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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 1141 by tim, Wed Apr 28 23:09:32 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  
17 + using namespace std;
18   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
19   const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
20   const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
21   const int maxIteration = 300;
22   const double tol = 1.0e-6;
23  
24 < class Integrator : public BaseIntegrator {
24 > template<typename T = BaseIntegrator> class Integrator : public T {
25  
26   public:
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31 +  virtual string getAdditionalParameters(void);
32  
25 –
33   protected:
34 <  
34 >
35    virtual void integrateStep( int calcPot, int calcStress );
36    virtual void preMove( void );
37    virtual void moveA( void );
# Line 32 | Line 39 | class Integrator : public BaseIntegrator { (protected)
39    virtual void constrainA( void );
40    virtual void constrainB( void );
41    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] );
42  
43 +  virtual void resetIntegrator( void ) { }
44  
45 +  virtual void calcForce( int calcPot, int calcStress );
46 +  virtual void thermalize();
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],
54 +         double A[3][3] );
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 48 | Line 64 | class Integrator : public BaseIntegrator { (protected)
64    int nMols;
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 <  
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 >
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  
66 –  double* pos;
67 –  double* vel;
68 –  double* frc;
69 –  double* trq;
70 –  double* Amat;
71 –
82    Thermo *tStats;
83    StatWriter*  statOut;
84    DumpWriter*  dumpOut;
85 <  
85 >
86   };
87  
88 < class NVE : public Integrator{
88 > typedef Integrator<BaseIntegrator> RealIntegrator;
89  
90 + template<typename T> class NVE : public T {
91 +
92   public:
93    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
94 <    Integrator( theInfo, the_ff ){}
94 >    T( theInfo, the_ff ){}
95    virtual ~NVE(){}
84 –
85 –  
86 –
96   };
97  
89 – class NVT : public Integrator{
98  
99 + template<typename T> class NVT : public T {
100 +
101   public:
102  
103    NVT ( SimInfo *theInfo, ForceFields* the_ff);
104 <  virtual ~NVT() {}
104 >  virtual ~NVT();
105  
106    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
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 103 | Line 116 | class NVT : public Integrator{ (protected)
116  
117    virtual int readyCheck();
118  
119 +  virtual void resetIntegrator( void );
120 +
121    // chi is a propagated degree of freedom.
122  
123    double chi;
124  
125 +  //integral of chi(t)dt
126 +  double integralOfChidt;
127 +
128    // targetTemp must be set.  tauThermostat must also be set;
129  
130    double targetTemp;
131    double tauThermostat;
132 <  
132 >
133    short int have_tau_thermostat, have_target_temp;
134  
135 +  double *oldVel;
136 +  double *oldJi;
137 +
138 +  double chiTolerance;
139 +  short int have_chi_tolerance;
140 +
141   };
142  
143  
120 – class NPTi : public Integrator{
144  
145 + template<typename T> class NPT : public T{
146 +
147   public:
148  
149 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
150 <  virtual ~NPTi() {};
149 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
150 >  virtual ~NPT();
151  
152    virtual void integrateStep( int calcPot, int calcStress ){
153      calcStress = 1;
154 <    Integrator::integrateStep( calcPot, calcStress );
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;}
165    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
166    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
167 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
168 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
169 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
170  
171   protected:
172  
# Line 141 | Line 175 | class NPTi : public Integrator{ (protected)
175  
176    virtual int readyCheck();
177  
178 +  virtual void resetIntegrator( void );
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],
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 +
190 +  virtual void evolveChiA( void );
191 +  virtual void evolveEtaA( void ) = 0;
192 +  virtual void evolveChiB( void );
193 +  virtual void evolveEtaB( void ) = 0;
194 +
195 +  virtual void scaleSimBox( void ) = 0;
196 +
197 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
198 +
199    // chi and eta are the propagated degrees of freedom
200  
201 +  double oldChi;
202 +  double prevChi;
203    double chi;
147 –  double eta;
204    double NkBT;
205 +  double fkBT;
206  
207 <  // targetTemp, targetPressure, and tauBarostat must be set.  
207 >  double tt2, tb2;
208 >  double instaTemp, instaPress, instaVol;
209 >  double press[3][3];
210 >
211 >  int Nparticles;
212 >
213 >  double integralOfChidt;
214 >
215 >  // targetTemp, targetPressure, and tauBarostat must be set.
216    // One of qmass or tauThermostat must be set;
217  
218    double targetTemp;
# Line 158 | Line 223 | class NPTi : public Integrator{ (protected)
223    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
224    short int have_target_pressure;
225  
226 +  double *oldPos;
227 +  double *oldVel;
228 +  double *oldJi;
229 +
230 +  double chiTolerance;
231 +  short int have_chi_tolerance;
232 +  double posIterTolerance;
233 +  short int have_pos_iter_tolerance;
234 +  double etaTolerance;
235 +  short int have_eta_tolerance;
236 +
237   };
238  
239 < class NPTim : public Integrator{
239 > template<typename T> class NPTi : public T{
240  
241   public:
242 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
243 +  ~NPTi();
244  
245 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
246 <  virtual ~NPTim() {};
247 <
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 <
245 >  virtual double getConservedQuantity(void);
246 >  virtual void resetIntegrator(void);
247 >  virtual string getAdditionalParameters(void);
248   protected:
249  
182 –  virtual void  moveA( void );
183 –  virtual void moveB( void );
250  
185 –  virtual int readyCheck();
251  
252 <  // chi and eta are the propagated degrees of freedom
252 >  virtual void evolveEtaA(void);
253 >  virtual void evolveEtaB(void);
254  
255 <  double chi;
190 <  double eta;
191 <  double NkBT;
255 >  virtual bool etaConverged( void );
256  
257 <  // targetTemp, targetPressure, and tauBarostat must be set.  
194 <  // One of qmass or tauThermostat must be set;
257 >  virtual void scaleSimBox( void );
258  
259 <  double targetTemp;
260 <  double targetPressure;
261 <  double tauThermostat;
262 <  double tauBarostat;
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],
262 >                           int index, double sc[3]);
263  
264 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
202 <  short int have_target_pressure;
264 >  virtual void calcVelScale( void );
265  
266 +  double eta, oldEta, prevEta;
267 +  double vScale;
268   };
269  
270 < class NPTf : public Integrator{
270 > template<typename T> class NPTf : public T{
271  
272   public:
273  
274    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
275 <  virtual ~NPTf() {};
275 >  virtual ~NPTf();
276  
277 <  virtual void integrateStep( int calcPot, int calcStress ){
278 <    calcStress = 1;
279 <    Integrator::integrateStep( calcPot, calcStress );
216 <  }
277 >  virtual double getConservedQuantity(void);
278 >  virtual string getAdditionalParameters(void);
279 >  virtual void resetIntegrator(void);
280  
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 –
281   protected:
282  
283 <  virtual void  moveA( void );
284 <  virtual void moveB( void );
283 >  virtual void evolveEtaA(void);
284 >  virtual void evolveEtaB(void);
285  
286 <  virtual int readyCheck();
286 >  virtual bool etaConverged( void );
287  
288 <  // chi and eta are the propagated degrees of freedom
288 >  virtual void scaleSimBox( void );
289  
290 <  double chi;
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],
293 >                           int index, double sc[3]);
294 >
295 >  virtual void calcVelScale( void );
296 >
297    double eta[3][3];
298 <  double NkBT;
298 >  double oldEta[3][3];
299 >  double prevEta[3][3];
300 >  double vScale[3][3];
301 > };
302  
303 <  // targetTemp, targetPressure, and tauBarostat must be set.  
237 <  // One of qmass or tauThermostat must be set;
303 > template<typename T> class NPTxyz : public T{
304  
305 <  double targetTemp;
240 <  double targetPressure;
241 <  double tauThermostat;
242 <  double tauBarostat;
305 > public:
306  
307 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
308 <  short int have_target_pressure;
307 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
308 >  virtual ~NPTxyz();
309 >
310 >  virtual double getConservedQuantity(void);
311 >  virtual string getAdditionalParameters(void);
312 >  virtual void resetIntegrator(void);
313 >
314 > protected:
315 >
316 >  virtual void evolveEtaA(void);
317 >  virtual void evolveEtaB(void);
318  
319 +  virtual bool etaConverged( void );
320 +
321 +  virtual void scaleSimBox( void );
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],
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  
249 – class NPTfm : public Integrator{
336  
337 + template<typename T> class ZConstraint : public T {
338 +
339 +  public:
340 +  class ForceSubtractionPolicy{
341 +    public:
342 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
343 +
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 +
350 +   protected:
351 +     ZConstraint<T>* zconsIntegrator;
352 +  };
353 +
354 +  class PolicyByNumber : public ForceSubtractionPolicy{
355 +
356 +    public:
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 +
364 +    private:
365 +      int totNumOfMovingAtoms;
366 +  };
367 +
368 +  class PolicyByMass : public ForceSubtractionPolicy{
369 +
370 +    public:
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);
377 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
378 +
379 +   private:
380 +     double totMassOfMovingAtoms;
381 +  };
382 +
383   public:
384  
385 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
386 <  virtual ~NPTfm() {};
385 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
386 >  ~ZConstraint();
387  
388 <  virtual void integrateStep( int calcPot, int calcStress ){
389 <    calcStress = 1;
258 <    Integrator::integrateStep( calcPot, calcStress );
259 <  }
388 >  void setZConsTime(double time)                  {this->zconsTime = time;}
389 >  void getZConsTime()                             {return zconsTime;}
390  
391 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
392 <  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;}
391 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
392 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
393  
394 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
395 +  string getZConsOutput()                         {return zconsOutput;}
396 +
397 +  virtual void integrate();
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};
405 +
406 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
407 +  vector<ZConsState> states;                 //state of z-constraint molecules
408 +
409 +
410 +
411 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
412 +  double totalMassOfUncons;                //total mas of unconstraint molecules
413 +
414 +
415   protected:
416  
268 –  virtual void  moveA( void );
269 –  virtual void moveB( void );
417  
271 –  virtual int readyCheck();
418  
419 <  // chi and eta are the propagated degrees of freedom
419 >  virtual void calcForce( int calcPot, int calcStress );
420 >  virtual void thermalize(void);
421  
422 <  double chi;
423 <  double eta[3][3];
424 <  double NkBT;
422 >  void zeroOutVel();
423 >  void doZconstraintForce();
424 >  void doHarmonic(vector<double>& resPos);
425 >  bool checkZConsState();
426  
427 <  // targetTemp, targetPressure, and tauBarostat must be set.  
428 <  // One of qmass or tauThermostat must be set;
427 >  bool haveFixedZMols();
428 >  bool haveMovingZMols();
429  
430 <  double targetTemp;
283 <  double targetPressure;
284 <  double tauThermostat;
285 <  double tauBarostat;
430 >  double calcZSys();
431  
432 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
288 <  short int have_target_pressure;
432 >  int isZConstraintMol(Molecule* mol);
433  
434 +
435 +  double zconsTime;                              //sample time
436 +  double zconsTol;                                 //tolerance of z-contratint
437 +  double zForceConst;                           //base force constant term
438 +                                                          //which is estimate by OOPSE
439 +
440 +
441 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
442 +  vector<double> kz;                              //force constant array
443 +
444 +  vector<double> zPos;                          //
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 +
453 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
454 +
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 +  double zconsFixTime;  
465 +  double zconsGap;
466 +  bool hasZConsGap;
467 +  vector<double> endFixTime;
468 +  
469 +  int whichDirection;                           //constraint direction
470 +
471 + private:
472 +
473 +  string zconsOutput;                         //filename of zconstraint output
474 +  ZConsWriter* fzOut;                         //z-constraint writer
475 +
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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