| 215 |
|
|
| 216 |
|
tt2 = tauThermostat * tauThermostat; |
| 217 |
|
tb2 = tauBarostat * tauBarostat; |
| 218 |
– |
|
| 218 |
|
|
| 219 |
|
// Set things up for the iteration: |
| 220 |
|
|
| 369 |
|
simError(); |
| 370 |
|
} |
| 371 |
|
|
| 372 |
< |
if (!have_eta_tolerance) { |
| 372 |
> |
if (!have_eta_tolerance) { |
| 373 |
|
sprintf( painCave.errMsg, |
| 374 |
|
"NPTi warning: setting eta tolerance to 1e-6\n"); |
| 375 |
|
etaTolerance = 1e-6; |
| 377 |
|
painCave.isFatal = 0; |
| 378 |
|
simError(); |
| 379 |
|
} |
| 380 |
< |
// We need NkBT a lot, so just set it here: |
| 381 |
< |
|
| 380 |
> |
|
| 381 |
> |
|
| 382 |
> |
// We need NkBT a lot, so just set it here: This is the RAW number |
| 383 |
> |
// of particles, so no subtraction or addition of constraints or |
| 384 |
> |
// orientational degrees of freedom: |
| 385 |
> |
|
| 386 |
|
NkBT = (double)Nparticles * kB * targetTemp; |
| 387 |
+ |
|
| 388 |
+ |
// fkBT is used because the thermostat operates on more degrees of freedom |
| 389 |
+ |
// than the barostat (when there are particles with orientational degrees |
| 390 |
+ |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
| 391 |
+ |
|
| 392 |
|
fkBT = (double)info->ndf * kB * targetTemp; |
| 393 |
|
|
| 394 |
|
return 1; |
| 397 |
|
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
| 398 |
|
|
| 399 |
|
double conservedQuantity; |
| 400 |
+ |
double Three_NkBT; |
| 401 |
+ |
double Energy; |
| 402 |
+ |
double thermostat_kinetic; |
| 403 |
+ |
double thermostat_potential; |
| 404 |
+ |
double barostat_kinetic; |
| 405 |
+ |
double barostat_potential; |
| 406 |
|
double tb2; |
| 407 |
< |
double eta2; |
| 394 |
< |
double E_NPT; |
| 395 |
< |
double U; |
| 396 |
< |
double TS; |
| 397 |
< |
double PV; |
| 398 |
< |
double extra; |
| 407 |
> |
double eta2; |
| 408 |
|
|
| 409 |
< |
U = tStats->getTotalE(); |
| 409 |
> |
Energy = tStats->getTotalE(); |
| 410 |
|
|
| 411 |
< |
TS = fkBT * |
| 412 |
< |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
| 411 |
> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 412 |
> |
(2.0 * eConvert); |
| 413 |
|
|
| 414 |
< |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
| 414 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 415 |
|
|
| 407 |
– |
tb2 = tauBarostat * tauBarostat; |
| 408 |
– |
eta2 = eta * eta; |
| 416 |
|
|
| 417 |
+ |
barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta / |
| 418 |
+ |
(2.0 * eConvert); |
| 419 |
+ |
|
| 420 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 421 |
+ |
eConvert; |
| 422 |
|
|
| 423 |
< |
extra = ((double)info->ndfTrans * kB * targetTemp * tb2 * eta2 / 2.0) / eConvert; |
| 424 |
< |
|
| 423 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 424 |
> |
barostat_kinetic + barostat_potential; |
| 425 |
> |
|
| 426 |
|
cout.width(8); |
| 427 |
|
cout.precision(8); |
| 428 |
|
|
| 429 |
< |
|
| 430 |
< |
// cout << info->getTime() << "\t" |
| 431 |
< |
// << chi << "\t" |
| 419 |
< |
// << eta << "\t" |
| 420 |
< |
// << U << "\t" |
| 421 |
< |
// << TS << "\t" |
| 422 |
< |
// << PV << "\t" |
| 423 |
< |
// << extra << "\t" |
| 424 |
< |
// << U+TS+PV+extra << endl; |
| 429 |
> |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 430 |
> |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 431 |
> |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 432 |
|
|
| 426 |
– |
conservedQuantity = U+TS+PV+extra; |
| 433 |
|
return conservedQuantity; |
| 434 |
|
} |
