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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 1198 by tim, Thu May 27 00:48:12 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 12 | Line 13
13   #include "Thermo.hpp"
14   #include "ReadWrite.hpp"
15   #include "ZConsWriter.hpp"
16 + #include "Restraints.hpp"
17  
18   using namespace std;
19   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
# Line 20 | Line 22 | const double tol = 1.0e-6;
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
23 –
25   template<typename T = BaseIntegrator> class Integrator : public T {
26  
27   public:
# Line 28 | Line 29 | template<typename T = BaseIntegrator> class Integrator
29    virtual ~Integrator();
30    void integrate( void );
31    virtual double  getConservedQuantity(void);
32 +  virtual string getAdditionalParameters(void);
33  
34   protected:
35  
# Line 40 | Line 42 | template<typename T = BaseIntegrator> class Integrator
42    virtual int  readyCheck( void ) { return 1; }
43  
44    virtual void resetIntegrator( void ) { }
45 <
46 <  virtual void calcForce( int calcPot, int calcStress );  
45 >
46 >  virtual void calcForce( int calcPot, int calcStress );
47    virtual void thermalize();
46 –  
47 –  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48  
49 +  virtual bool stopIntegrator() {return false;}
50 +
51 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
52 +
53    void checkConstraints( void );
54 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 >  void rotate( int axes1, int axes2, double angle, double j[3],
55           double A[3][3] );
56 <        
56 >
57    ForceFields* myFF;
58  
59    SimInfo *info; // all the info we'll ever need
60 +  vector<StuntDouble*> integrableObjects;
61    int nAtoms;  /* the number of atoms */
62    int oldAtoms;
63    Atom **atoms; /* array of atom pointers */
# Line 61 | Line 66 | template<typename T = BaseIntegrator> class Integrator
66  
67    int isConstrained; // boolean to know whether the systems contains
68           // constraints.
69 <  int nConstrained;  // counter for number of constraints
70 <  int *constrainedA; // the i of a constraint pair
71 <  int *constrainedB; // the j of a constraint pair
72 <  double *constrainedDsqr; // the square of the constraint distance
73 <  
69 >  int nConstrained;  // counter for number of constraints
70 >  int *constrainedA; // the i of a constraint pair
71 >  int *constrainedB; // the j of a constraint pair
72 >  double *constrainedDsqr; // the square of the constraint distance
73 >
74    int* moving; // tells whether we are moving atom i
75    int* moved;  // tells whether we have moved atom i
76 <  double* oldPos; // pre constrained positions
76 >  double* oldPos; // pre constrained positions
77  
78    short isFirst; /*boolean for the first time integrate is called */
79 <  
79 >
80    double dt;
81    double dt2;
82  
83    Thermo *tStats;
84    StatWriter*  statOut;
85    DumpWriter*  dumpOut;
86 <  
86 >
87   };
88  
89   typedef Integrator<BaseIntegrator> RealIntegrator;
90  
91 + // ansi instantiation
92 + template class Integrator<BaseIntegrator>;
93 +
94   template<typename T> class NVE : public T {
95  
96   public:
97    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
98      T( theInfo, the_ff ){}
99 <  virtual ~NVE(){}  
99 >  virtual ~NVE(){}
100   };
101  
102  
# Line 103 | Line 111 | template<typename T> class NVT : public T { (public)
111    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
112    void setChiTolerance(double tol) {chiTolerance = tol;}
113    virtual double  getConservedQuantity(void);
114 +  virtual string getAdditionalParameters(void);
115  
116   protected:
117  
# Line 124 | Line 133 | template<typename T> class NVT : public T { (public)
133  
134    double targetTemp;
135    double tauThermostat;
136 <  
136 >
137    short int have_tau_thermostat, have_target_temp;
138  
139    double *oldVel;
# Line 143 | Line 152 | template<typename T> class NPT : public T{ (public)
152  
153    NPT ( SimInfo *theInfo, ForceFields* the_ff);
154    virtual ~NPT();
155 <  
155 >
156    virtual void integrateStep( int calcPot, int calcStress ){
157      calcStress = 1;
158      T::integrateStep( calcPot, calcStress );
159    }
160  
161    virtual double getConservedQuantity(void) = 0;
162 +  virtual string getAdditionalParameters(void) = 0;
163 +  
164 +  double myTauThermo( void ) { return tauThermostat; }
165 +  double myTauBaro( void ) { return tauBarostat; }
166  
167    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
168    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
# Line 170 | Line 183 | template<typename T> class NPT : public T{ (public)
183  
184    virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
185    virtual void getVelScaleB( double sc[3], int index ) = 0;
186 <  virtual void getPosScale(double pos[3], double COM[3],
186 >  virtual void getPosScale(double pos[3], double COM[3],
187                             int index, double sc[3]) = 0;
188  
189 +  virtual void calcVelScale( void ) = 0;
190 +
191    virtual bool chiConverged( void );
192    virtual bool etaConverged( void ) = 0;
193 <  
193 >
194    virtual void evolveChiA( void );
195    virtual void evolveEtaA( void ) = 0;
196    virtual void evolveChiB( void );
# Line 201 | Line 216 | template<typename T> class NPT : public T{ (public)
216  
217    double integralOfChidt;
218  
219 <  // targetTemp, targetPressure, and tauBarostat must be set.  
219 >  // targetTemp, targetPressure, and tauBarostat must be set.
220    // One of qmass or tauThermostat must be set;
221  
222    double targetTemp;
# Line 226 | Line 241 | template<typename T> class NPTi : public T{
241   };
242  
243   template<typename T> class NPTi : public T{
244 <  
244 >
245   public:
246    NPTi( SimInfo *theInfo, ForceFields* the_ff);
247    ~NPTi();
248  
249    virtual double getConservedQuantity(void);
250    virtual void resetIntegrator(void);
251 <
251 >  virtual string getAdditionalParameters(void);
252   protected:
253  
239 –
254  
255 +
256    virtual void evolveEtaA(void);
257    virtual void evolveEtaB(void);
258  
# Line 247 | Line 262 | template<typename T> class NPTi : public T{
262  
263    virtual void getVelScaleA( double sc[3], double vel[3] );
264    virtual void getVelScaleB( double sc[3], int index );
265 <  virtual void getPosScale(double pos[3], double COM[3],
265 >  virtual void getPosScale(double pos[3], double COM[3],
266                             int index, double sc[3]);
267  
268 <  double eta, oldEta, prevEta;
254 < };
268 >  virtual void calcVelScale( void );
269  
270 < template<typename T> class NPTzm : public T{
271 <
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 <
270 >  double eta, oldEta, prevEta;
271 >  double vScale;
272   };
273  
274   template<typename T> class NPTf : public T{
# Line 310 | Line 279 | template<typename T> class NPTf : public T{ (public)
279    virtual ~NPTf();
280  
281    virtual double getConservedQuantity(void);
282 +  virtual string getAdditionalParameters(void);
283    virtual void resetIntegrator(void);
284  
285   protected:
# Line 323 | Line 293 | template<typename T> class NPTf : public T{ (public)
293  
294    virtual void getVelScaleA( double sc[3], double vel[3] );
295    virtual void getVelScaleB( double sc[3], int index );
296 <  virtual void getPosScale(double pos[3], double COM[3],
296 >  virtual void getPosScale(double pos[3], double COM[3],
297                             int index, double sc[3]);
298  
299 +  virtual void calcVelScale( void );
300 +
301    double eta[3][3];
302    double oldEta[3][3];
303    double prevEta[3][3];
304 +  double vScale[3][3];
305   };
306  
307 < template<typename T> class NPTxym : public T{
307 > template<typename T> class NPTxyz : public T{
308  
309   public:
310  
311 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
312 <  virtual ~NPTxym() {};
311 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
312 >  virtual ~NPTxyz();
313  
314 <  virtual void integrateStep( int calcPot, int calcStress ){
315 <    calcStress = 1;
316 <    T::integrateStep( calcPot, calcStress );
344 <  }
314 >  virtual double getConservedQuantity(void);
315 >  virtual string getAdditionalParameters(void);
316 >  virtual void resetIntegrator(void);
317  
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 –
318   protected:
319  
320 <  virtual void moveA( void );
321 <  virtual void moveB( void );
320 >  virtual void evolveEtaA(void);
321 >  virtual void evolveEtaB(void);
322  
323 <  virtual int readyCheck();
323 >  virtual bool etaConverged( void );
324  
325 <  virtual void resetIntegrator( void );
325 >  virtual void scaleSimBox( void );
326  
327 <  Molecule* myMolecules;
328 <  Atom** myAtoms;
327 >  virtual void getVelScaleA( double sc[3], double vel[3] );
328 >  virtual void getVelScaleB( double sc[3], int index );
329 >  virtual void getPosScale(double pos[3], double COM[3],
330 >                           int index, double sc[3]);
331  
332 <  // 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 <
398 <  virtual double getConservedQuantity(void);
399 <  
400 <  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;}
406 <
407 < protected:
332 >  virtual void calcVelScale( void );
333  
409 –  virtual void  moveA( void );
410 –  virtual void moveB( void );
411 –
412 –  virtual void resetIntegrator( void );
413 –
414 –  virtual int readyCheck();
415 –
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;
334    double eta[3][3];
335 <  double NkBT;
336 <  double integralOfChidt;
337 <
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 <
335 >  double oldEta[3][3];
336 >  double prevEta[3][3];
337 >  double vScale[3][3];
338   };
339  
340  
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 –
341   template<typename T> class ZConstraint : public T {
342 <  
343 <  public:
342 >
343 >  public:
344    class ForceSubtractionPolicy{
345      public:
346        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
347  
348 <      virtual void update() = 0;    
348 >      virtual void update() = 0;
349        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
350        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
351        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
353 <    
353 >
354     protected:
355 <     ZConstraint<T>* zconsIntegrator;;
355 >     ZConstraint<T>* zconsIntegrator;
356    };
357  
358    class PolicyByNumber : public ForceSubtractionPolicy{
359  
360      public:
361 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
362 <      virtual void update();    
361 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
362 >      virtual void update();
363        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
364        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
365        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
366        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
367 <    
367 >
368      private:
369        int totNumOfMovingAtoms;
370    };
# Line 529 | Line 372 | template<typename T> class ZConstraint : public T {
372    class PolicyByMass : public ForceSubtractionPolicy{
373  
374      public:
375 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
376 <      
377 <      virtual void update();    
375 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
376 >
377 >      virtual void update();
378        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
379        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
380        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 545 | Line 388 | template<typename T> class ZConstraint : public T {
388  
389    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
390    ~ZConstraint();
391 <    
391 >
392    void setZConsTime(double time)                  {this->zconsTime = time;}
393    void getZConsTime()                             {return zconsTime;}
394 <  
394 >
395    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
396    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
397 <  
397 >
398    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
399    string getZConsOutput()                         {return zconsOutput;}
400 <  
400 >
401    virtual void integrate();
559 –  
402  
403 +
404   #ifdef IS_MPI
405    virtual void update();                      //which is called to indicate the molecules' migration
406   #endif
407  
408 +  enum ZConsState {zcsMoving, zcsFixed};
409 +
410 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
411 +  vector<ZConsState> states;                 //state of z-constraint molecules
412 +
413 +
414 +
415 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
416 +  double totalMassOfUncons;                //total mas of unconstraint molecules
417 +
418 +
419   protected:
420  
421 <  enum ZConsState {zcsMoving, zcsFixed};  
422 <
423 <  virtual void calcForce( int calcPot, int calcStress );
421 >
422 >
423 >  virtual void calcForce( int calcPot, int calcStress );
424    virtual void thermalize(void);
425 <  
425 >
426    void zeroOutVel();
427    void doZconstraintForce();
428 <  void doHarmonic();
428 >  void doHarmonic(vector<double>& resPos);
429    bool checkZConsState();
430  
431    bool haveFixedZMols();
# Line 586 | Line 440 | template<typename T> class ZConstraint : public T {
440    double zconsTol;                                 //tolerance of z-contratint
441    double zForceConst;                           //base force constant term
442                                                            //which is estimate by OOPSE
443 <  
444 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
445 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
443 >
444 >
445 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
446    vector<double> kz;                              //force constant array
447 <  vector<ZConsState> states;                 //state of z-constraint molecules
447 >
448    vector<double> zPos;                          //
449 <  
450 <  
449 >
450 >
451    vector<Molecule*> unconsMols;           //unconstraint molecules array
452    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
599 –  double totalMassOfUncons;                //total mas of unconstraint molecules
453  
454 +
455    vector<ZConsParaItem>* parameters; //
456 <  
456 >
457    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
458  
459 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
460 <  double* fz;
461 <  double* curZPos;
608 <  
609 <  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
459 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
460 >  vector<double> fz;
461 >  vector<double> curZPos;
462  
463 <  int whichDirection;                           //constraint direction
463 >  bool usingSMD;
464 >  vector<double> prevCantPos;
465 >  vector<double> cantPos;
466 >  vector<double> cantVel;
467 >
468 >  double zconsFixTime;  
469 >  double zconsGap;
470 >  bool hasZConsGap;
471 >  vector<double> endFixTime;
472    
473 +  int whichDirection;                           //constraint direction
474 +
475   private:
476 <  
476 >
477    string zconsOutput;                         //filename of zconstraint output
478    ZConsWriter* fzOut;                         //z-constraint writer
479  
480 <  double curZconsTime;                      
480 >  double curZconsTime;
481  
482    double calcMovingMolsCOMVel();
483    double calcSysCOMVel();
484    double calcTotalForce();
485 +  void updateZPos();
486 +  void updateCantPos();
487    
488    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
489    friend class ForceSubtractionPolicy;

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