56 |
|
} |
57 |
|
|
58 |
|
template<typename T> void NPTi<T>::moveA() { |
59 |
– |
|
60 |
– |
|
61 |
– |
// int i, j; |
62 |
– |
// DirectionalAtom* dAtom; |
63 |
– |
// double Tb[3], ji[3]; |
64 |
– |
// double A[3][3], I[3][3]; |
65 |
– |
// double angle, mass; |
66 |
– |
// double vel[3], pos[3], frc[3]; |
67 |
– |
|
68 |
– |
// double rj[3]; |
69 |
– |
// double instaTemp, instaPress, instaVol; |
70 |
– |
// double tt2, tb2, scaleFactor; |
71 |
– |
|
72 |
– |
// tt2 = tauThermostat * tauThermostat; |
73 |
– |
// tb2 = tauBarostat * tauBarostat; |
74 |
– |
|
75 |
– |
// instaTemp = tStats->getTemperature(); |
76 |
– |
// instaPress = tStats->getPressure(); |
77 |
– |
// instaVol = tStats->getVolume(); |
78 |
– |
|
79 |
– |
// // first evolve chi a half step |
80 |
– |
|
81 |
– |
// chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
82 |
– |
// eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
83 |
– |
// (p_convert*NkBT*tb2)); |
84 |
– |
|
85 |
– |
// integralOfChidt += dt2* chi; |
86 |
– |
|
87 |
– |
// for( i=0; i<nAtoms; i++ ){ |
88 |
– |
// atoms[i]->getVel( vel ); |
89 |
– |
// atoms[i]->getPos( pos ); |
90 |
– |
// atoms[i]->getFrc( frc ); |
91 |
– |
|
92 |
– |
// mass = atoms[i]->getMass(); |
93 |
– |
|
94 |
– |
// for (j=0; j < 3; j++) { |
95 |
– |
// vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
96 |
– |
// rj[j] = pos[j]; |
97 |
– |
// } |
98 |
– |
|
99 |
– |
// atoms[i]->setVel( vel ); |
100 |
– |
|
101 |
– |
// info->wrapVector(rj); |
102 |
– |
|
103 |
– |
// for (j = 0; j < 3; j++) |
104 |
– |
// pos[j] += dt * (vel[j] + eta*rj[j]); |
105 |
– |
|
106 |
– |
// atoms[i]->setPos( pos ); |
107 |
– |
|
108 |
– |
// if( atoms[i]->isDirectional() ){ |
109 |
– |
|
110 |
– |
// dAtom = (DirectionalAtom *)atoms[i]; |
111 |
– |
|
112 |
– |
// // get and convert the torque to body frame |
113 |
– |
|
114 |
– |
// dAtom->getTrq( Tb ); |
115 |
– |
// dAtom->lab2Body( Tb ); |
116 |
– |
|
117 |
– |
// // get the angular momentum, and propagate a half step |
118 |
– |
|
119 |
– |
// dAtom->getJ( ji ); |
120 |
– |
|
121 |
– |
// for (j=0; j < 3; j++) |
122 |
– |
// ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
123 |
– |
|
124 |
– |
// // use the angular velocities to propagate the rotation matrix a |
125 |
– |
// // full time step |
126 |
– |
|
127 |
– |
// dAtom->getA(A); |
128 |
– |
// dAtom->getI(I); |
129 |
– |
|
130 |
– |
// // rotate about the x-axis |
131 |
– |
// angle = dt2 * ji[0] / I[0][0]; |
132 |
– |
// this->rotate( 1, 2, angle, ji, A ); |
133 |
– |
|
134 |
– |
// // rotate about the y-axis |
135 |
– |
// angle = dt2 * ji[1] / I[1][1]; |
136 |
– |
// this->rotate( 2, 0, angle, ji, A ); |
137 |
– |
|
138 |
– |
// // rotate about the z-axis |
139 |
– |
// angle = dt * ji[2] / I[2][2]; |
140 |
– |
// this->rotate( 0, 1, angle, ji, A); |
141 |
– |
|
142 |
– |
// // rotate about the y-axis |
143 |
– |
// angle = dt2 * ji[1] / I[1][1]; |
144 |
– |
// this->rotate( 2, 0, angle, ji, A ); |
145 |
– |
|
146 |
– |
// // rotate about the x-axis |
147 |
– |
// angle = dt2 * ji[0] / I[0][0]; |
148 |
– |
// this->rotate( 1, 2, angle, ji, A ); |
149 |
– |
|
150 |
– |
// dAtom->setJ( ji ); |
151 |
– |
// dAtom->setA( A ); |
152 |
– |
// } |
153 |
– |
|
154 |
– |
// } |
155 |
– |
|
156 |
– |
// // Scale the box after all the positions have been moved: |
157 |
– |
|
158 |
– |
// scaleFactor = exp(dt*eta); |
159 |
– |
|
160 |
– |
// if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
161 |
– |
// sprintf( painCave.errMsg, |
162 |
– |
// "NPTi error: Attempting a Box scaling of more than 10 percent" |
163 |
– |
// " check your tauBarostat, as it is probably too small!\n" |
164 |
– |
// " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
165 |
– |
// ); |
166 |
– |
// painCave.isFatal = 1; |
167 |
– |
// simError(); |
168 |
– |
// } else { |
169 |
– |
// info->scaleBox(exp(dt*eta)); |
170 |
– |
// } |
171 |
– |
|
59 |
|
|
60 |
|
//new version of NPTi |
61 |
|
int i, j, k; |
167 |
|
atoms[i]->getPos(pos); |
168 |
|
|
169 |
|
for(j = 0; j < 3; j++) |
170 |
< |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
284 |
< |
|
170 |
> |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
171 |
|
|
286 |
– |
//wrapVector(r(t)) = r(t)-R0 |
287 |
– |
//info->wrapVector(rj); |
288 |
– |
|
172 |
|
for(j = 0; j < 3; j++) |
173 |
|
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
174 |
|
|
175 |
|
atoms[i]->setPos( pos ); |
293 |
– |
|
176 |
|
} |
177 |
< |
|
177 |
> |
|
178 |
> |
if (nConstrained){ |
179 |
> |
constrainA(); |
180 |
> |
} |
181 |
|
} |
182 |
|
|
183 |
|
|
197 |
|
info->scaleBox(scaleFactor); |
198 |
|
} |
199 |
|
|
315 |
– |
//advance volume; |
316 |
– |
volume = volume * exp(dt*eta); |
200 |
|
} |
201 |
|
|
202 |
|
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; |
203 |
|
|
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 |
– |
*/ |
377 |
– |
|
204 |
|
//new version of NPTi |
205 |
|
int i, j, k; |
206 |
|
DirectionalAtom* dAtom; |
216 |
|
tt2 = tauThermostat * tauThermostat; |
217 |
|
tb2 = tauBarostat * tauBarostat; |
218 |
|
|
393 |
– |
|
219 |
|
// Set things up for the iteration: |
220 |
|
|
221 |
|
oldChi = chi; |
288 |
|
dAtom->setJ( ji ); |
289 |
|
} |
290 |
|
} |
291 |
< |
|
292 |
< |
if (fabs(prevChi - chi) <= chiTolerance && fabs(preEta -eta) <= etaTolerance) |
291 |
> |
|
292 |
> |
if (nConstrained){ |
293 |
> |
constrainB(); |
294 |
> |
} |
295 |
> |
|
296 |
> |
if (fabs(prevChi - chi) <= |
297 |
> |
chiTolerance && fabs(preEta -eta) <= etaTolerance) |
298 |
|
break; |
299 |
|
} |
300 |
|
|
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 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; |
563 |
< |
double E_NPT; |
564 |
< |
double U; |
565 |
< |
double TS; |
566 |
< |
double PV; |
567 |
< |
double extra; |
568 |
< |
|
569 |
< |
static double pre_U; |
570 |
< |
static double pre_TS; |
571 |
< |
static double pre_PV; |
572 |
< |
static double pre_extra; |
573 |
< |
static int hackCount = 0; |
407 |
> |
double eta2; |
408 |
|
|
409 |
< |
double delta_U; |
576 |
< |
double delta_TS; |
577 |
< |
double delta_PV; |
578 |
< |
double delta_extra; |
409 |
> |
Energy = tStats->getTotalE(); |
410 |
|
|
411 |
< |
U = tStats->getTotalE(); |
411 |
> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
412 |
> |
(2.0 * eConvert); |
413 |
|
|
414 |
< |
TS = fkBT * |
583 |
< |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
414 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
415 |
|
|
585 |
– |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
416 |
|
|
417 |
< |
tb2 = tauBarostat * tauBarostat; |
418 |
< |
eta2 = 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) / |
421 |
> |
eConvert; |
422 |
|
|
423 |
< |
extra = (fkBT * tb2 * eta2 / 2.0 ) / eConvert; |
424 |
< |
/* |
425 |
< |
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 |
< |
*/ |
423 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
424 |
> |
barostat_kinetic + barostat_potential; |
425 |
> |
|
426 |
|
cout.width(8); |
427 |
|
cout.precision(8); |
428 |
|
|
429 |
< |
|
430 |
< |
cout << info->getTime() << "\t" |
431 |
< |
<< chi << "\t" |
611 |
< |
<< eta << "\t" |
612 |
< |
<< U << "\t" |
613 |
< |
<< TS << "\t" |
614 |
< |
<< PV << "\t" |
615 |
< |
<< extra << "\t" |
616 |
< |
<< U+TS+PV+extra << endl; |
429 |
> |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
430 |
> |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
431 |
> |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
432 |
|
|
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; |
433 |
|
return conservedQuantity; |
434 |
|
} |