13 |
|
#include "mpiSimulation.hpp" |
14 |
|
#endif |
15 |
|
|
16 |
– |
|
16 |
|
// Basic isotropic thermostating and barostating via the Melchionna |
17 |
|
// modification of the Hoover algorithm: |
18 |
|
// |
87 |
|
mass = atoms[i]->getMass(); |
88 |
|
|
89 |
|
for (j=0; j < 3; j++) { |
90 |
< |
// velocity half step (use chi from previous step here): |
90 |
> |
// velocity half step |
91 |
|
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta)); |
93 |
– |
|
92 |
|
} |
93 |
|
|
94 |
|
atoms[i]->setVel( vel ); |
140 |
|
} |
141 |
|
} |
142 |
|
|
143 |
< |
// evolve chi and eta half step |
143 |
> |
// advance chi half step |
144 |
|
|
145 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
148 |
– |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
146 |
|
|
147 |
< |
//calculate the integral of chidt |
147 |
> |
// calculate the integral of chidt |
148 |
> |
|
149 |
|
integralOfChidt += dt2*chi; |
150 |
|
|
151 |
+ |
// advance eta half step |
152 |
+ |
|
153 |
+ |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
154 |
+ |
|
155 |
|
//save the old positions |
156 |
|
for(i = 0; i < nAtoms; i++){ |
157 |
|
atoms[i]->getPos(pos); |
210 |
|
double vel[3], frc[3]; |
211 |
|
double mass; |
212 |
|
|
213 |
< |
double instTemp, instPress, instVol; |
213 |
> |
double instaTemp, instaPress, instaVol; |
214 |
|
double tt2, tb2; |
215 |
|
double oldChi, prevChi; |
216 |
< |
double oldEta, preEta; |
216 |
> |
double oldEta, prevEta; |
217 |
|
|
218 |
|
tt2 = tauThermostat * tauThermostat; |
219 |
|
tb2 = tauBarostat * tauBarostat; |
244 |
|
|
245 |
|
// do the iteration: |
246 |
|
|
247 |
< |
instVol = tStats->getVolume(); |
247 |
> |
instaVol = tStats->getVolume(); |
248 |
|
|
249 |
|
for (k=0; k < 4; k++) { |
250 |
|
|
251 |
< |
instTemp = tStats->getTemperature(); |
252 |
< |
instPress = tStats->getPressure(); |
251 |
> |
instaTemp = tStats->getTemperature(); |
252 |
> |
instaPress = tStats->getPressure(); |
253 |
|
|
254 |
|
// evolve chi another half step using the temperature at t + dt/2 |
255 |
|
|
256 |
|
prevChi = chi; |
257 |
< |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
256 |
< |
(tauThermostat*tauThermostat); |
257 |
> |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
258 |
|
|
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 |
|
(p_convert*NkBT*tb2)); |
265 |
|
|
266 |
|
|
298 |
|
} |
299 |
|
|
300 |
|
if (fabs(prevChi - chi) <= |
301 |
< |
chiTolerance && fabs(preEta -eta) <= etaTolerance) |
301 |
> |
chiTolerance && fabs(prevEta -eta) <= etaTolerance) |
302 |
|
break; |
303 |
|
} |
304 |
|
|
305 |
< |
//calculate integral of chida |
305 |
> |
//calculate integral of chidt |
306 |
|
integralOfChidt += dt2*chi; |
307 |
|
|
304 |
– |
|
308 |
|
} |
309 |
|
|
310 |
|
template<typename T> void NPTi<T>::resetIntegrator() { |