30 |
|
virtual double getConservedQuantity(void); |
31 |
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|
32 |
|
protected: |
33 |
< |
|
33 |
> |
|
34 |
|
virtual void integrateStep( int calcPot, int calcStress ); |
35 |
|
virtual void preMove( void ); |
36 |
|
virtual void moveA( void ); |
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] ); |
137 |
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138 |
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139 |
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140 |
< |
template<typename T> class NPTi : public T{ |
140 |
> |
template<typename T> class NPT : public T{ |
141 |
|
|
142 |
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public: |
143 |
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|
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 ); |
148 |
– |
/* accIntegralOfChidt(); */ |
150 |
|
} |
151 |
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|
152 |
< |
virtual double getConservedQuantity(void); |
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;} |
168 |
|
|
169 |
|
virtual void resetIntegrator( void ); |
170 |
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|
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; |
175 |
– |
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; |
223 |
|
double etaTolerance; |
224 |
|
short int have_eta_tolerance; |
225 |
|
|
205 |
– |
double volume; |
206 |
– |
|
226 |
|
}; |
227 |
|
|
228 |
< |
template<typename T> class NPTim : public T{ |
229 |
< |
|
228 |
> |
template<typename T> class NPTi : public T{ |
229 |
> |
|
230 |
|
public: |
231 |
+ |
NPTi( SimInfo *theInfo, ForceFields* the_ff); |
232 |
+ |
~NPTi(); |
233 |
|
|
213 |
– |
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
214 |
– |
virtual ~NPTim() {} |
215 |
– |
|
216 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
217 |
– |
calcStress = 1; |
218 |
– |
T::integrateStep( calcPot, calcStress ); |
219 |
– |
accIntegralOfChidt(); |
220 |
– |
} |
221 |
– |
|
234 |
|
virtual double getConservedQuantity(void); |
235 |
+ |
virtual void resetIntegrator(void); |
236 |
|
|
224 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
225 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
226 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
227 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
228 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
229 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
230 |
– |
|
237 |
|
protected: |
238 |
|
|
239 |
< |
virtual void moveA( void ); |
234 |
< |
virtual void moveB( void ); |
239 |
> |
|
240 |
|
|
241 |
< |
virtual int readyCheck(); |
241 |
> |
virtual void evolveEtaA(void); |
242 |
> |
virtual void evolveEtaB(void); |
243 |
|
|
244 |
< |
virtual void resetIntegrator( void ); |
244 |
> |
virtual bool etaConverged( void ); |
245 |
|
|
246 |
< |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
241 |
< |
|
242 |
< |
Molecule* myMolecules; |
243 |
< |
Atom** myAtoms; |
246 |
> |
virtual void scaleSimBox( void ); |
247 |
|
|
248 |
< |
// chi and eta are the propagated degrees of freedom |
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 chi; |
248 |
< |
double eta; |
249 |
< |
double NkBT; |
250 |
< |
double integralOfChidt; |
251 |
< |
|
252 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
253 |
< |
// One of qmass or tauThermostat must be set; |
254 |
< |
|
255 |
< |
double targetTemp; |
256 |
< |
double targetPressure; |
257 |
< |
double tauThermostat; |
258 |
< |
double tauBarostat; |
259 |
< |
|
260 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
261 |
< |
short int have_target_pressure; |
262 |
< |
double chiTolerance; |
263 |
< |
short int have_chi_tolerance; |
264 |
< |
double posIterTolerance; |
265 |
< |
short int have_pos_iter_tolerance; |
266 |
< |
|
253 |
> |
double eta, oldEta, prevEta; |
254 |
|
}; |
255 |
|
|
256 |
|
template<typename T> class NPTzm : public T{ |
307 |
|
public: |
308 |
|
|
309 |
|
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
310 |
< |
virtual ~NPTf() {}; |
310 |
> |
virtual ~NPTf(); |
311 |
|
|
325 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
326 |
– |
calcStress = 1; |
327 |
– |
T::integrateStep( calcPot, calcStress ); |
328 |
– |
accIntegralOfChidt(); |
329 |
– |
} |
330 |
– |
|
312 |
|
virtual double getConservedQuantity(void); |
313 |
+ |
virtual void resetIntegrator(void); |
314 |
|
|
333 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
334 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
335 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
336 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
337 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
338 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
339 |
– |
|
315 |
|
protected: |
316 |
|
|
317 |
< |
virtual void moveA( void ); |
318 |
< |
virtual void moveB( void ); |
317 |
> |
virtual void evolveEtaA(void); |
318 |
> |
virtual void evolveEtaB(void); |
319 |
|
|
320 |
< |
virtual void resetIntegrator( void ); |
320 |
> |
virtual bool etaConverged( void ); |
321 |
|
|
322 |
< |
virtual int readyCheck(); |
322 |
> |
virtual void scaleSimBox( void ); |
323 |
|
|
324 |
< |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
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 |
|
|
351 |
– |
// chi and eta are the propagated degrees of freedom |
352 |
– |
|
353 |
– |
double chi; |
329 |
|
double eta[3][3]; |
330 |
< |
double NkBT; |
331 |
< |
|
357 |
< |
double integralOfChidt; |
358 |
< |
|
359 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
360 |
< |
// One of qmass or tauThermostat must be set; |
361 |
< |
|
362 |
< |
double targetTemp; |
363 |
< |
double targetPressure; |
364 |
< |
double tauThermostat; |
365 |
< |
double tauBarostat; |
366 |
< |
|
367 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
368 |
< |
short int have_target_pressure; |
369 |
< |
double chiTolerance; |
370 |
< |
short int have_chi_tolerance; |
371 |
< |
double posIterTolerance; |
372 |
< |
short int have_pos_iter_tolerance; |
373 |
< |
|
330 |
> |
double oldEta[3][3]; |
331 |
> |
double prevEta[3][3]; |
332 |
|
}; |
333 |
|
|
334 |
|
template<typename T> class NPTxym : public T{ |
381 |
|
|
382 |
|
}; |
383 |
|
|
426 |
– |
|
427 |
– |
template<typename T> class NPTfm : public T{ |
428 |
– |
|
429 |
– |
public: |
430 |
– |
|
431 |
– |
NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
432 |
– |
virtual ~NPTfm() {}; |
433 |
– |
|
434 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
435 |
– |
calcStress = 1; |
436 |
– |
T::integrateStep( calcPot, calcStress ); |
437 |
– |
accIntegralOfChidt(); |
438 |
– |
} |
439 |
– |
|
440 |
– |
virtual double getConservedQuantity(void); |
441 |
– |
|
442 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
443 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
444 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
445 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
446 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
447 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
448 |
– |
|
449 |
– |
protected: |
450 |
– |
|
451 |
– |
virtual void moveA( void ); |
452 |
– |
virtual void moveB( void ); |
453 |
– |
|
454 |
– |
virtual void resetIntegrator( void ); |
455 |
– |
|
456 |
– |
virtual int readyCheck(); |
457 |
– |
|
458 |
– |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
459 |
– |
|
460 |
– |
Molecule* myMolecules; |
461 |
– |
Atom** myAtoms; |
462 |
– |
|
463 |
– |
// chi and eta are the propagated degrees of freedom |
464 |
– |
|
465 |
– |
double chi; |
466 |
– |
double eta[3][3]; |
467 |
– |
double NkBT; |
468 |
– |
double integralOfChidt; |
469 |
– |
|
470 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
471 |
– |
// One of qmass or tauThermostat must be set; |
472 |
– |
|
473 |
– |
double targetTemp; |
474 |
– |
double targetPressure; |
475 |
– |
double tauThermostat; |
476 |
– |
double tauBarostat; |
477 |
– |
|
478 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
479 |
– |
short int have_target_pressure; |
480 |
– |
double chiTolerance; |
481 |
– |
short int have_chi_tolerance; |
482 |
– |
double posIterTolerance; |
483 |
– |
short int have_pos_iter_tolerance; |
484 |
– |
|
485 |
– |
}; |
486 |
– |
|
487 |
– |
|
488 |
– |
template<typename T> class NPTpr : public T{ |
489 |
– |
|
490 |
– |
public: |
491 |
– |
|
492 |
– |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
493 |
– |
virtual ~NPTpr() {}; |
494 |
– |
|
495 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
496 |
– |
calcStress = 1; |
497 |
– |
T::integrateStep( calcPot, calcStress ); |
498 |
– |
} |
499 |
– |
|
500 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
501 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
502 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
503 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
504 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
505 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
506 |
– |
|
507 |
– |
protected: |
508 |
– |
|
509 |
– |
virtual void moveA( void ); |
510 |
– |
virtual void moveB( void ); |
511 |
– |
|
512 |
– |
virtual int readyCheck(); |
513 |
– |
|
514 |
– |
virtual void resetIntegrator( void ); |
515 |
– |
|
516 |
– |
// chi and eta are the propagated degrees of freedom |
517 |
– |
|
518 |
– |
double chi; |
519 |
– |
double eta[3][3]; |
520 |
– |
double NkBT; |
521 |
– |
|
522 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
523 |
– |
// One of qmass or tauThermostat must be set; |
524 |
– |
|
525 |
– |
double targetTemp; |
526 |
– |
double targetPressure; |
527 |
– |
double tauThermostat; |
528 |
– |
double tauBarostat; |
529 |
– |
|
530 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
531 |
– |
short int have_target_pressure; |
532 |
– |
double chiTolerance; |
533 |
– |
short int have_chi_tolerance; |
534 |
– |
double posIterTolerance; |
535 |
– |
short int have_pos_iter_tolerance; |
536 |
– |
|
537 |
– |
}; |
538 |
– |
|
539 |
– |
|
384 |
|
template<typename T> class ZConstraint : public T { |
385 |
|
|
386 |
|
public: |