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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 597 by mmeineke, Mon Jul 14 21:28:54 2003 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 2004 UTC

# Line 1 | Line 1
1   #ifndef _INTEGRATOR_H_
2   #define _INTEGRATOR_H_
3  
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"
11   #include "SimInfo.hpp"
12   #include "ForceFields.hpp"
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
20   const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
21   const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
25 < class Integrator : public BaseIntegrator {
25 > template<typename T = BaseIntegrator> class Integrator : public T {
26  
27   public:
28    Integrator( SimInfo *theInfo, ForceFields* the_ff );
29    virtual ~Integrator();
30    void integrate( void );
31 +  virtual double  getConservedQuantity(void);
32 +  virtual string getAdditionalParameters(void);
33  
25 –
34   protected:
35 <  
35 >
36    virtual void integrateStep( int calcPot, int calcStress );
37    virtual void preMove( void );
38    virtual void moveA( void );
# Line 32 | Line 40 | class Integrator : public BaseIntegrator { (protected)
40    virtual void constrainA( void );
41    virtual void constrainB( void );
42    virtual int  readyCheck( void ) { return 1; }
35 –  
36 –  void checkConstraints( void );
37 –  void rotate( int axes1, int axes2, double angle, double j[3],
38 –               double A[9] );
43  
44 +  virtual void resetIntegrator( void ) { }
45  
46 +  virtual void calcForce( int calcPot, int calcStress );
47 +  virtual void thermalize();
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],
55 +         double A[3][3] );
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 48 | Line 65 | class Integrator : public BaseIntegrator { (protected)
65    int nMols;
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 <  
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 >
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  
66 –  double* pos;
67 –  double* vel;
68 –  double* frc;
69 –  double* trq;
70 –  double* Amat;
71 –
83    Thermo *tStats;
84    StatWriter*  statOut;
85    DumpWriter*  dumpOut;
86 <  
86 >
87   };
88  
89 < class NVE : public Integrator{
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 <    Integrator( theInfo, the_ff ){}
98 >    T( theInfo, the_ff ){}
99    virtual ~NVE(){}
84 –
85 –  
86 –
100   };
101  
89 – class NVT : public Integrator{
102  
103 + template<typename T> class NVT : public T {
104 +
105   public:
106  
107    NVT ( SimInfo *theInfo, ForceFields* the_ff);
108 <  virtual ~NVT() {}
108 >  virtual ~NVT();
109  
110    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
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 103 | Line 120 | class NVT : public Integrator{ (protected)
120  
121    virtual int readyCheck();
122  
123 +  virtual void resetIntegrator( void );
124 +
125    // chi is a propagated degree of freedom.
126  
127    double chi;
128  
129 +  //integral of chi(t)dt
130 +  double integralOfChidt;
131 +
132    // targetTemp must be set.  tauThermostat must also be set;
133  
134    double targetTemp;
135    double tauThermostat;
136 <  
136 >
137    short int have_tau_thermostat, have_target_temp;
138  
139 +  double *oldVel;
140 +  double *oldJi;
141 +
142 +  double chiTolerance;
143 +  short int have_chi_tolerance;
144 +
145   };
146  
147  
120 – class NPTi : public Integrator{
148  
149 + template<typename T> class NPT : public T{
150 +
151   public:
152  
153 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
154 <  virtual ~NPTi() {};
153 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
154 >  virtual ~NPT();
155  
156    virtual void integrateStep( int calcPot, int calcStress ){
157      calcStress = 1;
158 <    Integrator::integrateStep( calcPot, calcStress );
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;}
169    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
170    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
171 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
172 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
173 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
174  
175   protected:
176  
# Line 141 | Line 179 | class NPTi : public Integrator{ (protected)
179  
180    virtual int readyCheck();
181  
182 +  virtual void resetIntegrator( void );
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],
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 +
194 +  virtual void evolveChiA( void );
195 +  virtual void evolveEtaA( void ) = 0;
196 +  virtual void evolveChiB( void );
197 +  virtual void evolveEtaB( void ) = 0;
198 +
199 +  virtual void scaleSimBox( void ) = 0;
200 +
201 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
202 +
203    // chi and eta are the propagated degrees of freedom
204  
205 +  double oldChi;
206 +  double prevChi;
207    double chi;
147 –  double eta;
208    double NkBT;
209 +  double fkBT;
210  
211 <  // targetTemp, targetPressure, and tauBarostat must be set.  
211 >  double tt2, tb2;
212 >  double instaTemp, instaPress, instaVol;
213 >  double press[3][3];
214 >
215 >  int Nparticles;
216 >
217 >  double integralOfChidt;
218 >
219 >  // targetTemp, targetPressure, and tauBarostat must be set.
220    // One of qmass or tauThermostat must be set;
221  
222    double targetTemp;
# Line 158 | Line 227 | class NPTi : public Integrator{ (protected)
227    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
228    short int have_target_pressure;
229  
230 +  double *oldPos;
231 +  double *oldVel;
232 +  double *oldJi;
233 +
234 +  double chiTolerance;
235 +  short int have_chi_tolerance;
236 +  double posIterTolerance;
237 +  short int have_pos_iter_tolerance;
238 +  double etaTolerance;
239 +  short int have_eta_tolerance;
240 +
241   };
242  
243 < class NPTim : public Integrator{
243 > template<typename T> class NPTi : public T{
244  
245   public:
246 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
247 +  ~NPTi();
248  
249 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
250 <  virtual ~NPTim() {};
251 <
170 <  virtual void integrateStep( int calcPot, int calcStress ){
171 <    calcStress = 1;
172 <    Integrator::integrateStep( calcPot, calcStress );
173 <  }
174 <
175 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
176 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
177 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
178 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
179 <
249 >  virtual double getConservedQuantity(void);
250 >  virtual void resetIntegrator(void);
251 >  virtual string getAdditionalParameters(void);
252   protected:
253  
182 –  virtual void  moveA( void );
183 –  virtual void moveB( void );
254  
185 –  virtual int readyCheck();
255  
256 <  // chi and eta are the propagated degrees of freedom
256 >  virtual void evolveEtaA(void);
257 >  virtual void evolveEtaB(void);
258  
259 <  double chi;
190 <  double eta;
191 <  double NkBT;
259 >  virtual bool etaConverged( void );
260  
261 <  // targetTemp, targetPressure, and tauBarostat must be set.  
194 <  // One of qmass or tauThermostat must be set;
261 >  virtual void scaleSimBox( void );
262  
263 <  double targetTemp;
264 <  double targetPressure;
265 <  double tauThermostat;
266 <  double tauBarostat;
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],
266 >                           int index, double sc[3]);
267  
268 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
202 <  short int have_target_pressure;
268 >  virtual void calcVelScale( void );
269  
270 +  double eta, oldEta, prevEta;
271 +  double vScale;
272   };
273  
274 < class NPTf : public Integrator{
274 > template<typename T> class NPTf : public T{
275  
276   public:
277  
278    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
279 <  virtual ~NPTf() {};
279 >  virtual ~NPTf();
280  
281 <  virtual void integrateStep( int calcPot, int calcStress ){
282 <    calcStress = 1;
283 <    Integrator::integrateStep( calcPot, calcStress );
216 <  }
281 >  virtual double getConservedQuantity(void);
282 >  virtual string getAdditionalParameters(void);
283 >  virtual void resetIntegrator(void);
284  
218 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
219 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
220 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
221 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
222 –
285   protected:
286  
287 <  virtual void  moveA( void );
288 <  virtual void moveB( void );
287 >  virtual void evolveEtaA(void);
288 >  virtual void evolveEtaB(void);
289  
290 <  virtual int readyCheck();
290 >  virtual bool etaConverged( void );
291  
292 <  // chi and eta are the propagated degrees of freedom
292 >  virtual void scaleSimBox( void );
293  
294 <  double chi;
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],
297 >                           int index, double sc[3]);
298 >
299 >  virtual void calcVelScale( void );
300 >
301    double eta[3][3];
302 <  double NkBT;
302 >  double oldEta[3][3];
303 >  double prevEta[3][3];
304 >  double vScale[3][3];
305 > };
306  
307 <  // targetTemp, targetPressure, and tauBarostat must be set.  
237 <  // One of qmass or tauThermostat must be set;
307 > template<typename T> class NPTxyz : public T{
308  
309 <  double targetTemp;
240 <  double targetPressure;
241 <  double tauThermostat;
242 <  double tauBarostat;
309 > public:
310  
311 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
312 <  short int have_target_pressure;
311 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
312 >  virtual ~NPTxyz();
313 >
314 >  virtual double getConservedQuantity(void);
315 >  virtual string getAdditionalParameters(void);
316 >  virtual void resetIntegrator(void);
317 >
318 > protected:
319 >
320 >  virtual void evolveEtaA(void);
321 >  virtual void evolveEtaB(void);
322  
323 +  virtual bool etaConverged( void );
324 +
325 +  virtual void scaleSimBox( void );
326 +
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 +  virtual void calcVelScale( void );
333 +
334 +  double eta[3][3];
335 +  double oldEta[3][3];
336 +  double prevEta[3][3];
337 +  double vScale[3][3];
338   };
339  
249 – class NPTfm : public Integrator{
340  
341 + template<typename T> class ZConstraint : public T {
342 +
343 +  public:
344 +  class ForceSubtractionPolicy{
345 +    public:
346 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
347 +
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 +
354 +   protected:
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();
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 +
368 +    private:
369 +      int totNumOfMovingAtoms;
370 +  };
371 +
372 +  class PolicyByMass : public ForceSubtractionPolicy{
373 +
374 +    public:
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);
381 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
382 +
383 +   private:
384 +     double totMassOfMovingAtoms;
385 +  };
386 +
387   public:
388  
389 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
390 <  virtual ~NPTfm() {};
389 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
390 >  ~ZConstraint();
391  
392 <  virtual void integrateStep( int calcPot, int calcStress ){
393 <    calcStress = 1;
258 <    Integrator::integrateStep( calcPot, calcStress );
259 <  }
392 >  void setZConsTime(double time)                  {this->zconsTime = time;}
393 >  void getZConsTime()                             {return zconsTime;}
394  
395 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
396 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
263 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
264 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
395 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
396 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
397  
398 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
399 +  string getZConsOutput()                         {return zconsOutput;}
400 +
401 +  virtual void integrate();
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  
268 –  virtual void  moveA( void );
269 –  virtual void moveB( void );
421  
271 –  virtual int readyCheck();
422  
423 <  // chi and eta are the propagated degrees of freedom
423 >  virtual void calcForce( int calcPot, int calcStress );
424 >  virtual void thermalize(void);
425  
426 <  double chi;
427 <  double eta[3][3];
428 <  double NkBT;
426 >  void zeroOutVel();
427 >  void doZconstraintForce();
428 >  void doHarmonic(vector<double>& resPos);
429 >  bool checkZConsState();
430  
431 <  // targetTemp, targetPressure, and tauBarostat must be set.  
432 <  // One of qmass or tauThermostat must be set;
431 >  bool haveFixedZMols();
432 >  bool haveMovingZMols();
433  
434 <  double targetTemp;
283 <  double targetPressure;
284 <  double tauThermostat;
285 <  double tauBarostat;
434 >  double calcZSys();
435  
436 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
288 <  short int have_target_pressure;
436 >  int isZConstraintMol(Molecule* mol);
437  
438 +
439 +  double zconsTime;                              //sample time
440 +  double zconsTol;                                 //tolerance of z-contratint
441 +  double zForceConst;                           //base force constant term
442 +                                                          //which is estimate by OOPSE
443 +
444 +
445 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
446 +  vector<double> kz;                              //force constant array
447 +
448 +  vector<double> zPos;                          //
449 +
450 +
451 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
452 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
453 +
454 +
455 +  vector<ZConsParaItem>* parameters; //
456 +
457 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
458 +
459 +  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
460 +  vector<double> fz;
461 +  vector<double> curZPos;
462 +
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 +
477 +  string zconsOutput;                         //filename of zconstraint output
478 +  ZConsWriter* fzOut;                         //z-constraint writer
479 +
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;
490 +
491   };
492  
493 + /*
494 + template<typename T> class SingleZConstrain : public T{
495 +
496 +
497 + };
498 + */
499 +
500 + template<typename T> class NonEquMD : public T {
501 +  public:
502 +    
503 +
504 +
505 + };
506 +
507 +
508 + //
509 + template<typename T> class SingleZConstraint : public T{
510 +  public:
511 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
512 +    ~SingleZConstraint();
513 +    
514 +    bool stopIntegrator();
515 +    
516 +  protected:
517 +    
518 + };
519 +
520 + //Steered Molecular Dynamics, curret implement only support one steered molecule
521 + template<typename T> class SMD : public T{
522 +  public:
523 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
524 +    ~SMD();
525 +  
526 +    virtual void integrate();
527 +    virtual void calcForce( int calcPot, int calcStress );  
528 +    bool stopIntegrator();
529 +  private:
530 +    
531 + };
532 +
533 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
534 + //Driven Molecular Dynamics and ZConstraint Method.
535 + template<typename T> class CoordinateDriver : public T {
536 +  public:
537 +    typedef T ParentIntegrator;
538 +
539 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
540 +    ~CoordinateDriver();
541 +    
542 +    virtual void integrate();
543 +
544 +  private:    
545 +    BaseIntegrator* zconsIntegrator;
546 +    BaseIntegrator* drivenIntegrator;
547 +    
548 + };
549 +
550   #endif

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