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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 562 by gezelter, Fri Jun 20 20:50:17 2003 UTC vs.
Revision 1180 by chrisfen, Thu May 20 20:24:07 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  
24 –
34   protected:
35 <  
35 >
36    virtual void integrateStep( int calcPot, int calcStress );
37    virtual void preMove( void );
38    virtual void moveA( void );
# Line 31 | Line 40 | class Integrator : public BaseIntegrator { (protected)
40    virtual void constrainA( void );
41    virtual void constrainB( void );
42    virtual int  readyCheck( void ) { return 1; }
34 –  
35 –  void checkConstraints( void );
36 –  void rotate( int axes1, int axes2, double angle, double j[3],
37 –               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 47 | 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  
65 –  double* pos;
66 –  double* vel;
67 –  double* frc;
68 –  double* trq;
69 –  double* Amat;
70 –
83    Thermo *tStats;
84    StatWriter*  statOut;
85    DumpWriter*  dumpOut;
86 <  
86 >
87 >  int i; // just an int
88   };
89  
90 < class NVE : public Integrator{
90 > typedef Integrator<BaseIntegrator> RealIntegrator;
91  
92 + // ansi instantiation
93 + template class Integrator<BaseIntegrator>;
94 +
95 + template<typename T> class NVE : public T {
96 +
97   public:
98    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
99 <    Integrator( theInfo, the_ff ){}
99 >    T( theInfo, the_ff ){}
100    virtual ~NVE(){}
83 –
84 –  
85 –
101   };
102  
88 – class NVT : public Integrator{
103  
104 + template<typename T> class NVT : public T {
105 +
106   public:
107  
108    NVT ( SimInfo *theInfo, ForceFields* the_ff);
109 <  virtual ~NVT() {}
109 >  virtual ~NVT();
110  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
111    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
112    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
113 +  void setChiTolerance(double tol) {chiTolerance = tol;}
114 +  virtual double  getConservedQuantity(void);
115 +  virtual string getAdditionalParameters(void);
116  
117   protected:
118  
# Line 103 | Line 121 | class NVT : public Integrator{ (protected)
121  
122    virtual int readyCheck();
123  
124 <  // zeta is a propagated degree of freedom.
124 >  virtual void resetIntegrator( void );
125  
126 <  double zeta;
126 >  // chi is a propagated degree of freedom.
127  
128 <  // targetTemp must be set.  One of qmass or tauThermostat must be set;
128 >  double chi;
129  
130 <  double qmass;
130 >  //integral of chi(t)dt
131 >  double integralOfChidt;
132 >
133 >  // targetTemp must be set.  tauThermostat must also be set;
134 >
135    double targetTemp;
136    double tauThermostat;
137  
138 <  double NkBT;
117 <  
118 <  short int have_tau_thermostat, have_target_temp, have_qmass;
138 >  short int have_tau_thermostat, have_target_temp;
139  
140 +  double *oldVel;
141 +  double *oldJi;
142 +
143 +  double chiTolerance;
144 +  short int have_chi_tolerance;
145 +
146   };
147  
148  
123 – class NPT : public Integrator{
149  
150 + template<typename T> class NPT : public T{
151 +
152   public:
153  
154    NPT ( SimInfo *theInfo, ForceFields* the_ff);
155 <  virtual ~NPT() {};
155 >  virtual ~NPT();
156  
157 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
157 >  virtual void integrateStep( int calcPot, int calcStress ){
158 >    calcStress = 1;
159 >    T::integrateStep( calcPot, calcStress );
160 >  }
161 >
162 >  virtual double getConservedQuantity(void) = 0;
163 >  virtual string getAdditionalParameters(void) = 0;
164 >  
165 >  double myTauThermo( void ) { return tauThermostat; }
166 >  double myTauBaro( void ) { return tauBarostat; }
167 >
168    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
169    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
170    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
171    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
172 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
173 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
174 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
175  
176   protected:
177  
# Line 140 | Line 180 | class NPT : public Integrator{ (protected)
180  
181    virtual int readyCheck();
182  
183 <  // zeta and epsilonDot are the propagated degrees of freedom.
183 >  virtual void resetIntegrator( void );
184  
185 <  double zeta;
186 <  double epsilonDot;
185 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
186 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
187 >  virtual void getPosScale(double pos[3], double COM[3],
188 >                           int index, double sc[3]) = 0;
189  
190 <  // targetTemp, targetPressure, and tauBarostat must be set.  
190 >  virtual void calcVelScale( void ) = 0;
191 >
192 >  virtual bool chiConverged( void );
193 >  virtual bool etaConverged( void ) = 0;
194 >
195 >  virtual void evolveChiA( void );
196 >  virtual void evolveEtaA( void ) = 0;
197 >  virtual void evolveChiB( void );
198 >  virtual void evolveEtaB( void ) = 0;
199 >
200 >  virtual void scaleSimBox( void ) = 0;
201 >
202 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
203 >
204 >  // chi and eta are the propagated degrees of freedom
205 >
206 >  double oldChi;
207 >  double prevChi;
208 >  double chi;
209 >  double NkBT;
210 >  double fkBT;
211 >
212 >  double tt2, tb2;
213 >  double instaTemp, instaPress, instaVol;
214 >  double press[3][3];
215 >
216 >  int Nparticles;
217 >
218 >  double integralOfChidt;
219 >
220 >  // targetTemp, targetPressure, and tauBarostat must be set.
221    // One of qmass or tauThermostat must be set;
222  
151 –  double qmass;
223    double targetTemp;
224    double targetPressure;
225    double tauThermostat;
226    double tauBarostat;
227  
228    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
229 <  short int have_target_pressure, have_qmass;
229 >  short int have_target_pressure;
230  
231 +  double *oldPos;
232 +  double *oldVel;
233 +  double *oldJi;
234 +
235 +  double chiTolerance;
236 +  short int have_chi_tolerance;
237 +  double posIterTolerance;
238 +  short int have_pos_iter_tolerance;
239 +  double etaTolerance;
240 +  short int have_eta_tolerance;
241 +
242   };
243  
244 + template<typename T> class NPTi : public T{
245 +
246 + public:
247 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
248 +  ~NPTi();
249 +
250 +  virtual double getConservedQuantity(void);
251 +  virtual void resetIntegrator(void);
252 +  virtual string getAdditionalParameters(void);
253 + protected:
254 +
255 +
256 +
257 +  virtual void evolveEtaA(void);
258 +  virtual void evolveEtaB(void);
259 +
260 +  virtual bool etaConverged( void );
261 +
262 +  virtual void scaleSimBox( void );
263 +
264 +  virtual void getVelScaleA( double sc[3], double vel[3] );
265 +  virtual void getVelScaleB( double sc[3], int index );
266 +  virtual void getPosScale(double pos[3], double COM[3],
267 +                           int index, double sc[3]);
268 +
269 +  virtual void calcVelScale( void );
270 +
271 +  double eta, oldEta, prevEta;
272 +  double vScale;
273 + };
274 +
275 + template<typename T> class NPTf : public T{
276 +
277 + public:
278 +
279 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
280 +  virtual ~NPTf();
281 +
282 +  virtual double getConservedQuantity(void);
283 +  virtual string getAdditionalParameters(void);
284 +  virtual void resetIntegrator(void);
285 +
286 + protected:
287 +
288 +  virtual void evolveEtaA(void);
289 +  virtual void evolveEtaB(void);
290 +
291 +  virtual bool etaConverged( void );
292 +
293 +  virtual void scaleSimBox( void );
294 +
295 +  virtual void getVelScaleA( double sc[3], double vel[3] );
296 +  virtual void getVelScaleB( double sc[3], int index );
297 +  virtual void getPosScale(double pos[3], double COM[3],
298 +                           int index, double sc[3]);
299 +
300 +  virtual void calcVelScale( void );
301 +
302 +  double eta[3][3];
303 +  double oldEta[3][3];
304 +  double prevEta[3][3];
305 +  double vScale[3][3];
306 + };
307 +
308 + template<typename T> class NPTxyz : public T{
309 +
310 + public:
311 +
312 +  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
313 +  virtual ~NPTxyz();
314 +
315 +  virtual double getConservedQuantity(void);
316 +  virtual string getAdditionalParameters(void);
317 +  virtual void resetIntegrator(void);
318 +
319 + protected:
320 +
321 +  virtual void evolveEtaA(void);
322 +  virtual void evolveEtaB(void);
323 +
324 +  virtual bool etaConverged( void );
325 +
326 +  virtual void scaleSimBox( void );
327 +
328 +  virtual void getVelScaleA( double sc[3], double vel[3] );
329 +  virtual void getVelScaleB( double sc[3], int index );
330 +  virtual void getPosScale(double pos[3], double COM[3],
331 +                           int index, double sc[3]);
332 +
333 +  virtual void calcVelScale( void );
334 +
335 +  double eta[3][3];
336 +  double oldEta[3][3];
337 +  double prevEta[3][3];
338 +  double vScale[3][3];
339 + };
340 +
341 +
342 + template<typename T> class ZConstraint : public T {
343 +
344 +  public:
345 +  class ForceSubtractionPolicy{
346 +    public:
347 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
348 +
349 +      virtual void update() = 0;
350 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
351 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
352 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
353 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
354 +
355 +   protected:
356 +     ZConstraint<T>* zconsIntegrator;
357 +  };
358 +
359 +  class PolicyByNumber : public ForceSubtractionPolicy{
360 +
361 +    public:
362 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
363 +      virtual void update();
364 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
365 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
366 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
367 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
368 +
369 +    private:
370 +      int totNumOfMovingAtoms;
371 +  };
372 +
373 +  class PolicyByMass : public ForceSubtractionPolicy{
374 +
375 +    public:
376 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
377 +
378 +      virtual void update();
379 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
380 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
381 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
382 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
383 +
384 +   private:
385 +     double totMassOfMovingAtoms;
386 +  };
387 +
388 + public:
389 +
390 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
391 +  ~ZConstraint();
392 +
393 +  void setZConsTime(double time)                  {this->zconsTime = time;}
394 +  void getZConsTime()                             {return zconsTime;}
395 +
396 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
397 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
398 +
399 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
400 +  string getZConsOutput()                         {return zconsOutput;}
401 +
402 +  virtual void integrate();
403 +
404 +
405 + #ifdef IS_MPI
406 +  virtual void update();                      //which is called to indicate the molecules' migration
407   #endif
408 +
409 +  enum ZConsState {zcsMoving, zcsFixed};
410 +
411 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
412 +  vector<ZConsState> states;                 //state of z-constraint molecules
413 +
414 +
415 +
416 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
417 +  double totalMassOfUncons;                //total mas of unconstraint molecules
418 +
419 +
420 + protected:
421 +
422 +
423 +
424 +  virtual void calcForce( int calcPot, int calcStress );
425 +  virtual void thermalize(void);
426 +
427 +  void zeroOutVel();
428 +  void doZconstraintForce();
429 +  void doHarmonic(vector<double>& resPos);
430 +  bool checkZConsState();
431 +
432 +  bool haveFixedZMols();
433 +  bool haveMovingZMols();
434 +
435 +  double calcZSys();
436 +
437 +  int isZConstraintMol(Molecule* mol);
438 +
439 +
440 +  double zconsTime;                              //sample time
441 +  double zconsTol;                                 //tolerance of z-contratint
442 +  double zForceConst;                           //base force constant term
443 +                                                          //which is estimate by OOPSE
444 +
445 +
446 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
447 +  vector<double> kz;                              //force constant array
448 +
449 +  vector<double> zPos;                          //
450 +
451 +
452 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
453 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
454 +
455 +
456 +  vector<ZConsParaItem>* parameters; //
457 +
458 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
459 +
460 +  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
461 +  vector<double> fz;
462 +  vector<double> curZPos;
463 +
464 +  bool usingSMD;
465 +  vector<double> prevCantPos;
466 +  vector<double> cantPos;
467 +  vector<double> cantVel;
468 +
469 +  double zconsFixTime;  
470 +  double zconsGap;
471 +  bool hasZConsGap;
472 +  vector<double> endFixTime;
473 +  
474 +  int whichDirection;                           //constraint direction
475 +
476 + private:
477 +
478 +  string zconsOutput;                         //filename of zconstraint output
479 +  ZConsWriter* fzOut;                         //z-constraint writer
480 +
481 +  double curZconsTime;
482 +
483 +  double calcMovingMolsCOMVel();
484 +  double calcSysCOMVel();
485 +  double calcTotalForce();
486 +  void updateZPos();
487 +  void updateCantPos();
488 +  
489 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
490 +  friend class ForceSubtractionPolicy;
491 +
492 + };
493 +
494 + /*
495 + template<typename T> class SingleZConstrain : public T{
496 +
497 +
498 + };
499 + */
500 +
501 + template<typename T> class NonEquMD : public T {
502 +  public:
503 +    
504 +
505 +
506 + };
507 +
508 +
509 + //
510 + template<typename T> class SingleZConstraint : public T{
511 +  public:
512 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
513 +    ~SingleZConstraint();
514 +    
515 +    bool stopIntegrator();
516 +    
517 +  protected:
518 +    
519 + };
520 +
521 + //Steered Molecular Dynamics, curret implement only support one steered molecule
522 + template<typename T> class SMD : public T{
523 +  public:
524 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
525 +    ~SMD();
526 +  
527 +    virtual void integrate();
528 +    virtual void calcForce( int calcPot, int calcStress );  
529 +    bool stopIntegrator();
530 +  private:
531 +    
532 + };
533 +
534 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
535 + //Driven Molecular Dynamics and ZConstraint Method.
536 + template<typename T> class CoordinateDriver : public T {
537 +  public:
538 +    typedef T ParentIntegrator;
539 +
540 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
541 +    ~CoordinateDriver();
542 +    
543 +    virtual void integrate();
544 +
545 +  private:    
546 +    BaseIntegrator* zconsIntegrator;
547 +    BaseIntegrator* drivenIntegrator;
548 +    
549 + };
550 +
551 + #endif

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