typename T> class ZConstraint : public T {
415   protected:
416  
417  
418 <
419 <  virtual void calcForce( int calcPot, int calcStress );
418 >
419 >  virtual void calcForce( int calcPot, int calcStress );
420    virtual void thermalize(void);
421 <  
421 >
422    void zeroOutVel();
423    void doZconstraintForce();
424 <  void doHarmonic();
424 >  void doHarmonic(vector<double>& resPos);
425    bool checkZConsState();
426  
427    bool haveFixedZMols();
# Line 414 | Line 436 | template<typename T> class ZConstraint : public T {
436    double zconsTol;                                 //tolerance of z-contratint
437    double zForceConst;                           //base force constant term
438                                                            //which is estimate by OOPSE
417 –  
439  
440 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
440 >
441 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
442    vector<double> kz;                              //force constant array
443  
444    vector<double> zPos;                          //
445 <  
446 <  
445 >
446 >
447    vector<Molecule*> unconsMols;           //unconstraint molecules array
448    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
449  
450  
451    vector<ZConsParaItem>* parameters; //
452 <  
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;
436 <  
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 <  int whichDirection;                           //constraint direction
464 >  double zconsFixTime;  
465 >  double zconsGap;
466 >  bool hasZConsGap;
467 >  vector<double> endFixTime;
468    
469 +  int whichDirection;                           //constraint direction
470 +
471   private:
472 <  
472 >
473    string zconsOutput;                         //filename of zconstraint output
474    ZConsWriter* fzOut;                         //z-constraint writer
475  
476 <  double curZconsTime;                      
476 >  double curZconsTime;
477  
478    double calcMovingMolsCOMVel();
479    double calcSysCOMVel();
480    double calcTotalForce();
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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