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) / |