| 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 LkBT; |
| 393 |
< |
double fkBT; |
| 394 |
< |
double f1kBT; |
| 395 |
< |
double f2kBT; |
| 396 |
< |
double NkBT; |
| 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; |
| 407 |
> |
double eta2; |
| 408 |
|
|
| 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 |
– |
|
| 409 |
|
Energy = tStats->getTotalE(); |
| 410 |
|
|
| 411 |
|
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 414 |
|
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 415 |
|
|
| 416 |
|
|
| 417 |
< |
barostat_kinetic = fkBT * tauBarostat * tauBarostat * eta * eta / |
| 417 |
> |
barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta / |
| 418 |
|
(2.0 * eConvert); |
| 419 |
|
|
| 420 |
|
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
