13 |
|
#include "mpiSimulation.hpp" |
14 |
|
#endif |
15 |
|
|
16 |
– |
|
16 |
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// Basic isotropic thermostating and barostating via the Melchionna |
17 |
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// modification of the Hoover algorithm: |
18 |
|
// |
55 |
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} |
56 |
|
|
57 |
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template<typename T> void NPTi<T>::moveA() { |
59 |
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|
60 |
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|
61 |
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// int i, j; |
62 |
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// DirectionalAtom* dAtom; |
63 |
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// double Tb[3], ji[3]; |
64 |
– |
// double A[3][3], I[3][3]; |
65 |
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// double angle, mass; |
66 |
– |
// double vel[3], pos[3], frc[3]; |
67 |
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|
68 |
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// double rj[3]; |
69 |
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// double instaTemp, instaPress, instaVol; |
70 |
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// double tt2, tb2, scaleFactor; |
71 |
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|
72 |
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// tt2 = tauThermostat * tauThermostat; |
73 |
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// tb2 = tauBarostat * tauBarostat; |
74 |
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|
75 |
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// instaTemp = tStats->getTemperature(); |
76 |
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// instaPress = tStats->getPressure(); |
77 |
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// instaVol = tStats->getVolume(); |
78 |
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|
79 |
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// // first evolve chi a half step |
80 |
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|
81 |
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// chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
82 |
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// eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
83 |
– |
// (p_convert*NkBT*tb2)); |
84 |
– |
|
85 |
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// integralOfChidt += dt2* chi; |
86 |
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|
87 |
– |
// for( i=0; i<nAtoms; i++ ){ |
88 |
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// atoms[i]->getVel( vel ); |
89 |
– |
// atoms[i]->getPos( pos ); |
90 |
– |
// atoms[i]->getFrc( frc ); |
91 |
– |
|
92 |
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// mass = atoms[i]->getMass(); |
93 |
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|
94 |
– |
// for (j=0; j < 3; j++) { |
95 |
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// vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
96 |
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// rj[j] = pos[j]; |
97 |
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// } |
98 |
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|
99 |
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// atoms[i]->setVel( vel ); |
100 |
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|
101 |
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// info->wrapVector(rj); |
102 |
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|
103 |
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// for (j = 0; j < 3; j++) |
104 |
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// pos[j] += dt * (vel[j] + eta*rj[j]); |
105 |
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|
106 |
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// atoms[i]->setPos( pos ); |
107 |
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|
108 |
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// if( atoms[i]->isDirectional() ){ |
109 |
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|
110 |
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// dAtom = (DirectionalAtom *)atoms[i]; |
111 |
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|
112 |
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// // get and convert the torque to body frame |
113 |
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|
114 |
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// dAtom->getTrq( Tb ); |
115 |
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// dAtom->lab2Body( Tb ); |
116 |
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|
117 |
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// // get the angular momentum, and propagate a half step |
118 |
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|
119 |
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// dAtom->getJ( ji ); |
120 |
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|
121 |
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// for (j=0; j < 3; j++) |
122 |
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// ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
123 |
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|
124 |
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// // use the angular velocities to propagate the rotation matrix a |
125 |
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// // full time step |
126 |
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|
127 |
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// dAtom->getA(A); |
128 |
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// dAtom->getI(I); |
129 |
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|
130 |
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// // rotate about the x-axis |
131 |
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// angle = dt2 * ji[0] / I[0][0]; |
132 |
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// this->rotate( 1, 2, angle, ji, A ); |
133 |
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|
134 |
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// // rotate about the y-axis |
135 |
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// angle = dt2 * ji[1] / I[1][1]; |
136 |
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// this->rotate( 2, 0, angle, ji, A ); |
137 |
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|
138 |
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// // rotate about the z-axis |
139 |
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// angle = dt * ji[2] / I[2][2]; |
140 |
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// this->rotate( 0, 1, angle, ji, A); |
141 |
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|
142 |
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// // rotate about the y-axis |
143 |
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// angle = dt2 * ji[1] / I[1][1]; |
144 |
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// this->rotate( 2, 0, angle, ji, A ); |
145 |
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|
146 |
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// // rotate about the x-axis |
147 |
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// angle = dt2 * ji[0] / I[0][0]; |
148 |
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// this->rotate( 1, 2, angle, ji, A ); |
149 |
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|
150 |
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// dAtom->setJ( ji ); |
151 |
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// dAtom->setA( A ); |
152 |
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// } |
153 |
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|
154 |
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// } |
155 |
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|
156 |
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// // Scale the box after all the positions have been moved: |
157 |
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|
158 |
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// scaleFactor = exp(dt*eta); |
159 |
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|
160 |
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// if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
161 |
– |
// sprintf( painCave.errMsg, |
162 |
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// "NPTi error: Attempting a Box scaling of more than 10 percent" |
163 |
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// " check your tauBarostat, as it is probably too small!\n" |
164 |
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// " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
165 |
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// ); |
166 |
– |
// painCave.isFatal = 1; |
167 |
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// simError(); |
168 |
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// } else { |
169 |
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// info->scaleBox(exp(dt*eta)); |
170 |
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// } |
171 |
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|
58 |
|
|
59 |
|
//new version of NPTi |
60 |
|
int i, j, k; |
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)); |
206 |
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|
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; |
261 |
– |
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); |
169 |
|
atoms[i]->getPos(pos); |
170 |
|
|
171 |
|
for(j = 0; j < 3; j++) |
172 |
< |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
284 |
< |
|
172 |
> |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
173 |
|
|
286 |
– |
//wrapVector(r(t)) = r(t)-R0 |
287 |
– |
//info->wrapVector(rj); |
288 |
– |
|
174 |
|
for(j = 0; j < 3; j++) |
175 |
|
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
176 |
|
|
177 |
|
atoms[i]->setPos( pos ); |
293 |
– |
|
178 |
|
} |
179 |
< |
|
179 |
> |
|
180 |
> |
if (nConstrained){ |
181 |
> |
constrainA(); |
182 |
> |
} |
183 |
|
} |
184 |
|
|
185 |
|
|
199 |
|
info->scaleBox(scaleFactor); |
200 |
|
} |
201 |
|
|
315 |
– |
//advance volume; |
316 |
– |
volume = volume * exp(dt*eta); |
202 |
|
} |
203 |
|
|
204 |
|
template<typename T> void NPTi<T>::moveB( void ){ |
320 |
– |
|
321 |
– |
/* |
322 |
– |
int i, j; |
323 |
– |
DirectionalAtom* dAtom; |
324 |
– |
double Tb[3], ji[3]; |
325 |
– |
double vel[3], frc[3]; |
326 |
– |
double mass; |
327 |
– |
|
328 |
– |
double instaTemp, instaPress, instaVol; |
329 |
– |
double tt2, tb2; |
330 |
– |
|
331 |
– |
tt2 = tauThermostat * tauThermostat; |
332 |
– |
tb2 = tauBarostat * tauBarostat; |
333 |
– |
|
334 |
– |
instaTemp = tStats->getTemperature(); |
335 |
– |
instaPress = tStats->getPressure(); |
336 |
– |
instaVol = tStats->getVolume(); |
337 |
– |
|
338 |
– |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
339 |
– |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
340 |
– |
(p_convert*NkBT*tb2)); |
341 |
– |
integralOfChidt += dt2*chi; |
342 |
– |
|
343 |
– |
for( i=0; i<nAtoms; i++ ){ |
344 |
– |
|
345 |
– |
atoms[i]->getVel( vel ); |
346 |
– |
atoms[i]->getFrc( frc ); |
347 |
– |
|
348 |
– |
mass = atoms[i]->getMass(); |
349 |
– |
|
350 |
– |
// velocity half step |
351 |
– |
for (j=0; j < 3; j++) |
352 |
– |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
353 |
– |
|
354 |
– |
atoms[i]->setVel( vel ); |
355 |
– |
|
356 |
– |
if( atoms[i]->isDirectional() ){ |
357 |
– |
|
358 |
– |
dAtom = (DirectionalAtom *)atoms[i]; |
359 |
– |
|
360 |
– |
// get and convert the torque to body frame |
361 |
– |
|
362 |
– |
dAtom->getTrq( Tb ); |
363 |
– |
dAtom->lab2Body( Tb ); |
364 |
– |
|
365 |
– |
// get the angular momentum, and propagate a half step |
366 |
– |
|
367 |
– |
dAtom->getJ( ji ); |
368 |
– |
|
369 |
– |
for (j=0; j < 3; j++) |
370 |
– |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
371 |
– |
|
372 |
– |
dAtom->setJ( ji ); |
373 |
– |
} |
374 |
– |
} |
375 |
– |
|
376 |
– |
*/ |
205 |
|
|
206 |
|
//new version of NPTi |
207 |
|
int i, j, k; |
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; |
220 |
|
|
393 |
– |
|
221 |
|
// Set things up for the iteration: |
222 |
|
|
223 |
|
oldChi = chi; |
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) / |
431 |
< |
(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 |
|
|
292 |
|
dAtom->setJ( ji ); |
293 |
|
} |
294 |
|
} |
295 |
< |
|
296 |
< |
if (fabs(prevChi - chi) <= chiTolerance && fabs(preEta -eta) <= etaTolerance) |
295 |
> |
|
296 |
> |
if (nConstrained){ |
297 |
> |
constrainB(); |
298 |
> |
} |
299 |
> |
|
300 |
> |
if (fabs(prevChi - chi) <= |
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 |
|
|
474 |
– |
|
308 |
|
} |
309 |
|
|
310 |
|
template<typename T> void NPTi<T>::resetIntegrator() { |
372 |
|
simError(); |
373 |
|
} |
374 |
|
|
375 |
< |
if (!have_eta_tolerance) { |
375 |
> |
if (!have_eta_tolerance) { |
376 |
|
sprintf( painCave.errMsg, |
377 |
|
"NPTi warning: setting eta tolerance to 1e-6\n"); |
378 |
|
etaTolerance = 1e-6; |
380 |
|
painCave.isFatal = 0; |
381 |
|
simError(); |
382 |
|
} |
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 |
|
|
397 |
|
return 1; |
400 |
|
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
401 |
|
|
402 |
|
double conservedQuantity; |
403 |
< |
double tb2; |
404 |
< |
double eta2; |
405 |
< |
double E_NPT; |
406 |
< |
double U; |
407 |
< |
double TS; |
408 |
< |
double PV; |
409 |
< |
double extra; |
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; |
411 |
|
|
412 |
< |
static double pre_U; |
570 |
< |
static double pre_TS; |
571 |
< |
static double pre_PV; |
572 |
< |
static double pre_extra; |
573 |
< |
static int hackCount = 0; |
412 |
> |
Energy = tStats->getTotalE(); |
413 |
|
|
414 |
< |
double delta_U; |
415 |
< |
double delta_TS; |
577 |
< |
double delta_PV; |
578 |
< |
double delta_extra; |
414 |
> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
415 |
> |
(2.0 * eConvert); |
416 |
|
|
417 |
< |
U = tStats->getTotalE(); |
417 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
418 |
|
|
582 |
– |
TS = fkBT * |
583 |
– |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
419 |
|
|
420 |
< |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
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 |
< |
tb2 = tauBarostat * tauBarostat; |
427 |
< |
eta2 = eta * eta; |
428 |
< |
|
590 |
< |
extra = (fkBT * tb2 * eta2 / 2.0 ) / eConvert; |
591 |
< |
/* |
592 |
< |
if(hackCount == 0){ |
593 |
< |
pre_U = U; |
594 |
< |
pre_TS =TS; |
595 |
< |
pre_PV = PV; |
596 |
< |
pre_extra =extra; |
597 |
< |
hackCount ++; |
598 |
< |
} |
599 |
< |
|
600 |
< |
delta_U = U - pre_U; |
601 |
< |
delta_TS = TS - pre_TS; |
602 |
< |
delta_PV = PV - pre_PV; |
603 |
< |
delta_extra = extra - pre_extra; |
604 |
< |
*/ |
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" |
611 |
< |
<< eta << "\t" |
612 |
< |
<< U << "\t" |
613 |
< |
<< TS << "\t" |
614 |
< |
<< PV << "\t" |
615 |
< |
<< extra << "\t" |
616 |
< |
<< 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 |
|
|
618 |
– |
/* |
619 |
– |
pre_U = U; |
620 |
– |
pre_TS =TS; |
621 |
– |
pre_PV = PV; |
622 |
– |
pre_extra =extra; |
623 |
– |
|
624 |
– |
|
625 |
– |
cout << info->getTime() << "\t" |
626 |
– |
<< U << "\t" |
627 |
– |
<< U+TS << "\t" |
628 |
– |
<< U+TS+PV << "\t" |
629 |
– |
<< U+TS+PV+extra << endl; |
630 |
– |
*/ |
631 |
– |
conservedQuantity = U+TS+PV+extra; |
436 |
|
return conservedQuantity; |
437 |
|
} |