20 |
|
// |
21 |
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
22 |
|
|
23 |
< |
NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
24 |
< |
Integrator( theInfo, the_ff ) |
23 |
> |
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
24 |
> |
T( theInfo, the_ff ) |
25 |
|
{ |
26 |
|
int i, j; |
27 |
|
chi = 0.0; |
28 |
+ |
integralOfChidt = 0.0; |
29 |
|
|
30 |
|
for(i = 0; i < 3; i++) |
31 |
|
for (j = 0; j < 3; j++) |
35 |
|
have_tau_barostat = 0; |
36 |
|
have_target_temp = 0; |
37 |
|
have_target_pressure = 0; |
38 |
+ |
|
39 |
+ |
have_chi_tolerance = 0; |
40 |
+ |
have_eta_tolerance = 0; |
41 |
+ |
have_pos_iter_tolerance = 0; |
42 |
+ |
|
43 |
+ |
oldPos = new double[3*nAtoms]; |
44 |
+ |
oldVel = new double[3*nAtoms]; |
45 |
+ |
oldJi = new double[3*nAtoms]; |
46 |
+ |
#ifdef IS_MPI |
47 |
+ |
Nparticles = mpiSim->getTotAtoms(); |
48 |
+ |
#else |
49 |
+ |
Nparticles = theInfo->n_atoms; |
50 |
+ |
#endif |
51 |
|
} |
52 |
|
|
53 |
< |
void NPTf::moveA() { |
53 |
> |
template<typename T> NPTf<T>::~NPTf() { |
54 |
> |
delete[] oldPos; |
55 |
> |
delete[] oldVel; |
56 |
> |
delete[] oldJi; |
57 |
> |
} |
58 |
> |
|
59 |
> |
template<typename T> void NPTf<T>::moveA() { |
60 |
|
|
61 |
|
int i, j, k; |
62 |
|
DirectionalAtom* dAtom; |
72 |
|
double eta2ij; |
73 |
|
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
74 |
|
double bigScale, smallScale, offDiagMax; |
75 |
+ |
double COM[3]; |
76 |
|
|
77 |
|
tt2 = tauThermostat * tauThermostat; |
78 |
|
tb2 = tauBarostat * tauBarostat; |
80 |
|
instaTemp = tStats->getTemperature(); |
81 |
|
tStats->getPressureTensor(press); |
82 |
|
instaVol = tStats->getVolume(); |
62 |
– |
|
63 |
– |
// first evolve chi a half step |
83 |
|
|
84 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
84 |
> |
tStats->getCOM(COM); |
85 |
|
|
86 |
+ |
//calculate scale factor of veloity |
87 |
|
for (i = 0; i < 3; i++ ) { |
88 |
|
for (j = 0; j < 3; j++ ) { |
89 |
+ |
vScale[i][j] = eta[i][j]; |
90 |
+ |
|
91 |
|
if (i == j) { |
92 |
< |
|
93 |
< |
eta[i][j] += dt2 * instaVol * |
72 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
73 |
< |
|
74 |
< |
vScale[i][j] = eta[i][j] + chi; |
75 |
< |
|
76 |
< |
} else { |
77 |
< |
|
78 |
< |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
79 |
< |
|
80 |
< |
vScale[i][j] = eta[i][j]; |
81 |
< |
|
82 |
< |
} |
92 |
> |
vScale[i][j] += chi; |
93 |
> |
} |
94 |
|
} |
95 |
|
} |
96 |
< |
|
96 |
> |
|
97 |
> |
//evolve velocity half step |
98 |
|
for( i=0; i<nAtoms; i++ ){ |
99 |
|
|
100 |
|
atoms[i]->getVel( vel ); |
89 |
– |
atoms[i]->getPos( pos ); |
101 |
|
atoms[i]->getFrc( frc ); |
102 |
|
|
103 |
|
mass = atoms[i]->getMass(); |
104 |
|
|
94 |
– |
// velocity half step |
95 |
– |
|
105 |
|
info->matVecMul3( vScale, vel, sc ); |
106 |
< |
|
107 |
< |
for (j = 0; j < 3; j++) { |
106 |
> |
|
107 |
> |
for (j=0; j < 3; j++) { |
108 |
> |
// velocity half step (use chi from previous step here): |
109 |
|
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
110 |
< |
rj[j] = pos[j]; |
110 |
> |
|
111 |
|
} |
112 |
|
|
113 |
|
atoms[i]->setVel( vel ); |
104 |
– |
|
105 |
– |
// position whole step |
106 |
– |
|
107 |
– |
info->wrapVector(rj); |
108 |
– |
|
109 |
– |
info->matVecMul3( eta, rj, sc ); |
110 |
– |
|
111 |
– |
for (j = 0; j < 3; j++ ) |
112 |
– |
pos[j] += dt * (vel[j] + sc[j]); |
113 |
– |
|
114 |
– |
atoms[i]->setPos( pos ); |
114 |
|
|
115 |
|
if( atoms[i]->isDirectional() ){ |
116 |
|
|
117 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
118 |
< |
|
118 |
> |
|
119 |
|
// get and convert the torque to body frame |
120 |
|
|
121 |
|
dAtom->getTrq( Tb ); |
156 |
|
|
157 |
|
dAtom->setJ( ji ); |
158 |
|
dAtom->setA( A ); |
159 |
< |
} |
159 |
> |
} |
160 |
|
} |
161 |
+ |
|
162 |
+ |
// advance chi half step |
163 |
+ |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
164 |
+ |
|
165 |
+ |
//calculate the integral of chidt |
166 |
+ |
integralOfChidt += dt2*chi; |
167 |
+ |
|
168 |
+ |
//advance eta half step |
169 |
+ |
for(i = 0; i < 3; i ++) |
170 |
+ |
for(j = 0; j < 3; j++){ |
171 |
+ |
if( i == j) |
172 |
+ |
eta[i][j] += dt2 * instaVol * |
173 |
+ |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
174 |
+ |
else |
175 |
+ |
eta[i][j] += dt2 * instaVol * press[i][j] / ( NkBT*tb2); |
176 |
+ |
} |
177 |
+ |
|
178 |
+ |
//save the old positions |
179 |
+ |
for(i = 0; i < nAtoms; i++){ |
180 |
+ |
atoms[i]->getPos(pos); |
181 |
+ |
for(j = 0; j < 3; j++) |
182 |
+ |
oldPos[i*3 + j] = pos[j]; |
183 |
+ |
} |
184 |
|
|
185 |
+ |
//the first estimation of r(t+dt) is equal to r(t) |
186 |
+ |
|
187 |
+ |
for(k = 0; k < 4; k ++){ |
188 |
+ |
|
189 |
+ |
for(i =0 ; i < nAtoms; i++){ |
190 |
+ |
|
191 |
+ |
atoms[i]->getVel(vel); |
192 |
+ |
atoms[i]->getPos(pos); |
193 |
+ |
|
194 |
+ |
for(j = 0; j < 3; j++) |
195 |
+ |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
196 |
+ |
|
197 |
+ |
info->matVecMul3( eta, rj, sc ); |
198 |
+ |
|
199 |
+ |
for(j = 0; j < 3; j++) |
200 |
+ |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
201 |
+ |
|
202 |
+ |
atoms[i]->setPos( pos ); |
203 |
+ |
|
204 |
+ |
} |
205 |
+ |
|
206 |
+ |
} |
207 |
+ |
|
208 |
+ |
|
209 |
|
// Scale the box after all the positions have been moved: |
210 |
|
|
211 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
235 |
|
if (i != j) |
236 |
|
if (fabs(scaleMat[i][j]) > offDiagMax) |
237 |
|
offDiagMax = fabs(scaleMat[i][j]); |
192 |
– |
|
238 |
|
} |
239 |
|
|
240 |
|
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
273 |
|
|
274 |
|
} |
275 |
|
|
276 |
< |
void NPTf::moveB( void ){ |
276 |
> |
template<typename T> void NPTf<T>::moveB( void ){ |
277 |
|
|
278 |
< |
int i, j; |
278 |
> |
int i, j, k; |
279 |
|
DirectionalAtom* dAtom; |
280 |
|
double Tb[3], ji[3]; |
281 |
|
double vel[3], frc[3]; |
285 |
|
double tt2, tb2; |
286 |
|
double sc[3]; |
287 |
|
double press[3][3], vScale[3][3]; |
288 |
+ |
double oldChi, prevChi; |
289 |
+ |
double oldEta[3][3], preEta[3][3], diffEta; |
290 |
|
|
291 |
|
tt2 = tauThermostat * tauThermostat; |
292 |
|
tb2 = tauBarostat * tauBarostat; |
293 |
|
|
247 |
– |
instaTemp = tStats->getTemperature(); |
248 |
– |
tStats->getPressureTensor(press); |
249 |
– |
instaVol = tStats->getVolume(); |
250 |
– |
|
251 |
– |
// first evolve chi a half step |
252 |
– |
|
253 |
– |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
254 |
– |
|
255 |
– |
for (i = 0; i < 3; i++ ) { |
256 |
– |
for (j = 0; j < 3; j++ ) { |
257 |
– |
if (i == j) { |
294 |
|
|
295 |
< |
eta[i][j] += dt2 * instaVol * |
260 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
295 |
> |
// Set things up for the iteration: |
296 |
|
|
297 |
< |
vScale[i][j] = eta[i][j] + chi; |
298 |
< |
|
299 |
< |
} else { |
300 |
< |
|
301 |
< |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
297 |
> |
oldChi = chi; |
298 |
> |
|
299 |
> |
for(i = 0; i < 3; i++) |
300 |
> |
for(j = 0; j < 3; j++) |
301 |
> |
oldEta[i][j] = eta[i][j]; |
302 |
|
|
268 |
– |
vScale[i][j] = eta[i][j]; |
269 |
– |
|
270 |
– |
} |
271 |
– |
} |
272 |
– |
} |
273 |
– |
|
303 |
|
for( i=0; i<nAtoms; i++ ){ |
304 |
|
|
305 |
|
atoms[i]->getVel( vel ); |
277 |
– |
atoms[i]->getFrc( frc ); |
306 |
|
|
307 |
< |
mass = atoms[i]->getMass(); |
308 |
< |
|
281 |
< |
// velocity half step |
282 |
< |
|
283 |
< |
info->matVecMul3( vScale, vel, sc ); |
284 |
< |
|
285 |
< |
for (j = 0; j < 3; j++) { |
286 |
< |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
287 |
< |
} |
307 |
> |
for (j=0; j < 3; j++) |
308 |
> |
oldVel[3*i + j] = vel[j]; |
309 |
|
|
289 |
– |
atoms[i]->setVel( vel ); |
290 |
– |
|
310 |
|
if( atoms[i]->isDirectional() ){ |
311 |
|
|
312 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
313 |
< |
|
314 |
< |
// get and convert the torque to body frame |
313 |
> |
|
314 |
> |
dAtom->getJ( ji ); |
315 |
> |
|
316 |
> |
for (j=0; j < 3; j++) |
317 |
> |
oldJi[3*i + j] = ji[j]; |
318 |
> |
|
319 |
> |
} |
320 |
> |
} |
321 |
> |
|
322 |
> |
// do the iteration: |
323 |
> |
|
324 |
> |
instaVol = tStats->getVolume(); |
325 |
> |
|
326 |
> |
for (k=0; k < 4; k++) { |
327 |
> |
|
328 |
> |
instaTemp = tStats->getTemperature(); |
329 |
> |
tStats->getPressureTensor(press); |
330 |
> |
|
331 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
332 |
> |
|
333 |
> |
prevChi = chi; |
334 |
> |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
335 |
> |
|
336 |
> |
for(i = 0; i < 3; i++) |
337 |
> |
for(j = 0; j < 3; j++) |
338 |
> |
preEta[i][j] = eta[i][j]; |
339 |
> |
|
340 |
> |
//advance eta half step and calculate scale factor for velocity |
341 |
> |
for(i = 0; i < 3; i ++) |
342 |
> |
for(j = 0; j < 3; j++){ |
343 |
> |
if( i == j){ |
344 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
345 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
346 |
> |
vScale[i][j] = eta[i][j] + chi; |
347 |
> |
} |
348 |
> |
else |
349 |
> |
{ |
350 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
351 |
> |
vScale[i][j] = eta[i][j]; |
352 |
> |
} |
353 |
> |
} |
354 |
> |
|
355 |
> |
//advance velocity half step |
356 |
> |
for( i=0; i<nAtoms; i++ ){ |
357 |
> |
|
358 |
> |
atoms[i]->getFrc( frc ); |
359 |
> |
atoms[i]->getVel(vel); |
360 |
|
|
361 |
< |
dAtom->getTrq( Tb ); |
298 |
< |
dAtom->lab2Body( Tb ); |
361 |
> |
mass = atoms[i]->getMass(); |
362 |
|
|
363 |
< |
// get the angular momentum, and propagate a half step |
363 |
> |
info->matVecMul3( vScale, vel, sc ); |
364 |
> |
|
365 |
> |
for (j=0; j < 3; j++) { |
366 |
> |
// velocity half step (use chi from previous step here): |
367 |
> |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
368 |
> |
} |
369 |
|
|
370 |
< |
dAtom->getJ( ji ); |
370 |
> |
atoms[i]->setVel( vel ); |
371 |
|
|
372 |
< |
for (j=0; j < 3; j++) |
373 |
< |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
372 |
> |
if( atoms[i]->isDirectional() ){ |
373 |
> |
|
374 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
375 |
> |
|
376 |
> |
// get and convert the torque to body frame |
377 |
> |
|
378 |
> |
dAtom->getTrq( Tb ); |
379 |
> |
dAtom->lab2Body( Tb ); |
380 |
> |
|
381 |
> |
for (j=0; j < 3; j++) |
382 |
> |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
383 |
|
|
384 |
< |
dAtom->setJ( ji ); |
384 |
> |
dAtom->setJ( ji ); |
385 |
> |
} |
386 |
> |
} |
387 |
|
|
388 |
< |
} |
388 |
> |
|
389 |
> |
diffEta = 0; |
390 |
> |
for(i = 0; i < 3; i++) |
391 |
> |
diffEta += pow(preEta[i][i] - eta[i][i], 2); |
392 |
> |
|
393 |
> |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
394 |
> |
break; |
395 |
|
} |
396 |
+ |
|
397 |
+ |
//calculate integral of chida |
398 |
+ |
integralOfChidt += dt2*chi; |
399 |
+ |
|
400 |
+ |
|
401 |
|
} |
402 |
|
|
403 |
< |
int NPTf::readyCheck() { |
403 |
> |
template<typename T> void NPTf<T>::resetIntegrator() { |
404 |
> |
int i,j; |
405 |
> |
|
406 |
> |
chi = 0.0; |
407 |
> |
|
408 |
> |
for(i = 0; i < 3; i++) |
409 |
> |
for (j = 0; j < 3; j++) |
410 |
> |
eta[i][j] = 0.0; |
411 |
> |
|
412 |
> |
} |
413 |
> |
|
414 |
> |
template<typename T> int NPTf<T>::readyCheck() { |
415 |
> |
|
416 |
> |
//check parent's readyCheck() first |
417 |
> |
if (T::readyCheck() == -1) |
418 |
> |
return -1; |
419 |
|
|
420 |
|
// First check to see if we have a target temperature. |
421 |
|
// Not having one is fatal. |
464 |
|
|
465 |
|
// We need NkBT a lot, so just set it here: |
466 |
|
|
467 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
467 |
> |
NkBT = (double)Nparticles * kB * targetTemp; |
468 |
> |
fkBT = (double)info->ndf * kB * targetTemp; |
469 |
|
|
470 |
|
return 1; |
471 |
|
} |
472 |
+ |
|
473 |
+ |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
474 |
+ |
|
475 |
+ |
double conservedQuantity; |
476 |
+ |
double tb2; |
477 |
+ |
double trEta; |
478 |
+ |
double U; |
479 |
+ |
double thermo; |
480 |
+ |
double integral; |
481 |
+ |
double baro; |
482 |
+ |
double PV; |
483 |
+ |
|
484 |
+ |
U = tStats->getTotalE(); |
485 |
+ |
thermo = (fkBT * tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
486 |
+ |
|
487 |
+ |
tb2 = tauBarostat * tauBarostat; |
488 |
+ |
trEta = info->matTrace3(eta); |
489 |
+ |
baro = ((double)info->ndfTrans * kB * targetTemp * tb2 * trEta * trEta / 2.0) / eConvert; |
490 |
+ |
|
491 |
+ |
integral = ((double)(info->ndf + 1) * kB * targetTemp * integralOfChidt) /eConvert; |
492 |
+ |
|
493 |
+ |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
494 |
+ |
|
495 |
+ |
|
496 |
+ |
cout.width(8); |
497 |
+ |
cout.precision(8); |
498 |
+ |
|
499 |
+ |
cout << info->getTime() << "\t" |
500 |
+ |
<< chi << "\t" |
501 |
+ |
<< trEta << "\t" |
502 |
+ |
<< U << "\t" |
503 |
+ |
<< thermo << "\t" |
504 |
+ |
<< baro << "\t" |
505 |
+ |
<< integral << "\t" |
506 |
+ |
<< PV << "\t" |
507 |
+ |
<< U+thermo+integral+PV+baro << endl; |
508 |
+ |
|
509 |
+ |
conservedQuantity = U+thermo+integral+PV+baro; |
510 |
+ |
return conservedQuantity; |
511 |
+ |
|
512 |
+ |
} |