26 |
|
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
27 |
|
T( theInfo, the_ff ) |
28 |
|
{ |
29 |
< |
int i, j; |
30 |
< |
chi = 0.0; |
31 |
< |
integralOfChidt = 0.0; |
32 |
< |
|
33 |
< |
for(i = 0; i < 3; i++) |
34 |
< |
for (j = 0; j < 3; j++) |
29 |
> |
|
30 |
> |
int i,j; |
31 |
> |
|
32 |
> |
for(i = 0; i < 3; i++){ |
33 |
> |
for (j = 0; j < 3; j++){ |
34 |
> |
|
35 |
|
eta[i][j] = 0.0; |
36 |
+ |
oldEta[i][j] = 0.0; |
37 |
+ |
} |
38 |
+ |
} |
39 |
+ |
} |
40 |
|
|
41 |
< |
have_tau_thermostat = 0; |
38 |
< |
have_tau_barostat = 0; |
39 |
< |
have_target_temp = 0; |
40 |
< |
have_target_pressure = 0; |
41 |
> |
template<typename T> NPTf<T>::~NPTf() { |
42 |
|
|
43 |
< |
have_chi_tolerance = 0; |
44 |
< |
have_eta_tolerance = 0; |
44 |
< |
have_pos_iter_tolerance = 0; |
43 |
> |
// empty for now |
44 |
> |
} |
45 |
|
|
46 |
< |
oldPos = new double[3*nAtoms]; |
47 |
< |
oldVel = new double[3*nAtoms]; |
48 |
< |
oldJi = new double[3*nAtoms]; |
49 |
< |
#ifdef IS_MPI |
50 |
< |
Nparticles = mpiSim->getTotAtoms(); |
51 |
< |
#else |
52 |
< |
Nparticles = theInfo->n_atoms; |
53 |
< |
#endif |
54 |
< |
|
46 |
> |
template<typename T> void NPTf<T>::resetIntegrator() { |
47 |
> |
|
48 |
> |
int i, j; |
49 |
> |
|
50 |
> |
for(i = 0; i < 3; i++) |
51 |
> |
for (j = 0; j < 3; j++) |
52 |
> |
eta[i][j] = 0.0; |
53 |
> |
|
54 |
> |
T::resetIntegrator(); |
55 |
|
} |
56 |
|
|
57 |
< |
template<typename T> NPTf<T>::~NPTf() { |
58 |
< |
delete[] oldPos; |
59 |
< |
delete[] oldVel; |
60 |
< |
delete[] oldJi; |
57 |
> |
template<typename T> void NPTf<T>::evolveEtaA() { |
58 |
> |
|
59 |
> |
int i, j; |
60 |
> |
|
61 |
> |
for(i = 0; i < 3; i ++){ |
62 |
> |
for(j = 0; j < 3; j++){ |
63 |
> |
if( i == j) |
64 |
> |
eta[i][j] += dt2 * instaVol * |
65 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
66 |
> |
else |
67 |
> |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
68 |
> |
} |
69 |
> |
} |
70 |
> |
|
71 |
> |
for(i = 0; i < 3; i++) |
72 |
> |
for (j = 0; j < 3; j++) |
73 |
> |
oldEta[i][j] = eta[i][j]; |
74 |
|
} |
75 |
|
|
76 |
< |
template<typename T> void NPTf<T>::moveA() { |
76 |
> |
template<typename T> void NPTf<T>::evolveEtaB() { |
77 |
> |
|
78 |
> |
int i,j; |
79 |
|
|
80 |
< |
// new version of NPTf |
81 |
< |
int i, j, k; |
82 |
< |
DirectionalAtom* dAtom; |
68 |
< |
double Tb[3], ji[3]; |
80 |
> |
for(i = 0; i < 3; i++) |
81 |
> |
for (j = 0; j < 3; j++) |
82 |
> |
prevEta[i][j] = eta[i][j]; |
83 |
|
|
84 |
< |
double mass; |
85 |
< |
double vel[3], pos[3], frc[3]; |
84 |
> |
for(i = 0; i < 3; i ++){ |
85 |
> |
for(j = 0; j < 3; j++){ |
86 |
> |
if( i == j) { |
87 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
88 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
89 |
> |
} else { |
90 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
91 |
> |
} |
92 |
> |
} |
93 |
> |
} |
94 |
> |
} |
95 |
|
|
96 |
< |
double rj[3]; |
97 |
< |
double instaTemp, instaPress, instaVol; |
98 |
< |
double tt2, tb2; |
76 |
< |
double sc[3]; |
77 |
< |
double eta2ij; |
78 |
< |
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
79 |
< |
double bigScale, smallScale, offDiagMax; |
80 |
< |
double COM[3]; |
96 |
> |
template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
97 |
> |
int i,j; |
98 |
> |
double vScale[3][3]; |
99 |
|
|
82 |
– |
tt2 = tauThermostat * tauThermostat; |
83 |
– |
tb2 = tauBarostat * tauBarostat; |
84 |
– |
|
85 |
– |
instaTemp = tStats->getTemperature(); |
86 |
– |
tStats->getPressureTensor(press); |
87 |
– |
instaVol = tStats->getVolume(); |
88 |
– |
|
89 |
– |
tStats->getCOM(COM); |
90 |
– |
|
91 |
– |
//calculate scale factor of veloity |
100 |
|
for (i = 0; i < 3; i++ ) { |
101 |
|
for (j = 0; j < 3; j++ ) { |
102 |
|
vScale[i][j] = eta[i][j]; |
107 |
|
} |
108 |
|
} |
109 |
|
|
110 |
< |
//evolve velocity half step |
111 |
< |
for( i=0; i<nAtoms; i++ ){ |
110 |
> |
info->matVecMul3( vScale, vel, sc ); |
111 |
> |
} |
112 |
|
|
113 |
< |
atoms[i]->getVel( vel ); |
114 |
< |
atoms[i]->getFrc( frc ); |
113 |
> |
template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
114 |
> |
int i,j; |
115 |
> |
double myVel[3]; |
116 |
> |
double vScale[3][3]; |
117 |
|
|
118 |
< |
mass = atoms[i]->getMass(); |
119 |
< |
|
120 |
< |
info->matVecMul3( vScale, vel, sc ); |
111 |
< |
|
112 |
< |
for (j=0; j < 3; j++) { |
113 |
< |
// velocity half step |
114 |
< |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
115 |
< |
} |
116 |
< |
|
117 |
< |
atoms[i]->setVel( vel ); |
118 |
< |
|
119 |
< |
if( atoms[i]->isDirectional() ){ |
120 |
< |
|
121 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
122 |
< |
|
123 |
< |
// get and convert the torque to body frame |
118 |
> |
for (i = 0; i < 3; i++ ) { |
119 |
> |
for (j = 0; j < 3; j++ ) { |
120 |
> |
vScale[i][j] = eta[i][j]; |
121 |
|
|
122 |
< |
dAtom->getTrq( Tb ); |
123 |
< |
dAtom->lab2Body( Tb ); |
124 |
< |
|
128 |
< |
// get the angular momentum, and propagate a half step |
129 |
< |
|
130 |
< |
dAtom->getJ( ji ); |
131 |
< |
|
132 |
< |
for (j=0; j < 3; j++) |
133 |
< |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
134 |
< |
|
135 |
< |
this->rotationPropagation( dAtom, ji ); |
136 |
< |
|
137 |
< |
dAtom->setJ( ji ); |
138 |
< |
} |
139 |
< |
} |
140 |
< |
|
141 |
< |
// advance chi half step |
142 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
143 |
< |
|
144 |
< |
// calculate the integral of chidt |
145 |
< |
integralOfChidt += dt2*chi; |
146 |
< |
|
147 |
< |
// advance eta half step |
148 |
< |
|
149 |
< |
for(i = 0; i < 3; i ++) |
150 |
< |
for(j = 0; j < 3; j++){ |
151 |
< |
if( i == j) |
152 |
< |
eta[i][j] += dt2 * instaVol * |
153 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
154 |
< |
else |
155 |
< |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
122 |
> |
if (i == j) { |
123 |
> |
vScale[i][j] += chi; |
124 |
> |
} |
125 |
|
} |
157 |
– |
|
158 |
– |
//save the old positions |
159 |
– |
for(i = 0; i < nAtoms; i++){ |
160 |
– |
atoms[i]->getPos(pos); |
161 |
– |
for(j = 0; j < 3; j++) |
162 |
– |
oldPos[i*3 + j] = pos[j]; |
126 |
|
} |
127 |
|
|
128 |
< |
//the first estimation of r(t+dt) is equal to r(t) |
129 |
< |
|
167 |
< |
for(k = 0; k < 4; k ++){ |
128 |
> |
for (j = 0; j < 3; j++) |
129 |
> |
myVel[j] = oldVel[3*index + j]; |
130 |
|
|
131 |
< |
for(i =0 ; i < nAtoms; i++){ |
131 |
> |
info->matVecMul3( vScale, myVel, sc ); |
132 |
> |
} |
133 |
|
|
134 |
< |
atoms[i]->getVel(vel); |
135 |
< |
atoms[i]->getPos(pos); |
134 |
> |
template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
135 |
> |
int index, double sc[3]){ |
136 |
> |
int j; |
137 |
> |
double rj[3]; |
138 |
|
|
139 |
< |
for(j = 0; j < 3; j++) |
140 |
< |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
176 |
< |
|
177 |
< |
info->matVecMul3( eta, rj, sc ); |
178 |
< |
|
179 |
< |
for(j = 0; j < 3; j++) |
180 |
< |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
139 |
> |
for(j=0; j<3; j++) |
140 |
> |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
141 |
|
|
142 |
< |
atoms[i]->setPos( pos ); |
142 |
> |
info->matVecMul3( eta, rj, sc ); |
143 |
> |
} |
144 |
|
|
145 |
< |
} |
145 |
> |
template<typename T> void NPTf<T>::scaleSimBox( void ){ |
146 |
|
|
147 |
< |
if (nConstrained) { |
148 |
< |
constrainA(); |
149 |
< |
} |
150 |
< |
} |
147 |
> |
int i,j,k; |
148 |
> |
double scaleMat[3][3]; |
149 |
> |
double eta2ij; |
150 |
> |
double bigScale, smallScale, offDiagMax; |
151 |
> |
double hm[3][3], hmnew[3][3]; |
152 |
> |
|
153 |
|
|
154 |
< |
|
154 |
> |
|
155 |
|
// Scale the box after all the positions have been moved: |
156 |
|
|
157 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
216 |
|
info->matMul3(hm, scaleMat, hmnew); |
217 |
|
info->setBoxM(hmnew); |
218 |
|
} |
256 |
– |
|
219 |
|
} |
220 |
|
|
221 |
< |
template<typename T> void NPTf<T>::moveB( void ){ |
222 |
< |
|
223 |
< |
//new version of NPTf |
262 |
< |
int i, j, k; |
263 |
< |
DirectionalAtom* dAtom; |
264 |
< |
double Tb[3], ji[3]; |
265 |
< |
double vel[3], myVel[3], frc[3]; |
266 |
< |
double mass; |
221 |
> |
template<typename T> bool NPTf<T>::etaConverged() { |
222 |
> |
int i; |
223 |
> |
double diffEta, sumEta; |
224 |
|
|
225 |
< |
double instaTemp, instaPress, instaVol; |
269 |
< |
double tt2, tb2; |
270 |
< |
double sc[3]; |
271 |
< |
double press[3][3], vScale[3][3]; |
272 |
< |
double oldChi, prevChi; |
273 |
< |
double oldEta[3][3], prevEta[3][3], diffEta; |
274 |
< |
|
275 |
< |
tt2 = tauThermostat * tauThermostat; |
276 |
< |
tb2 = tauBarostat * tauBarostat; |
277 |
< |
|
278 |
< |
// Set things up for the iteration: |
279 |
< |
|
280 |
< |
oldChi = chi; |
281 |
< |
|
225 |
> |
sumEta = 0; |
226 |
|
for(i = 0; i < 3; i++) |
227 |
< |
for(j = 0; j < 3; j++) |
284 |
< |
oldEta[i][j] = eta[i][j]; |
285 |
< |
|
286 |
< |
for( i=0; i<nAtoms; i++ ){ |
287 |
< |
|
288 |
< |
atoms[i]->getVel( vel ); |
289 |
< |
|
290 |
< |
for (j=0; j < 3; j++) |
291 |
< |
oldVel[3*i + j] = vel[j]; |
292 |
< |
|
293 |
< |
if( atoms[i]->isDirectional() ){ |
294 |
< |
|
295 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
296 |
< |
|
297 |
< |
dAtom->getJ( ji ); |
298 |
< |
|
299 |
< |
for (j=0; j < 3; j++) |
300 |
< |
oldJi[3*i + j] = ji[j]; |
301 |
< |
|
302 |
< |
} |
303 |
< |
} |
304 |
< |
|
305 |
< |
// do the iteration: |
306 |
< |
|
307 |
< |
instaVol = tStats->getVolume(); |
227 |
> |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
228 |
|
|
229 |
< |
for (k=0; k < 4; k++) { |
310 |
< |
|
311 |
< |
instaTemp = tStats->getTemperature(); |
312 |
< |
tStats->getPressureTensor(press); |
313 |
< |
|
314 |
< |
// evolve chi another half step using the temperature at t + dt/2 |
315 |
< |
|
316 |
< |
prevChi = chi; |
317 |
< |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
318 |
< |
|
319 |
< |
for(i = 0; i < 3; i++) |
320 |
< |
for(j = 0; j < 3; j++) |
321 |
< |
prevEta[i][j] = eta[i][j]; |
322 |
< |
|
323 |
< |
//advance eta half step and calculate scale factor for velocity |
324 |
< |
|
325 |
< |
for(i = 0; i < 3; i ++) |
326 |
< |
for(j = 0; j < 3; j++){ |
327 |
< |
if( i == j) { |
328 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
329 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
330 |
< |
vScale[i][j] = eta[i][j] + chi; |
331 |
< |
} else { |
332 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
333 |
< |
vScale[i][j] = eta[i][j]; |
334 |
< |
} |
335 |
< |
} |
336 |
< |
|
337 |
< |
for( i=0; i<nAtoms; i++ ){ |
338 |
< |
|
339 |
< |
atoms[i]->getFrc( frc ); |
340 |
< |
atoms[i]->getVel(vel); |
341 |
< |
|
342 |
< |
mass = atoms[i]->getMass(); |
343 |
< |
|
344 |
< |
for (j = 0; j < 3; j++) |
345 |
< |
myVel[j] = oldVel[3*i + j]; |
346 |
< |
|
347 |
< |
info->matVecMul3( vScale, myVel, sc ); |
348 |
< |
|
349 |
< |
// velocity half step |
350 |
< |
for (j=0; j < 3; j++) { |
351 |
< |
// velocity half step (use chi from previous step here): |
352 |
< |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
353 |
< |
} |
354 |
< |
|
355 |
< |
atoms[i]->setVel( vel ); |
356 |
< |
|
357 |
< |
if( atoms[i]->isDirectional() ){ |
358 |
< |
|
359 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
229 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
230 |
|
|
231 |
< |
// get and convert the torque to body frame |
362 |
< |
|
363 |
< |
dAtom->getTrq( Tb ); |
364 |
< |
dAtom->lab2Body( Tb ); |
365 |
< |
|
366 |
< |
for (j=0; j < 3; j++) |
367 |
< |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
368 |
< |
|
369 |
< |
dAtom->setJ( ji ); |
370 |
< |
} |
371 |
< |
} |
372 |
< |
|
373 |
< |
if (nConstrained) { |
374 |
< |
constrainB(); |
375 |
< |
} |
376 |
< |
|
377 |
< |
diffEta = 0; |
378 |
< |
for(i = 0; i < 3; i++) |
379 |
< |
diffEta += pow(prevEta[i][i] - eta[i][i], 2); |
380 |
< |
|
381 |
< |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
382 |
< |
break; |
383 |
< |
} |
384 |
< |
|
385 |
< |
//calculate integral of chidt |
386 |
< |
integralOfChidt += dt2*chi; |
387 |
< |
|
231 |
> |
return ( diffEta <= etaTolerance ); |
232 |
|
} |
233 |
|
|
390 |
– |
template<typename T> void NPTf<T>::resetIntegrator() { |
391 |
– |
int i,j; |
392 |
– |
|
393 |
– |
chi = 0.0; |
394 |
– |
|
395 |
– |
for(i = 0; i < 3; i++) |
396 |
– |
for (j = 0; j < 3; j++) |
397 |
– |
eta[i][j] = 0.0; |
398 |
– |
|
399 |
– |
} |
400 |
– |
|
401 |
– |
template<typename T> int NPTf<T>::readyCheck() { |
402 |
– |
|
403 |
– |
//check parent's readyCheck() first |
404 |
– |
if (T::readyCheck() == -1) |
405 |
– |
return -1; |
406 |
– |
|
407 |
– |
// First check to see if we have a target temperature. |
408 |
– |
// Not having one is fatal. |
409 |
– |
|
410 |
– |
if (!have_target_temp) { |
411 |
– |
sprintf( painCave.errMsg, |
412 |
– |
"NPTf error: You can't use the NPTf integrator\n" |
413 |
– |
" without a targetTemp!\n" |
414 |
– |
); |
415 |
– |
painCave.isFatal = 1; |
416 |
– |
simError(); |
417 |
– |
return -1; |
418 |
– |
} |
419 |
– |
|
420 |
– |
if (!have_target_pressure) { |
421 |
– |
sprintf( painCave.errMsg, |
422 |
– |
"NPTf error: You can't use the NPTf integrator\n" |
423 |
– |
" without a targetPressure!\n" |
424 |
– |
); |
425 |
– |
painCave.isFatal = 1; |
426 |
– |
simError(); |
427 |
– |
return -1; |
428 |
– |
} |
429 |
– |
|
430 |
– |
// We must set tauThermostat. |
431 |
– |
|
432 |
– |
if (!have_tau_thermostat) { |
433 |
– |
sprintf( painCave.errMsg, |
434 |
– |
"NPTf error: If you use the NPTf\n" |
435 |
– |
" integrator, you must set tauThermostat.\n"); |
436 |
– |
painCave.isFatal = 1; |
437 |
– |
simError(); |
438 |
– |
return -1; |
439 |
– |
} |
440 |
– |
|
441 |
– |
// We must set tauBarostat. |
442 |
– |
|
443 |
– |
if (!have_tau_barostat) { |
444 |
– |
sprintf( painCave.errMsg, |
445 |
– |
"NPTf error: If you use the NPTf\n" |
446 |
– |
" integrator, you must set tauBarostat.\n"); |
447 |
– |
painCave.isFatal = 1; |
448 |
– |
simError(); |
449 |
– |
return -1; |
450 |
– |
} |
451 |
– |
|
452 |
– |
|
453 |
– |
// We need NkBT a lot, so just set it here: This is the RAW number |
454 |
– |
// of particles, so no subtraction or addition of constraints or |
455 |
– |
// orientational degrees of freedom: |
456 |
– |
|
457 |
– |
NkBT = (double)Nparticles * kB * targetTemp; |
458 |
– |
|
459 |
– |
// fkBT is used because the thermostat operates on more degrees of freedom |
460 |
– |
// than the barostat (when there are particles with orientational degrees |
461 |
– |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
462 |
– |
|
463 |
– |
fkBT = (double)info->ndf * kB * targetTemp; |
464 |
– |
|
465 |
– |
return 1; |
466 |
– |
} |
467 |
– |
|
234 |
|
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
235 |
< |
|
235 |
> |
|
236 |
|
double conservedQuantity; |
237 |
|
double Energy; |
238 |
|
double thermostat_kinetic; |
244 |
|
|
245 |
|
Energy = tStats->getTotalE(); |
246 |
|
|
247 |
< |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
247 |
> |
thermostat_kinetic = fkBT* tt2 * chi * chi / |
248 |
|
(2.0 * eConvert); |
249 |
|
|
250 |
|
thermostat_potential = fkBT* integralOfChidt / eConvert; |
253 |
|
info->matMul3(a, eta, b); |
254 |
|
trEta = info->matTrace3(b); |
255 |
|
|
256 |
< |
barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / |
256 |
> |
barostat_kinetic = NkBT * tb2 * trEta / |
257 |
|
(2.0 * eConvert); |
258 |
|
|
259 |
|
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
262 |
|
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
263 |
|
barostat_kinetic + barostat_potential; |
264 |
|
|
265 |
< |
cout.width(8); |
266 |
< |
cout.precision(8); |
265 |
> |
// cout.width(8); |
266 |
> |
// cout.precision(8); |
267 |
|
|
268 |
< |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
269 |
< |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
270 |
< |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
268 |
> |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
269 |
> |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
270 |
> |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
271 |
|
|
272 |
|
return conservedQuantity; |
273 |
+ |
|
274 |
|
} |