| 13 |
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#include "mpiSimulation.hpp" |
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#endif |
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– |
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// Basic isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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// |
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mass = atoms[i]->getMass(); |
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|
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for (j=0; j < 3; j++) { |
| 90 |
< |
// velocity half step (use chi from previous step here): |
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> |
// velocity half step |
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vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta)); |
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} |
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atoms[i]->setVel( vel ); |
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} |
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} |
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< |
// evolve chi and eta half step |
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> |
// advance chi half step |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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– |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
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|
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< |
//calculate the integral of chidt |
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> |
// calculate the integral of chidt |
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> |
|
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integralOfChidt += dt2*chi; |
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+ |
// advance eta half step |
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+ |
|
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+ |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
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+ |
|
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//save the old positions |
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for(i = 0; i < nAtoms; i++){ |
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atoms[i]->getPos(pos); |
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double vel[3], frc[3]; |
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double mass; |
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< |
double instTemp, instPress, instVol; |
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> |
double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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double oldChi, prevChi; |
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< |
double oldEta, preEta; |
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> |
double oldEta, prevEta; |
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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// Set things up for the iteration: |
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oldChi = chi; |
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// do the iteration: |
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< |
instVol = tStats->getVolume(); |
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> |
instaVol = tStats->getVolume(); |
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| 249 |
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for (k=0; k < 4; k++) { |
| 250 |
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| 251 |
< |
instTemp = tStats->getTemperature(); |
| 252 |
< |
instPress = tStats->getPressure(); |
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> |
instaTemp = tStats->getTemperature(); |
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> |
instaPress = tStats->getPressure(); |
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// evolve chi another half step using the temperature at t + dt/2 |
| 255 |
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prevChi = chi; |
| 257 |
< |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
| 257 |
< |
(tauThermostat*tauThermostat); |
| 257 |
> |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 258 |
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|
| 259 |
< |
preEta = eta; |
| 260 |
< |
eta = oldEta + dt2 * ( instVol * (instPress - targetPressure) / |
| 259 |
> |
prevEta = eta; |
| 260 |
> |
|
| 261 |
> |
// advance eta half step and calculate scale factor for velocity |
| 262 |
> |
|
| 263 |
> |
eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
| 264 |
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(p_convert*NkBT*tb2)); |
| 265 |
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| 266 |
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| 298 |
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} |
| 299 |
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| 300 |
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if (fabs(prevChi - chi) <= |
| 301 |
< |
chiTolerance && fabs(preEta -eta) <= etaTolerance) |
| 301 |
> |
chiTolerance && fabs(prevEta -eta) <= etaTolerance) |
| 302 |
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break; |
| 303 |
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} |
| 304 |
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|
| 305 |
< |
//calculate integral of chida |
| 305 |
> |
//calculate integral of chidt |
| 306 |
|
integralOfChidt += dt2*chi; |
| 307 |
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|
| 305 |
– |
|
| 308 |
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} |
| 309 |
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|
| 310 |
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template<typename T> void NPTi<T>::resetIntegrator() { |
| 372 |
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simError(); |
| 373 |
|
} |
| 374 |
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|
| 375 |
< |
if (!have_eta_tolerance) { |
| 375 |
> |
if (!have_eta_tolerance) { |
| 376 |
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sprintf( painCave.errMsg, |
| 377 |
|
"NPTi warning: setting eta tolerance to 1e-6\n"); |
| 378 |
|
etaTolerance = 1e-6; |
| 380 |
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painCave.isFatal = 0; |
| 381 |
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simError(); |
| 382 |
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} |
| 383 |
< |
// We need NkBT a lot, so just set it here: |
| 384 |
< |
|
| 383 |
> |
|
| 384 |
> |
|
| 385 |
> |
// We need NkBT a lot, so just set it here: This is the RAW number |
| 386 |
> |
// of particles, so no subtraction or addition of constraints or |
| 387 |
> |
// orientational degrees of freedom: |
| 388 |
> |
|
| 389 |
|
NkBT = (double)Nparticles * kB * targetTemp; |
| 390 |
+ |
|
| 391 |
+ |
// fkBT is used because the thermostat operates on more degrees of freedom |
| 392 |
+ |
// than the barostat (when there are particles with orientational degrees |
| 393 |
+ |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
| 394 |
+ |
|
| 395 |
|
fkBT = (double)info->ndf * kB * targetTemp; |
| 396 |
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|
| 397 |
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return 1; |
| 400 |
|
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
| 401 |
|
|
| 402 |
|
double conservedQuantity; |
| 403 |
+ |
double Three_NkBT; |
| 404 |
+ |
double Energy; |
| 405 |
+ |
double thermostat_kinetic; |
| 406 |
+ |
double thermostat_potential; |
| 407 |
+ |
double barostat_kinetic; |
| 408 |
+ |
double barostat_potential; |
| 409 |
|
double tb2; |
| 410 |
< |
double eta2; |
| 394 |
< |
double E_NPT; |
| 395 |
< |
double U; |
| 396 |
< |
double TS; |
| 397 |
< |
double PV; |
| 398 |
< |
double extra; |
| 410 |
> |
double eta2; |
| 411 |
|
|
| 412 |
< |
U = tStats->getTotalE(); |
| 412 |
> |
Energy = tStats->getTotalE(); |
| 413 |
|
|
| 414 |
< |
TS = fkBT * |
| 415 |
< |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
| 414 |
> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 415 |
> |
(2.0 * eConvert); |
| 416 |
|
|
| 417 |
< |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
| 417 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 418 |
|
|
| 407 |
– |
tb2 = tauBarostat * tauBarostat; |
| 408 |
– |
eta2 = eta * eta; |
| 419 |
|
|
| 420 |
+ |
barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta / |
| 421 |
+ |
(2.0 * eConvert); |
| 422 |
+ |
|
| 423 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 424 |
+ |
eConvert; |
| 425 |
|
|
| 426 |
< |
extra = ((double)info->ndfTrans * kB * targetTemp * tb2 * eta2 / 2.0) / eConvert; |
| 427 |
< |
|
| 426 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 427 |
> |
barostat_kinetic + barostat_potential; |
| 428 |
> |
|
| 429 |
|
cout.width(8); |
| 430 |
|
cout.precision(8); |
| 431 |
|
|
| 432 |
< |
|
| 433 |
< |
// cout << info->getTime() << "\t" |
| 434 |
< |
// << chi << "\t" |
| 419 |
< |
// << eta << "\t" |
| 420 |
< |
// << U << "\t" |
| 421 |
< |
// << TS << "\t" |
| 422 |
< |
// << PV << "\t" |
| 423 |
< |
// << extra << "\t" |
| 424 |
< |
// << U+TS+PV+extra << endl; |
| 432 |
> |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 433 |
> |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 434 |
> |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 435 |
|
|
| 426 |
– |
conservedQuantity = U+TS+PV+extra; |
| 436 |
|
return conservedQuantity; |
| 437 |
|
} |
