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 |
|
void checkConstraints( void ); |
48 |
|
void rotate( int axes1, int axes2, double angle, double j[3], |
49 |
< |
double A[3][3] ); |
50 |
< |
|
49 |
> |
double A[3][3] ); |
50 |
> |
|
51 |
|
ForceFields* myFF; |
52 |
|
|
53 |
|
SimInfo *info; // all the info we'll ever need |
58 |
|
int nMols; |
59 |
|
|
60 |
|
int isConstrained; // boolean to know whether the systems contains |
61 |
< |
// constraints. |
61 |
> |
// constraints. |
62 |
|
int nConstrained; // counter for number of constraints |
63 |
|
int *constrainedA; // the i of a constraint pair |
64 |
|
int *constrainedB; // the j of a constraint pair |
107 |
|
|
108 |
|
virtual int readyCheck(); |
109 |
|
|
110 |
+ |
virtual void resetIntegrator( void ); |
111 |
+ |
|
112 |
|
// chi is a propagated degree of freedom. |
113 |
|
|
114 |
|
double chi; |
148 |
|
|
149 |
|
virtual int readyCheck(); |
150 |
|
|
151 |
+ |
virtual void resetIntegrator( void ); |
152 |
+ |
|
153 |
|
// chi and eta are the propagated degrees of freedom |
154 |
|
|
155 |
|
double chi; |
175 |
|
|
176 |
|
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
177 |
|
virtual ~NPTim() {}; |
178 |
+ |
|
179 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
180 |
+ |
calcStress = 1; |
181 |
+ |
T::integrateStep( calcPot, calcStress ); |
182 |
+ |
} |
183 |
+ |
|
184 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
185 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
186 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
187 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
188 |
+ |
|
189 |
+ |
protected: |
190 |
+ |
|
191 |
+ |
virtual void moveA( void ); |
192 |
+ |
virtual void moveB( void ); |
193 |
+ |
|
194 |
+ |
virtual int readyCheck(); |
195 |
+ |
|
196 |
+ |
virtual void resetIntegrator( void ); |
197 |
+ |
|
198 |
+ |
Molecule* myMolecules; |
199 |
+ |
Atom** myAtoms; |
200 |
|
|
201 |
+ |
// chi and eta are the propagated degrees of freedom |
202 |
+ |
|
203 |
+ |
double chi; |
204 |
+ |
double eta; |
205 |
+ |
double NkBT; |
206 |
+ |
|
207 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
208 |
+ |
// One of qmass or tauThermostat must be set; |
209 |
+ |
|
210 |
+ |
double targetTemp; |
211 |
+ |
double targetPressure; |
212 |
+ |
double tauThermostat; |
213 |
+ |
double tauBarostat; |
214 |
+ |
|
215 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
216 |
+ |
short int have_target_pressure; |
217 |
+ |
|
218 |
+ |
}; |
219 |
+ |
|
220 |
+ |
template<typename T> class NPTzm : public T{ |
221 |
+ |
|
222 |
+ |
public: |
223 |
+ |
|
224 |
+ |
NPTzm ( SimInfo *theInfo, ForceFields* the_ff); |
225 |
+ |
virtual ~NPTzm() {}; |
226 |
+ |
|
227 |
|
virtual void integrateStep( int calcPot, int calcStress ){ |
228 |
|
calcStress = 1; |
229 |
|
T::integrateStep( calcPot, calcStress ); |
241 |
|
|
242 |
|
virtual int readyCheck(); |
243 |
|
|
244 |
+ |
virtual void resetIntegrator( void ); |
245 |
+ |
|
246 |
|
Molecule* myMolecules; |
247 |
|
Atom** myAtoms; |
248 |
|
|
250 |
|
|
251 |
|
double chi; |
252 |
|
double eta; |
253 |
+ |
double etaZ; |
254 |
|
double NkBT; |
255 |
|
|
256 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
288 |
|
virtual void moveA( void ); |
289 |
|
virtual void moveB( void ); |
290 |
|
|
291 |
+ |
virtual void resetIntegrator( void ); |
292 |
+ |
|
293 |
|
virtual int readyCheck(); |
294 |
|
|
295 |
|
// chi and eta are the propagated degrees of freedom |
296 |
|
|
297 |
|
double chi; |
298 |
|
double eta[3][3]; |
299 |
+ |
double NkBT; |
300 |
+ |
|
301 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
302 |
+ |
// One of qmass or tauThermostat must be set; |
303 |
+ |
|
304 |
+ |
double targetTemp; |
305 |
+ |
double targetPressure; |
306 |
+ |
double tauThermostat; |
307 |
+ |
double tauBarostat; |
308 |
+ |
|
309 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
310 |
+ |
short int have_target_pressure; |
311 |
+ |
|
312 |
+ |
}; |
313 |
+ |
|
314 |
+ |
template<typename T> class NPTxym : public T{ |
315 |
+ |
|
316 |
+ |
public: |
317 |
+ |
|
318 |
+ |
NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
319 |
+ |
virtual ~NPTxym() {}; |
320 |
+ |
|
321 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
322 |
+ |
calcStress = 1; |
323 |
+ |
T::integrateStep( calcPot, calcStress ); |
324 |
+ |
} |
325 |
+ |
|
326 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
327 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
328 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
329 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
330 |
+ |
|
331 |
+ |
protected: |
332 |
+ |
|
333 |
+ |
virtual void moveA( void ); |
334 |
+ |
virtual void moveB( void ); |
335 |
+ |
|
336 |
+ |
virtual int readyCheck(); |
337 |
+ |
|
338 |
+ |
virtual void resetIntegrator( void ); |
339 |
+ |
|
340 |
+ |
Molecule* myMolecules; |
341 |
+ |
Atom** myAtoms; |
342 |
+ |
|
343 |
+ |
// chi and eta are the propagated degrees of freedom |
344 |
+ |
|
345 |
+ |
double chi; |
346 |
+ |
double eta; |
347 |
+ |
double etaX; |
348 |
+ |
double etaY; |
349 |
|
double NkBT; |
350 |
|
|
351 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
361 |
|
|
362 |
|
}; |
363 |
|
|
364 |
+ |
|
365 |
|
template<typename T> class NPTfm : public T{ |
366 |
|
|
367 |
|
public: |
384 |
|
virtual void moveA( void ); |
385 |
|
virtual void moveB( void ); |
386 |
|
|
387 |
+ |
virtual void resetIntegrator( void ); |
388 |
+ |
|
389 |
|
virtual int readyCheck(); |
390 |
|
|
391 |
|
Molecule* myMolecules; |
392 |
|
Atom** myAtoms; |
393 |
+ |
|
394 |
+ |
// chi and eta are the propagated degrees of freedom |
395 |
+ |
|
396 |
+ |
double chi; |
397 |
+ |
double eta[3][3]; |
398 |
+ |
double NkBT; |
399 |
+ |
|
400 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
401 |
+ |
// One of qmass or tauThermostat must be set; |
402 |
+ |
|
403 |
+ |
double targetTemp; |
404 |
+ |
double targetPressure; |
405 |
+ |
double tauThermostat; |
406 |
+ |
double tauBarostat; |
407 |
+ |
|
408 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
409 |
+ |
short int have_target_pressure; |
410 |
|
|
411 |
+ |
}; |
412 |
+ |
|
413 |
+ |
|
414 |
+ |
template<typename T> class NPTpr : public T{ |
415 |
+ |
|
416 |
+ |
public: |
417 |
+ |
|
418 |
+ |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
419 |
+ |
virtual ~NPTpr() {}; |
420 |
+ |
|
421 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
422 |
+ |
calcStress = 1; |
423 |
+ |
T::integrateStep( calcPot, calcStress ); |
424 |
+ |
} |
425 |
+ |
|
426 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
427 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
428 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
429 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
430 |
+ |
|
431 |
+ |
protected: |
432 |
+ |
|
433 |
+ |
virtual void moveA( void ); |
434 |
+ |
virtual void moveB( void ); |
435 |
+ |
|
436 |
+ |
virtual int readyCheck(); |
437 |
+ |
|
438 |
+ |
virtual void resetIntegrator( void ); |
439 |
+ |
|
440 |
|
// chi and eta are the propagated degrees of freedom |
441 |
|
|
442 |
|
double chi; |
456 |
|
|
457 |
|
}; |
458 |
|
|
459 |
+ |
|
460 |
|
template<typename T> class ZConstraint : public T { |
461 |
+ |
|
462 |
+ |
public: |
463 |
+ |
class ForceSubtractionPolicy{ |
464 |
+ |
public: |
465 |
+ |
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
466 |
|
|
467 |
+ |
virtual void update() = 0; |
468 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
469 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
470 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
471 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
472 |
+ |
|
473 |
+ |
protected: |
474 |
+ |
ZConstraint<T>* zconsIntegrator;; |
475 |
+ |
}; |
476 |
+ |
|
477 |
+ |
class PolicyByNumber : public ForceSubtractionPolicy{ |
478 |
+ |
|
479 |
+ |
public: |
480 |
+ |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
481 |
+ |
virtual void update(); |
482 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
483 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
484 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
485 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
486 |
+ |
|
487 |
+ |
private: |
488 |
+ |
int totNumOfMovingAtoms; |
489 |
+ |
}; |
490 |
+ |
|
491 |
+ |
class PolicyByMass : public ForceSubtractionPolicy{ |
492 |
+ |
|
493 |
+ |
public: |
494 |
+ |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
495 |
+ |
|
496 |
+ |
virtual void update(); |
497 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
498 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
499 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
500 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
501 |
+ |
|
502 |
+ |
private: |
503 |
+ |
double totMassOfMovingAtoms; |
504 |
+ |
}; |
505 |
+ |
|
506 |
|
public: |
507 |
|
|
508 |
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
511 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
512 |
|
void getZConsTime() {return zconsTime;} |
513 |
|
|
514 |
< |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
515 |
< |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
514 |
> |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
515 |
> |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
516 |
|
|
517 |
< |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
517 |
> |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
518 |
|
string getZConsOutput() {return zconsOutput;} |
519 |
|
|
520 |
|
virtual void integrate(); |
521 |
|
|
522 |
|
|
523 |
|
#ifdef IS_MPI |
524 |
< |
virtual void update(); //which is called to indicate the molecules' migration |
524 |
> |
virtual void update(); //which is called to indicate the molecules' migration |
525 |
|
#endif |
526 |
|
|
527 |
|
protected: |
528 |
|
|
529 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
327 |
< |
|
328 |
< |
|
529 |
> |
enum ZConsState {zcsMoving, zcsFixed}; |
530 |
|
|
531 |
|
virtual void calcForce( int calcPot, int calcStress ); |
532 |
|
virtual void thermalize(void); |
544 |
|
int isZConstraintMol(Molecule* mol); |
545 |
|
|
546 |
|
|
547 |
< |
double zconsTime; |
548 |
< |
double zconsTol; |
549 |
< |
double zForceConst; |
547 |
> |
double zconsTime; //sample time |
548 |
> |
double zconsTol; //tolerance of z-contratint |
549 |
> |
double zForceConst; //base force constant term |
550 |
> |
//which is estimate by OOPSE |
551 |
|
|
552 |
< |
vector<Molecule*> zconsMols; |
553 |
< |
vector<double> massOfZConsMols; |
554 |
< |
vector<double> kz; |
555 |
< |
vector<ZConsState> states; |
556 |
< |
vector<double> zPos; |
552 |
> |
vector<Molecule*> zconsMols; //z-constraint molecules array |
553 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
554 |
> |
vector<double> kz; //force constant array |
555 |
> |
vector<ZConsState> states; //state of z-constraint molecules |
556 |
> |
vector<double> zPos; // |
557 |
|
|
558 |
|
|
559 |
< |
vector<Molecule*> unconsMols; |
560 |
< |
vector<double> massOfUnconsMols; |
561 |
< |
double totalMassOfUncons; |
559 |
> |
vector<Molecule*> unconsMols; //unconstraint molecules array |
560 |
> |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
561 |
> |
double totalMassOfUncons; //total mas of unconstraint molecules |
562 |
|
|
563 |
< |
vector<ZConsParaItem>* parameters; |
563 |
> |
vector<ZConsParaItem>* parameters; // |
564 |
|
|
565 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
566 |
|
|
567 |
|
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
568 |
|
double* fz; |
569 |
+ |
double* curZPos; |
570 |
|
|
571 |
< |
int totNumOfUnconsAtoms; |
571 |
> |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
572 |
|
|
573 |
|
int whichDirection; //constraint direction |
574 |
|
|
575 |
|
private: |
576 |
|
|
577 |
< |
string zconsOutput; |
578 |
< |
ZConsWriter* fzOut; |
577 |
> |
string zconsOutput; //filename of zconstraint output |
578 |
> |
ZConsWriter* fzOut; //z-constraint writer |
579 |
|
|
580 |
+ |
double curZconsTime; |
581 |
+ |
|
582 |
|
double calcMovingMolsCOMVel(); |
583 |
|
double calcSysCOMVel(); |
584 |
|
double calcTotalForce(); |
585 |
+ |
|
586 |
+ |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
587 |
+ |
friend class ForceSubtractionPolicy; |
588 |
|
|
589 |
|
}; |
590 |
|
|