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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 588 by gezelter, Thu Jul 10 17:10:56 2003 UTC vs.
Revision 788 by mmeineke, Thu Sep 25 21:17:16 2003 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 "Molecule.hpp"
8   #include "SRI.hpp"
9   #include "AbstractClasses.hpp"
10   #include "SimInfo.hpp"
11   #include "ForceFields.hpp"
12   #include "Thermo.hpp"
13   #include "ReadWrite.hpp"
14 + #include "ZConsWriter.hpp"
15  
16 + using namespace std;
17   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
18   const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19   const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
20   const int maxIteration = 300;
21   const double tol = 1.0e-6;
22  
18 – class Integrator : public BaseIntegrator {
23  
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  
25 –
32   protected:
33 <  
33 >
34    virtual void integrateStep( int calcPot, int calcStress );
35    virtual void preMove( void );
36    virtual void moveA( void );
# Line 32 | Line 38 | class Integrator : public BaseIntegrator { (protected)
38    virtual void constrainA( void );
39    virtual void constrainB( void );
40    virtual int  readyCheck( void ) { return 1; }
41 +
42 +  virtual void resetIntegrator( void ) { }
43 +
44 +  virtual void calcForce( int calcPot, int calcStress );  
45 +  virtual void thermalize();
46    
47 +  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48 +
49    void checkConstraints( void );
50    void rotate( int axes1, int axes2, double angle, double j[3],
51 <               double A[9] );
52 <
40 <
51 >         double A[3][3] );
52 >        
53    ForceFields* myFF;
54  
55    SimInfo *info; // all the info we'll ever need
# Line 48 | Line 60 | class Integrator : public BaseIntegrator { (protected)
60    int nMols;
61  
62    int isConstrained; // boolean to know whether the systems contains
63 <                     // constraints.
63 >         // constraints.
64    int nConstrained;  // counter for number of constraints
65    int *constrainedA; // the i of a constraint pair
66    int *constrainedB; // the j of a constraint pair
# Line 63 | Line 75 | class Integrator : public BaseIntegrator { (protected)
75    double dt;
76    double dt2;
77  
66 –  double* pos;
67 –  double* vel;
68 –  double* frc;
69 –  double* trq;
70 –  double* Amat;
71 –
78    Thermo *tStats;
79    StatWriter*  statOut;
80    DumpWriter*  dumpOut;
81    
82   };
83  
84 < class NVE : public Integrator{
84 > typedef Integrator<BaseIntegrator> RealIntegrator;
85  
86 + template<typename T> class NVE : public T {
87 +
88   public:
89    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
90 <    Integrator( theInfo, the_ff ){}
91 <  virtual ~NVE(){}
84 <
85 <  
86 <
90 >    T( theInfo, the_ff ){}
91 >  virtual ~NVE(){}  
92   };
93  
89 – class NVT : public Integrator{
94  
95 + template<typename T> class NVT : public T {
96 +
97   public:
98  
99    NVT ( SimInfo *theInfo, ForceFields* the_ff);
100 <  virtual ~NVT() {}
100 >  virtual ~NVT();
101  
102    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
103    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
104 +  void setChiTolerance(double tol) {chiTolerance = tol;}
105 +  virtual double  getConservedQuantity(void);
106  
107   protected:
108  
# Line 103 | Line 111 | class NVT : public Integrator{ (protected)
111  
112    virtual int readyCheck();
113  
114 +  virtual void resetIntegrator( void );
115 +
116    // chi is a propagated degree of freedom.
117  
118    double chi;
119  
120 +  //integral of chi(t)dt
121 +  double integralOfChidt;
122 +
123    // targetTemp must be set.  tauThermostat must also be set;
124  
125    double targetTemp;
# Line 114 | Line 127 | class NVT : public Integrator{ (protected)
127    
128    short int have_tau_thermostat, have_target_temp;
129  
130 +  double *oldVel;
131 +  double *oldJi;
132 +
133 +  double chiTolerance;
134 +  short int have_chi_tolerance;
135 +
136   };
137  
138  
120 – class NPTi : public Integrator{
139  
140 + template<typename T> class NPT : public T{
141 +
142   public:
143  
144 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
145 <  virtual ~NPTi() {};
144 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
145 >  virtual ~NPT();
146 >  
147 >  virtual void integrateStep( int calcPot, int calcStress ){
148 >    calcStress = 1;
149 >    T::integrateStep( calcPot, calcStress );
150 >  }
151  
152 +  virtual double getConservedQuantity(void) = 0;
153 +
154    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
155    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
156    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
157    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
158 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
159 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
160 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
161  
162   protected:
163  
# Line 136 | Line 166 | class NPTi : public Integrator{ (protected)
166  
167    virtual int readyCheck();
168  
169 +  virtual void resetIntegrator( void );
170 +
171 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
172 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
173 +  virtual void getPosScale(double pos[3], double COM[3],
174 +                           int index, double sc[3]) = 0;
175 +
176 +  virtual bool chiConverged( void );
177 +  virtual bool etaConverged( void ) = 0;
178 +  
179 +  virtual void evolveChiA( void );
180 +  virtual void evolveEtaA( void ) = 0;
181 +  virtual void evolveChiB( void );
182 +  virtual void evolveEtaB( void ) = 0;
183 +
184 +  virtual void scaleSimBox( void ) = 0;
185 +
186 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
187 +
188    // chi and eta are the propagated degrees of freedom
189  
190 +  double oldChi;
191 +  double prevChi;
192    double chi;
142 –  double eta;
193    double NkBT;
194 +  double fkBT;
195  
196 +  double tt2, tb2;
197 +  double instaTemp, instaPress, instaVol;
198 +  double press[3][3];
199 +
200 +  int Nparticles;
201 +
202 +  double integralOfChidt;
203 +
204    // targetTemp, targetPressure, and tauBarostat must be set.  
205    // One of qmass or tauThermostat must be set;
206  
# Line 153 | Line 212 | class NPTi : public Integrator{ (protected)
212    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
213    short int have_target_pressure;
214  
215 +  double *oldPos;
216 +  double *oldVel;
217 +  double *oldJi;
218 +
219 +  double chiTolerance;
220 +  short int have_chi_tolerance;
221 +  double posIterTolerance;
222 +  short int have_pos_iter_tolerance;
223 +  double etaTolerance;
224 +  short int have_eta_tolerance;
225 +
226   };
227  
228 < class NPTf : public Integrator{
228 > template<typename T> class NPTi : public T{
229 >  
230 > public:
231 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
232 >  ~NPTi();
233  
234 +  virtual double getConservedQuantity(void);
235 +  virtual void resetIntegrator(void);
236 +
237 + protected:
238 +
239 +
240 +
241 +  virtual void evolveEtaA(void);
242 +  virtual void evolveEtaB(void);
243 +
244 +  virtual bool etaConverged( void );
245 +
246 +  virtual void scaleSimBox( void );
247 +
248 +  virtual void getVelScaleA( double sc[3], double vel[3] );
249 +  virtual void getVelScaleB( double sc[3], int index );
250 +  virtual void getPosScale(double pos[3], double COM[3],
251 +                           int index, double sc[3]);
252 +
253 +  double eta, oldEta, prevEta;
254 + };
255 +
256 + template<typename T> class NPTzm : public T{
257 +
258   public:
259  
260 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
261 <  virtual ~NPTf() {};
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;}
# Line 169 | Line 272 | class NPTf : public Integrator{ (protected)
272  
273   protected:
274  
275 <  virtual void  moveA( void );
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 +
303 + };
304 +
305 + template<typename T> class NPTf : public T{
306 +
307 + public:
308 +
309 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
310 +  virtual ~NPTf();
311 +
312 +  virtual double getConservedQuantity(void);
313 +  virtual void resetIntegrator(void);
314 +
315 + protected:
316 +
317 +  virtual void evolveEtaA(void);
318 +  virtual void evolveEtaB(void);
319 +
320 +  virtual bool etaConverged( void );
321 +
322 +  virtual void scaleSimBox( void );
323 +
324 +  virtual void getVelScaleA( double sc[3], double vel[3] );
325 +  virtual void getVelScaleB( double sc[3], int index );
326 +  virtual void getPosScale(double pos[3], double COM[3],
327 +                           int index, double sc[3]);
328 +
329    double eta[3][3];
330 +  double oldEta[3][3];
331 +  double prevEta[3][3];
332 + };
333 +
334 + template<typename T> class NPTxym : public T{
335 +
336 + public:
337 +
338 +  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
339 +  virtual ~NPTxym() {};
340 +
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.  
# Line 193 | Line 381 | class NPTf : public Integrator{ (protected)
381  
382   };
383  
384 + template<typename T> class ZConstraint : public T {
385 +  
386 +  public:
387 +  class ForceSubtractionPolicy{
388 +    public:
389 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
390 +
391 +      virtual void update() = 0;    
392 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
393 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
394 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
395 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
396 +    
397 +   protected:
398 +     ZConstraint<T>* zconsIntegrator;
399 +  };
400 +
401 +  class PolicyByNumber : public ForceSubtractionPolicy{
402 +
403 +    public:
404 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
405 +      virtual void update();    
406 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
407 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
408 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
409 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
410 +    
411 +    private:
412 +      int totNumOfMovingAtoms;
413 +  };
414 +
415 +  class PolicyByMass : public ForceSubtractionPolicy{
416 +
417 +    public:
418 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
419 +      
420 +      virtual void update();    
421 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
422 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
423 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
424 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
425 +
426 +   private:
427 +     double totMassOfMovingAtoms;
428 +  };
429 +
430 + public:
431 +
432 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
433 +  ~ZConstraint();
434 +    
435 +  void setZConsTime(double time)                  {this->zconsTime = time;}
436 +  void getZConsTime()                             {return zconsTime;}
437 +  
438 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
439 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
440 +  
441 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
442 +  string getZConsOutput()                         {return zconsOutput;}
443 +  
444 +  virtual void integrate();
445 +  
446 +
447 + #ifdef IS_MPI
448 +  virtual void update();                      //which is called to indicate the molecules' migration
449   #endif
450 +
451 + protected:
452 +
453 +  enum ZConsState {zcsMoving, zcsFixed};  
454 +
455 +  virtual void calcForce( int calcPot, int calcStress );
456 +  virtual void thermalize(void);
457 +  
458 +  void zeroOutVel();
459 +  void doZconstraintForce();
460 +  void doHarmonic();
461 +  bool checkZConsState();
462 +
463 +  bool haveFixedZMols();
464 +  bool haveMovingZMols();
465 +
466 +  double calcZSys();
467 +
468 +  int isZConstraintMol(Molecule* mol);
469 +
470 +
471 +  double zconsTime;                              //sample time
472 +  double zconsTol;                                 //tolerance of z-contratint
473 +  double zForceConst;                           //base force constant term
474 +                                                          //which is estimate by OOPSE
475 +  
476 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
477 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
478 +  vector<double> kz;                              //force constant array
479 +  vector<ZConsState> states;                 //state of z-constraint molecules
480 +  vector<double> zPos;                          //
481 +  
482 +  
483 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
484 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
485 +  double totalMassOfUncons;                //total mas of unconstraint molecules
486 +
487 +  vector<ZConsParaItem>* parameters; //
488 +  
489 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
490 +
491 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
492 +  double* fz;
493 +  double* curZPos;
494 +  
495 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
496 +
497 +  int whichDirection;                           //constraint direction
498 +  
499 + private:
500 +  
501 +  string zconsOutput;                         //filename of zconstraint output
502 +  ZConsWriter* fzOut;                         //z-constraint writer
503 +
504 +  double curZconsTime;                      
505 +
506 +  double calcMovingMolsCOMVel();
507 +  double calcSysCOMVel();
508 +  double calcTotalForce();
509 +  
510 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
511 +  friend class ForceSubtractionPolicy;
512 +
513 + };
514 +
515 + #endif

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