| 173 |
|
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
| 174 |
|
|
| 175 |
|
atoms[i]->setPos( pos ); |
| 176 |
– |
|
| 176 |
|
} |
| 177 |
< |
|
| 177 |
> |
|
| 178 |
> |
if (nConstrained){ |
| 179 |
> |
constrainA(); |
| 180 |
> |
} |
| 181 |
|
} |
| 182 |
|
|
| 183 |
|
|
| 289 |
|
dAtom->setJ( ji ); |
| 290 |
|
} |
| 291 |
|
} |
| 292 |
< |
|
| 293 |
< |
if (fabs(prevChi - chi) <= chiTolerance && fabs(preEta -eta) <= etaTolerance) |
| 292 |
> |
|
| 293 |
> |
if (nConstrained){ |
| 294 |
> |
constrainB(); |
| 295 |
> |
} |
| 296 |
> |
|
| 297 |
> |
if (fabs(prevChi - chi) <= |
| 298 |
> |
chiTolerance && fabs(preEta -eta) <= etaTolerance) |
| 299 |
|
break; |
| 300 |
|
} |
| 301 |
|
|
| 389 |
|
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
| 390 |
|
|
| 391 |
|
double conservedQuantity; |
| 392 |
+ |
double LkBT; |
| 393 |
+ |
double fkBT; |
| 394 |
+ |
double f1kBT; |
| 395 |
+ |
double f2kBT; |
| 396 |
+ |
double NkBT; |
| 397 |
+ |
double Energy; |
| 398 |
+ |
double thermostat_kinetic; |
| 399 |
+ |
double thermostat_potential; |
| 400 |
+ |
double barostat_kinetic; |
| 401 |
+ |
double barostat_potential; |
| 402 |
|
double tb2; |
| 403 |
|
double eta2; |
| 387 |
– |
double E_NPT; |
| 388 |
– |
double U; |
| 389 |
– |
double TS; |
| 390 |
– |
double PV; |
| 391 |
– |
double extra; |
| 404 |
|
|
| 405 |
< |
U = tStats->getTotalE(); |
| 405 |
> |
LkBT = (double)(info->getNDF() + 4) * kB * targetTemp; // 3N + 1 |
| 406 |
> |
fkBT = (double)(info->getNDF() ) * kB * targetTemp; // 3N - 3 |
| 407 |
> |
f1kBT = (double)(info->getNDF()+ 1) * kB * targetTemp; // 3N - 3 + 1 |
| 408 |
> |
NkBT = (double)(info->getNDF() + 3) * kB * targetTemp; // 3N |
| 409 |
> |
f2kBT = (double)(info->getNDF()+ 2) * kB * targetTemp; // 3N - 3 + 1 |
| 410 |
|
|
| 411 |
< |
TS = fkBT * |
| 396 |
< |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
| 411 |
> |
Energy = tStats->getTotalE(); |
| 412 |
|
|
| 413 |
< |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
| 413 |
> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 414 |
> |
(2.0 * eConvert); |
| 415 |
|
|
| 416 |
< |
tb2 = tauBarostat * tauBarostat; |
| 401 |
< |
eta2 = eta * eta; |
| 416 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 417 |
|
|
| 418 |
|
|
| 419 |
< |
extra = ((double)info->ndfTrans * kB * targetTemp * tb2 * eta2 / 2.0) / eConvert; |
| 419 |
> |
barostat_kinetic = fkBT * tauBarostat * tauBarostat * eta * eta / |
| 420 |
> |
(2.0 * eConvert); |
| 421 |
> |
|
| 422 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 423 |
> |
eConvert; |
| 424 |
|
|
| 425 |
+ |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 426 |
+ |
barostat_kinetic + barostat_potential; |
| 427 |
+ |
|
| 428 |
|
cout.width(8); |
| 429 |
|
cout.precision(8); |
| 430 |
|
|
| 431 |
< |
|
| 432 |
< |
cout << info->getTime() << "\t" |
| 433 |
< |
<< chi << "\t" |
| 412 |
< |
<< eta << "\t" |
| 413 |
< |
<< U << "\t" |
| 414 |
< |
<< TS << "\t" |
| 415 |
< |
<< PV << "\t" |
| 416 |
< |
<< extra << "\t" |
| 417 |
< |
<< U+TS+PV+extra << endl; |
| 431 |
> |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 432 |
> |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 433 |
> |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 434 |
|
|
| 419 |
– |
conservedQuantity = U+TS+PV+extra; |
| 435 |
|
return conservedQuantity; |
| 436 |
|
} |
