27 |
|
Integrator( SimInfo *theInfo, ForceFields* the_ff ); |
28 |
|
virtual ~Integrator(); |
29 |
|
void integrate( void ); |
30 |
+ |
virtual double getConservedQuantity(void); |
31 |
|
|
31 |
– |
|
32 |
|
protected: |
33 |
< |
|
33 |
> |
|
34 |
|
virtual void integrateStep( int calcPot, int calcStress ); |
35 |
|
virtual void preMove( void ); |
36 |
|
virtual void moveA( void ); |
40 |
|
virtual int readyCheck( void ) { return 1; } |
41 |
|
|
42 |
|
virtual void resetIntegrator( void ) { } |
43 |
< |
|
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[3][3] ); |
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 |
|
|
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; |
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 |
|
|
139 |
|
|
140 |
< |
template<typename T> class NPTi : public T{ |
140 |
> |
template<typename T> class NPT : public T{ |
141 |
|
|
142 |
|
public: |
143 |
|
|
144 |
< |
NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
145 |
< |
virtual ~NPTi() {}; |
146 |
< |
|
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 |
|
|
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; |
156 |
– |
double eta; |
193 |
|
double NkBT; |
194 |
+ |
double fkBT; |
195 |
|
|
196 |
+ |
double tt2, tb2; |
197 |
+ |
double instaTemp, instaPress, instaVol; |
198 |
+ |
|
199 |
+ |
int Nparticles; |
200 |
+ |
|
201 |
+ |
double integralOfChidt; |
202 |
+ |
|
203 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
204 |
|
// One of qmass or tauThermostat must be set; |
205 |
|
|
210 |
|
|
211 |
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
212 |
|
short int have_target_pressure; |
213 |
+ |
|
214 |
+ |
double *oldPos; |
215 |
+ |
double *oldVel; |
216 |
+ |
double *oldJi; |
217 |
|
|
218 |
+ |
double chiTolerance; |
219 |
+ |
short int have_chi_tolerance; |
220 |
+ |
double posIterTolerance; |
221 |
+ |
short int have_pos_iter_tolerance; |
222 |
+ |
double etaTolerance; |
223 |
+ |
short int have_eta_tolerance; |
224 |
+ |
|
225 |
|
}; |
226 |
|
|
227 |
+ |
template<typename T> class NPTi : public T{ |
228 |
+ |
|
229 |
+ |
public: |
230 |
+ |
NPTi( SimInfo *theInfo, ForceFields* the_ff); |
231 |
+ |
~NPTi(); |
232 |
+ |
|
233 |
+ |
virtual double getConservedQuantity(void); |
234 |
+ |
virtual void resetIntegrator(void); |
235 |
+ |
|
236 |
+ |
protected: |
237 |
+ |
|
238 |
+ |
|
239 |
+ |
|
240 |
+ |
virtual void evolveEtaA(void); |
241 |
+ |
virtual void evolveEtaB(void); |
242 |
+ |
|
243 |
+ |
virtual bool etaConverged( void ); |
244 |
+ |
|
245 |
+ |
virtual void scaleSimBox( void ); |
246 |
+ |
|
247 |
+ |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
248 |
+ |
virtual void getVelScaleB( double sc[3], int index ); |
249 |
+ |
virtual void getPosScale(double pos[3], double COM[3], |
250 |
+ |
int index, double sc[3]); |
251 |
+ |
|
252 |
+ |
double eta, oldEta, prevEta; |
253 |
+ |
}; |
254 |
+ |
|
255 |
+ |
|
256 |
|
template<typename T> class NPTim : public T{ |
257 |
|
|
258 |
|
public: |
259 |
|
|
260 |
|
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
261 |
< |
virtual ~NPTim() {}; |
261 |
> |
virtual ~NPTim() {} |
262 |
|
|
263 |
|
virtual void integrateStep( int calcPot, int calcStress ){ |
264 |
|
calcStress = 1; |
265 |
|
T::integrateStep( calcPot, calcStress ); |
266 |
+ |
accIntegralOfChidt(); |
267 |
|
} |
268 |
|
|
269 |
+ |
virtual double getConservedQuantity(void); |
270 |
+ |
|
271 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
272 |
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
273 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
274 |
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
275 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol;} |
276 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
277 |
|
|
278 |
|
protected: |
279 |
|
|
284 |
|
|
285 |
|
virtual void resetIntegrator( void ); |
286 |
|
|
287 |
+ |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
288 |
+ |
|
289 |
|
Molecule* myMolecules; |
290 |
|
Atom** myAtoms; |
291 |
|
|
294 |
|
double chi; |
295 |
|
double eta; |
296 |
|
double NkBT; |
297 |
+ |
double integralOfChidt; |
298 |
|
|
299 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
300 |
|
// One of qmass or tauThermostat must be set; |
306 |
|
|
307 |
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
308 |
|
short int have_target_pressure; |
309 |
+ |
double chiTolerance; |
310 |
+ |
short int have_chi_tolerance; |
311 |
+ |
double posIterTolerance; |
312 |
+ |
short int have_pos_iter_tolerance; |
313 |
|
|
314 |
|
}; |
315 |
|
|
316 |
+ |
template<typename T> class NPTzm : public T{ |
317 |
+ |
|
318 |
+ |
public: |
319 |
+ |
|
320 |
+ |
NPTzm ( SimInfo *theInfo, ForceFields* the_ff); |
321 |
+ |
virtual ~NPTzm() {}; |
322 |
+ |
|
323 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
324 |
+ |
calcStress = 1; |
325 |
+ |
T::integrateStep( calcPot, calcStress ); |
326 |
+ |
} |
327 |
+ |
|
328 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
329 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
330 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
331 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
332 |
+ |
|
333 |
+ |
protected: |
334 |
+ |
|
335 |
+ |
virtual void moveA( void ); |
336 |
+ |
virtual void moveB( void ); |
337 |
+ |
|
338 |
+ |
virtual int readyCheck(); |
339 |
+ |
|
340 |
+ |
virtual void resetIntegrator( void ); |
341 |
+ |
|
342 |
+ |
Molecule* myMolecules; |
343 |
+ |
Atom** myAtoms; |
344 |
+ |
|
345 |
+ |
// chi and eta are the propagated degrees of freedom |
346 |
+ |
|
347 |
+ |
double chi; |
348 |
+ |
double eta; |
349 |
+ |
double etaZ; |
350 |
+ |
double NkBT; |
351 |
+ |
|
352 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
353 |
+ |
// One of qmass or tauThermostat must be set; |
354 |
+ |
|
355 |
+ |
double targetTemp; |
356 |
+ |
double targetPressure; |
357 |
+ |
double tauThermostat; |
358 |
+ |
double tauBarostat; |
359 |
+ |
|
360 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
361 |
+ |
short int have_target_pressure; |
362 |
+ |
|
363 |
+ |
}; |
364 |
+ |
|
365 |
|
template<typename T> class NPTf : public T{ |
366 |
|
|
367 |
|
public: |
368 |
|
|
369 |
|
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
370 |
< |
virtual ~NPTf() {}; |
370 |
> |
virtual ~NPTf(); |
371 |
|
|
372 |
|
virtual void integrateStep( int calcPot, int calcStress ){ |
373 |
|
calcStress = 1; |
374 |
|
T::integrateStep( calcPot, calcStress ); |
375 |
|
} |
376 |
+ |
|
377 |
+ |
virtual double getConservedQuantity(void); |
378 |
|
|
379 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
380 |
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
381 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
382 |
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
383 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol;} |
384 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
385 |
|
|
386 |
|
protected: |
387 |
|
|
392 |
|
|
393 |
|
virtual int readyCheck(); |
394 |
|
|
395 |
+ |
|
396 |
|
// chi and eta are the propagated degrees of freedom |
397 |
|
|
398 |
|
double chi; |
399 |
|
double eta[3][3]; |
400 |
+ |
double NkBT; |
401 |
+ |
double fkBT; |
402 |
+ |
|
403 |
+ |
int Nparticles; |
404 |
+ |
|
405 |
+ |
double *oldPos; |
406 |
+ |
double *oldVel; |
407 |
+ |
double *oldJi; |
408 |
+ |
|
409 |
+ |
double integralOfChidt; |
410 |
+ |
|
411 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
412 |
+ |
// One of qmass or tauThermostat must be set; |
413 |
+ |
|
414 |
+ |
double targetTemp; |
415 |
+ |
double targetPressure; |
416 |
+ |
double tauThermostat; |
417 |
+ |
double tauBarostat; |
418 |
+ |
|
419 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
420 |
+ |
short int have_target_pressure; |
421 |
+ |
double chiTolerance; |
422 |
+ |
short int have_chi_tolerance; |
423 |
+ |
double posIterTolerance; |
424 |
+ |
short int have_pos_iter_tolerance; |
425 |
+ |
double etaTolerance; |
426 |
+ |
short int have_eta_tolerance; |
427 |
+ |
}; |
428 |
+ |
|
429 |
+ |
template<typename T> class NPTxym : public T{ |
430 |
+ |
|
431 |
+ |
public: |
432 |
+ |
|
433 |
+ |
NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
434 |
+ |
virtual ~NPTxym() {}; |
435 |
+ |
|
436 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
437 |
+ |
calcStress = 1; |
438 |
+ |
T::integrateStep( calcPot, calcStress ); |
439 |
+ |
} |
440 |
+ |
|
441 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
442 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
443 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
444 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
445 |
+ |
|
446 |
+ |
protected: |
447 |
+ |
|
448 |
+ |
virtual void moveA( void ); |
449 |
+ |
virtual void moveB( void ); |
450 |
+ |
|
451 |
+ |
virtual int readyCheck(); |
452 |
+ |
|
453 |
+ |
virtual void resetIntegrator( void ); |
454 |
+ |
|
455 |
+ |
Molecule* myMolecules; |
456 |
+ |
Atom** myAtoms; |
457 |
+ |
|
458 |
+ |
// chi and eta are the propagated degrees of freedom |
459 |
+ |
|
460 |
+ |
double chi; |
461 |
+ |
double eta; |
462 |
+ |
double etaX; |
463 |
+ |
double etaY; |
464 |
|
double NkBT; |
465 |
|
|
466 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
476 |
|
|
477 |
|
}; |
478 |
|
|
479 |
+ |
|
480 |
|
template<typename T> class NPTfm : public T{ |
481 |
|
|
482 |
|
public: |
487 |
|
virtual void integrateStep( int calcPot, int calcStress ){ |
488 |
|
calcStress = 1; |
489 |
|
T::integrateStep( calcPot, calcStress ); |
490 |
+ |
accIntegralOfChidt(); |
491 |
|
} |
492 |
|
|
493 |
+ |
virtual double getConservedQuantity(void); |
494 |
+ |
|
495 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
496 |
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
497 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
498 |
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
499 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol;} |
500 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
501 |
|
|
502 |
|
protected: |
503 |
|
|
508 |
|
|
509 |
|
virtual int readyCheck(); |
510 |
|
|
511 |
+ |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
512 |
+ |
|
513 |
|
Molecule* myMolecules; |
514 |
|
Atom** myAtoms; |
515 |
|
|
518 |
|
double chi; |
519 |
|
double eta[3][3]; |
520 |
|
double NkBT; |
521 |
+ |
double integralOfChidt; |
522 |
|
|
523 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
524 |
|
// One of qmass or tauThermostat must be set; |
530 |
|
|
531 |
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
532 |
|
short int have_target_pressure; |
533 |
+ |
double chiTolerance; |
534 |
+ |
short int have_chi_tolerance; |
535 |
+ |
double posIterTolerance; |
536 |
+ |
short int have_pos_iter_tolerance; |
537 |
|
|
538 |
|
}; |
539 |
|
|
554 |
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
555 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
556 |
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
557 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol;} |
558 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
559 |
|
|
560 |
|
protected: |
561 |
|
|
582 |
|
|
583 |
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
584 |
|
short int have_target_pressure; |
585 |
+ |
double chiTolerance; |
586 |
+ |
short int have_chi_tolerance; |
587 |
+ |
double posIterTolerance; |
588 |
+ |
short int have_pos_iter_tolerance; |
589 |
|
|
590 |
|
}; |
591 |
|
|
618 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
619 |
|
|
620 |
|
private: |
621 |
< |
int totNumOfMovingAtoms; |
621 |
> |
int totNumOfMovingAtoms; |
622 |
|
}; |
623 |
|
|
624 |
|
class PolicyByMass : public ForceSubtractionPolicy{ |