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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 780 by mmeineke, Mon Sep 22 21:23:25 2003 UTC vs.
Revision 843 by mmeineke, Wed Oct 29 20:41:39 2003 UTC

# 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();
47 <  
47 >
48    virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
49  
50    void checkConstraints( void );
51 <  void rotate( int axes1, int axes2, double angle, double j[3],
51 >  void rotate( int axes1, int axes2, double angle, double j[3],
52           double A[3][3] );
53 <        
53 >
54    ForceFields* myFF;
55  
56    SimInfo *info; // all the info we'll ever need
# Line 61 | Line 62 | template<typename T = BaseIntegrator> class Integrator
62  
63    int isConstrained; // boolean to know whether the systems contains
64           // constraints.
65 <  int nConstrained;  // counter for number of constraints
66 <  int *constrainedA; // the i of a constraint pair
67 <  int *constrainedB; // the j of a constraint pair
68 <  double *constrainedDsqr; // the square of the constraint distance
69 <  
65 >  int nConstrained;  // counter for number of constraints
66 >  int *constrainedA; // the i of a constraint pair
67 >  int *constrainedB; // the j of a constraint pair
68 >  double *constrainedDsqr; // the square of the constraint distance
69 >
70    int* moving; // tells whether we are moving atom i
71    int* moved;  // tells whether we have moved atom i
72 <  double* oldPos; // pre constrained positions
72 >  double* oldPos; // pre constrained positions
73  
74    short isFirst; /*boolean for the first time integrate is called */
75 <  
75 >
76    double dt;
77    double dt2;
78  
79    Thermo *tStats;
80    StatWriter*  statOut;
81    DumpWriter*  dumpOut;
82 <  
82 >
83   };
84  
85   typedef Integrator<BaseIntegrator> RealIntegrator;
# Line 88 | Line 89 | template<typename T> class NVE : public T { (public)
89   public:
90    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
91      T( theInfo, the_ff ){}
92 <  virtual ~NVE(){}  
92 >  virtual ~NVE(){}
93   };
94  
95  
# Line 103 | Line 104 | template<typename T> class NVT : public T { (public)
104    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
105    void setChiTolerance(double tol) {chiTolerance = tol;}
106    virtual double  getConservedQuantity(void);
107 +  virtual string getAdditionalParameters(void);
108  
109   protected:
110  
# Line 124 | Line 126 | template<typename T> class NVT : public T { (public)
126  
127    double targetTemp;
128    double tauThermostat;
129 <  
129 >
130    short int have_tau_thermostat, have_target_temp;
131  
132    double *oldVel;
# Line 143 | Line 145 | template<typename T> class NPT : public T{ (public)
145  
146    NPT ( SimInfo *theInfo, ForceFields* the_ff);
147    virtual ~NPT();
148 <  
148 >
149    virtual void integrateStep( int calcPot, int calcStress ){
150      calcStress = 1;
151      T::integrateStep( calcPot, calcStress );
152    }
153  
154    virtual double getConservedQuantity(void) = 0;
155 +  virtual string getAdditionalParameters(void) = 0;
156 +  
157 +  double myTauThermo( void ) { return tauThermostat; }
158 +  double myTauBaro( void ) { return tauBarostat; }
159  
160    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
161    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
# Line 170 | Line 176 | template<typename T> class NPT : public T{ (public)
176  
177    virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
178    virtual void getVelScaleB( double sc[3], int index ) = 0;
179 <  virtual void getPosScale(double pos[3], double COM[3],
179 >  virtual void getPosScale(double pos[3], double COM[3],
180                             int index, double sc[3]) = 0;
181  
182    virtual bool chiConverged( void );
183    virtual bool etaConverged( void ) = 0;
184 <  
184 >
185    virtual void evolveChiA( void );
186    virtual void evolveEtaA( void ) = 0;
187    virtual void evolveChiB( void );
# Line 201 | Line 207 | template<typename T> class NPT : public T{ (public)
207  
208    double integralOfChidt;
209  
210 <  // targetTemp, targetPressure, and tauBarostat must be set.  
210 >  // targetTemp, targetPressure, and tauBarostat must be set.
211    // One of qmass or tauThermostat must be set;
212  
213    double targetTemp;
# Line 226 | Line 232 | template<typename T> class NPTi : public T{
232   };
233  
234   template<typename T> class NPTi : public T{
235 <  
235 >
236   public:
237    NPTi( SimInfo *theInfo, ForceFields* the_ff);
238    ~NPTi();
239  
240    virtual double getConservedQuantity(void);
241    virtual void resetIntegrator(void);
242 <
242 >  virtual string getAdditionalParameters(void);
243   protected:
244  
239 –
245  
246 +
247    virtual void evolveEtaA(void);
248    virtual void evolveEtaB(void);
249  
# Line 247 | Line 253 | template<typename T> class NPTi : public T{
253  
254    virtual void getVelScaleA( double sc[3], double vel[3] );
255    virtual void getVelScaleB( double sc[3], int index );
256 <  virtual void getPosScale(double pos[3], double COM[3],
256 >  virtual void getPosScale(double pos[3], double COM[3],
257                             int index, double sc[3]);
258  
259    double eta, oldEta, prevEta;
254 – };
255 –
256 – template<typename T> class NPTzm : public T{
257 –
258 – public:
259 –
260 –  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
261 –  virtual ~NPTzm() {};
262 –
263 –  virtual void integrateStep( int calcPot, int calcStress ){
264 –    calcStress = 1;
265 –    T::integrateStep( calcPot, calcStress );
266 –  }
267 –
268 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
269 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
270 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
271 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
272 –
273 – protected:
274 –
275 –  virtual void moveA( void );
276 –  virtual void moveB( void );
277 –
278 –  virtual int readyCheck();
279 –
280 –  virtual void resetIntegrator( void );
281 –
282 –  Molecule* myMolecules;
283 –  Atom** myAtoms;
284 –
285 –  // chi and eta are the propagated degrees of freedom
286 –
287 –  double chi;
288 –  double eta;
289 –  double etaZ;
290 –  double NkBT;
291 –
292 –  // targetTemp, targetPressure, and tauBarostat must be set.  
293 –  // One of qmass or tauThermostat must be set;
294 –
295 –  double targetTemp;
296 –  double targetPressure;
297 –  double tauThermostat;
298 –  double tauBarostat;
299 –
300 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
301 –  short int have_target_pressure;
302 –
260   };
261  
262   template<typename T> class NPTf : public T{
# Line 310 | Line 267 | template<typename T> class NPTf : public T{ (public)
267    virtual ~NPTf();
268  
269    virtual double getConservedQuantity(void);
270 +  virtual string getAdditionalParameters(void);
271    virtual void resetIntegrator(void);
272  
273   protected:
# Line 323 | Line 281 | template<typename T> class NPTf : public T{ (public)
281  
282    virtual void getVelScaleA( double sc[3], double vel[3] );
283    virtual void getVelScaleB( double sc[3], int index );
284 <  virtual void getPosScale(double pos[3], double COM[3],
284 >  virtual void getPosScale(double pos[3], double COM[3],
285                             int index, double sc[3]);
286  
287    double eta[3][3];
# Line 331 | Line 289 | template<typename T> class NPTxym : public T{
289    double prevEta[3][3];
290   };
291  
292 < template<typename T> class NPTxym : public T{
292 > template<typename T> class NPTxyz : public T{
293  
294   public:
295  
296 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
297 <  virtual ~NPTxym() {};
296 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
297 >  virtual ~NPTxyz();
298  
341 –  virtual void integrateStep( int calcPot, int calcStress ){
342 –    calcStress = 1;
343 –    T::integrateStep( calcPot, calcStress );
344 –  }
345 –
346 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
347 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
348 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
349 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
350 –
351 – protected:
352 –
353 –  virtual void moveA( void );
354 –  virtual void moveB( void );
355 –
356 –  virtual int readyCheck();
357 –
358 –  virtual void resetIntegrator( void );
359 –
360 –  Molecule* myMolecules;
361 –  Atom** myAtoms;
362 –
363 –  // chi and eta are the propagated degrees of freedom
364 –
365 –  double chi;
366 –  double eta;
367 –  double etaX;
368 –  double etaY;
369 –  double NkBT;
370 –
371 –  // targetTemp, targetPressure, and tauBarostat must be set.  
372 –  // One of qmass or tauThermostat must be set;
373 –
374 –  double targetTemp;
375 –  double targetPressure;
376 –  double tauThermostat;
377 –  double tauBarostat;
378 –
379 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
380 –  short int have_target_pressure;
381 –
382 – };
383 –
384 –
385 – template<typename T> class NPTfm : public T{
386 –
387 – public:
388 –
389 –  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
390 –  virtual ~NPTfm() {};
391 –
392 –  virtual void integrateStep( int calcPot, int calcStress ){
393 –    calcStress = 1;
394 –    T::integrateStep( calcPot, calcStress );
395 –    accIntegralOfChidt();
396 –  }
397 –
299    virtual double getConservedQuantity(void);
300 <  
301 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
401 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
402 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
403 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
404 <  void setChiTolerance(double tol) {chiTolerance = tol;}
405 <  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
300 >  virtual string getAdditionalParameters(void);
301 >  virtual void resetIntegrator(void);
302  
303   protected:
304  
305 <  virtual void  moveA( void );
306 <  virtual void moveB( void );
305 >  virtual void evolveEtaA(void);
306 >  virtual void evolveEtaB(void);
307  
308 <  virtual void resetIntegrator( void );
308 >  virtual bool etaConverged( void );
309  
310 <  virtual int readyCheck();
310 >  virtual void scaleSimBox( void );
311 >
312 >  virtual void getVelScaleA( double sc[3], double vel[3] );
313 >  virtual void getVelScaleB( double sc[3], int index );
314 >  virtual void getPosScale(double pos[3], double COM[3],
315 >                           int index, double sc[3]);
316  
416 –  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
417 –
418 –  Molecule* myMolecules;
419 –  Atom** myAtoms;
420 –
421 –  // chi and eta are the propagated degrees of freedom
422 –
423 –  double chi;
317    double eta[3][3];
318 <  double NkBT;
319 <  double integralOfChidt;
427 <
428 <  // targetTemp, targetPressure, and tauBarostat must be set.  
429 <  // One of qmass or tauThermostat must be set;
430 <
431 <  double targetTemp;
432 <  double targetPressure;
433 <  double tauThermostat;
434 <  double tauBarostat;
435 <
436 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
437 <  short int have_target_pressure;
438 <  double chiTolerance;
439 <  short int have_chi_tolerance;
440 <  double posIterTolerance;
441 <  short int have_pos_iter_tolerance;
442 <
318 >  double oldEta[3][3];
319 >  double prevEta[3][3];
320   };
321  
322  
446 – template<typename T> class NPTpr : public T{
447 –
448 – public:
449 –
450 –  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
451 –  virtual ~NPTpr() {};
452 –
453 –  virtual void integrateStep( int calcPot, int calcStress ){
454 –    calcStress = 1;
455 –    T::integrateStep( calcPot, calcStress );
456 –  }
457 –
458 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
459 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
460 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
461 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
462 –  void setChiTolerance(double tol) {chiTolerance = tol;}
463 –  void setPosIterTolerance(double tol) {posIterTolerance = tol;}
464 –
465 – protected:
466 –
467 –  virtual void  moveA( void );
468 –  virtual void moveB( void );
469 –
470 –  virtual int readyCheck();
471 –
472 –  virtual void resetIntegrator( void );
473 –
474 –  // chi and eta are the propagated degrees of freedom
475 –
476 –  double chi;
477 –  double eta[3][3];
478 –  double NkBT;
479 –
480 –  // targetTemp, targetPressure, and tauBarostat must be set.  
481 –  // One of qmass or tauThermostat must be set;
482 –
483 –  double targetTemp;
484 –  double targetPressure;
485 –  double tauThermostat;
486 –  double tauBarostat;
487 –
488 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
489 –  short int have_target_pressure;
490 –  double chiTolerance;
491 –  short int have_chi_tolerance;
492 –  double posIterTolerance;
493 –  short int have_pos_iter_tolerance;
494 –
495 – };
496 –
497 –
323   template<typename T> class ZConstraint : public T {
324 <  
325 <  public:
324 >
325 >  public:
326    class ForceSubtractionPolicy{
327      public:
328        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
329  
330 <      virtual void update() = 0;    
330 >      virtual void update() = 0;
331        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
332        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
333        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
334        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
335 <    
335 >
336     protected:
337 <     ZConstraint<T>* zconsIntegrator;;
337 >     ZConstraint<T>* zconsIntegrator;
338    };
339  
340    class PolicyByNumber : public ForceSubtractionPolicy{
341  
342      public:
343 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
344 <      virtual void update();    
343 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
344 >      virtual void update();
345        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
346        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
347        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
348        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
349 <    
349 >
350      private:
351        int totNumOfMovingAtoms;
352    };
# Line 529 | Line 354 | template<typename T> class ZConstraint : public T {
354    class PolicyByMass : public ForceSubtractionPolicy{
355  
356      public:
357 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
358 <      
359 <      virtual void update();    
357 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358 >
359 >      virtual void update();
360        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
361        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
362        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 545 | Line 370 | template<typename T> class ZConstraint : public T {
370  
371    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
372    ~ZConstraint();
373 <    
373 >
374    void setZConsTime(double time)                  {this->zconsTime = time;}
375    void getZConsTime()                             {return zconsTime;}
376 <  
376 >
377    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
378    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
379 <  
379 >
380    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
381    string getZConsOutput()                         {return zconsOutput;}
382 <  
382 >
383    virtual void integrate();
559 –  
384  
385 +
386   #ifdef IS_MPI
387    virtual void update();                      //which is called to indicate the molecules' migration
388   #endif
389  
390 +  enum ZConsState {zcsMoving, zcsFixed};
391 +
392 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
393 +  vector<ZConsState> states;                 //state of z-constraint molecules
394 +
395 +
396 +
397 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
398 +  double totalMassOfUncons;                //total mas of unconstraint molecules
399 +
400 +
401   protected:
402  
403 <  enum ZConsState {zcsMoving, zcsFixed};  
404 <
405 <  virtual void calcForce( int calcPot, int calcStress );
403 >
404 >
405 >  virtual void calcForce( int calcPot, int calcStress );
406    virtual void thermalize(void);
407 <  
407 >
408    void zeroOutVel();
409    void doZconstraintForce();
410    void doHarmonic();
# Line 586 | Line 422 | template<typename T> class ZConstraint : public T {
422    double zconsTol;                                 //tolerance of z-contratint
423    double zForceConst;                           //base force constant term
424                                                            //which is estimate by OOPSE
425 <  
426 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
427 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
425 >
426 >
427 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
428    vector<double> kz;                              //force constant array
429 <  vector<ZConsState> states;                 //state of z-constraint molecules
429 >
430    vector<double> zPos;                          //
431 <  
432 <  
431 >
432 >
433    vector<Molecule*> unconsMols;           //unconstraint molecules array
434    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
599 –  double totalMassOfUncons;                //total mas of unconstraint molecules
435  
436 +
437    vector<ZConsParaItem>* parameters; //
438 <  
438 >
439    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
440  
441 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
441 >  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
442    double* fz;
443    double* curZPos;
608 –  
609 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
444  
445 <  int whichDirection;                           //constraint direction
446 <  
445 >
446 >
447 >  int whichDirection;                           //constraint direction
448 >
449   private:
450 <  
450 >
451    string zconsOutput;                         //filename of zconstraint output
452    ZConsWriter* fzOut;                         //z-constraint writer
453  
454 <  double curZconsTime;                      
454 >  double curZconsTime;
455  
456    double calcMovingMolsCOMVel();
457    double calcSysCOMVel();
458    double calcTotalForce();
459 <  
459 >
460    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
461    friend class ForceSubtractionPolicy;
462  

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