26 |
|
template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
27 |
|
T( theInfo, the_ff ) |
28 |
|
{ |
29 |
– |
chi = 0.0; |
29 |
|
eta = 0.0; |
30 |
< |
integralOfChidt = 0.0; |
32 |
< |
have_tau_thermostat = 0; |
33 |
< |
have_tau_barostat = 0; |
34 |
< |
have_target_temp = 0; |
35 |
< |
have_target_pressure = 0; |
36 |
< |
have_chi_tolerance = 0; |
37 |
< |
have_eta_tolerance = 0; |
38 |
< |
have_pos_iter_tolerance = 0; |
39 |
< |
|
40 |
< |
oldPos = new double[3*nAtoms]; |
41 |
< |
oldVel = new double[3*nAtoms]; |
42 |
< |
oldJi = new double[3*nAtoms]; |
43 |
< |
#ifdef IS_MPI |
44 |
< |
Nparticles = mpiSim->getTotAtoms(); |
45 |
< |
#else |
46 |
< |
Nparticles = theInfo->n_atoms; |
47 |
< |
#endif |
48 |
< |
|
30 |
> |
oldEta = 0.0; |
31 |
|
} |
32 |
|
|
33 |
|
template<typename T> NPTi<T>::~NPTi() { |
34 |
< |
delete[] oldPos; |
53 |
< |
delete[] oldVel; |
54 |
< |
delete[] oldJi; |
34 |
> |
//nothing for now |
35 |
|
} |
36 |
|
|
37 |
< |
template<typename T> void NPTi<T>::moveA() { |
38 |
< |
|
39 |
< |
//new version of NPTi |
40 |
< |
int i, j, k; |
61 |
< |
DirectionalAtom* dAtom; |
62 |
< |
double Tb[3], ji[3]; |
63 |
< |
double A[3][3], I[3][3]; |
64 |
< |
double angle, mass; |
65 |
< |
double vel[3], pos[3], frc[3]; |
37 |
> |
template<typename T> void NPTi<T>::resetIntegrator() { |
38 |
> |
eta = 0.0; |
39 |
> |
T::resetIntegrator(); |
40 |
> |
} |
41 |
|
|
42 |
< |
double rj[3]; |
43 |
< |
double instaTemp, instaPress, instaVol; |
44 |
< |
double tt2, tb2, scaleFactor; |
45 |
< |
double COM[3]; |
42 |
> |
template<typename T> void NPTi<T>::evolveEtaA() { |
43 |
> |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
44 |
> |
(p_convert*NkBT*tb2)); |
45 |
> |
oldEta = eta; |
46 |
> |
} |
47 |
|
|
48 |
< |
tt2 = tauThermostat * tauThermostat; |
73 |
< |
tb2 = tauBarostat * tauBarostat; |
74 |
< |
|
75 |
< |
instaTemp = tStats->getTemperature(); |
76 |
< |
instaPress = tStats->getPressure(); |
77 |
< |
instaVol = tStats->getVolume(); |
48 |
> |
template<typename T> void NPTi<T>::evolveEtaB() { |
49 |
|
|
50 |
< |
tStats->getCOM(COM); |
51 |
< |
|
52 |
< |
//evolve velocity half step |
53 |
< |
for( i=0; i<nAtoms; i++ ){ |
50 |
> |
prevEta = eta; |
51 |
> |
eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
52 |
> |
(p_convert*NkBT*tb2)); |
53 |
> |
} |
54 |
|
|
55 |
< |
atoms[i]->getVel( vel ); |
56 |
< |
atoms[i]->getFrc( frc ); |
55 |
> |
template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) { |
56 |
> |
int i; |
57 |
|
|
58 |
< |
mass = atoms[i]->getMass(); |
58 |
> |
for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta ); |
59 |
> |
} |
60 |
|
|
61 |
< |
for (j=0; j < 3; j++) { |
62 |
< |
// velocity half step |
91 |
< |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta)); |
92 |
< |
} |
61 |
> |
template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){ |
62 |
> |
int i; |
63 |
|
|
64 |
< |
atoms[i]->setVel( vel ); |
65 |
< |
|
96 |
< |
if( atoms[i]->isDirectional() ){ |
64 |
> |
for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta ); |
65 |
> |
} |
66 |
|
|
98 |
– |
dAtom = (DirectionalAtom *)atoms[i]; |
67 |
|
|
68 |
< |
// get and convert the torque to body frame |
69 |
< |
|
70 |
< |
dAtom->getTrq( Tb ); |
103 |
< |
dAtom->lab2Body( Tb ); |
104 |
< |
|
105 |
< |
// get the angular momentum, and propagate a half step |
68 |
> |
template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3], |
69 |
> |
int index, double sc[3]){ |
70 |
> |
int j; |
71 |
|
|
72 |
< |
dAtom->getJ( ji ); |
72 |
> |
for(j=0; j<3; j++) |
73 |
> |
sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
74 |
|
|
75 |
< |
for (j=0; j < 3; j++) |
76 |
< |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
77 |
< |
|
112 |
< |
// use the angular velocities to propagate the rotation matrix a |
113 |
< |
// full time step |
75 |
> |
for(j=0; j<3; j++) |
76 |
> |
sc[j] *= eta; |
77 |
> |
} |
78 |
|
|
79 |
< |
dAtom->getA(A); |
116 |
< |
dAtom->getI(I); |
117 |
< |
|
118 |
< |
// rotate about the x-axis |
119 |
< |
angle = dt2 * ji[0] / I[0][0]; |
120 |
< |
this->rotate( 1, 2, angle, ji, A ); |
79 |
> |
template<typename T> void NPTi<T>::scaleSimBox( void ){ |
80 |
|
|
81 |
< |
// rotate about the y-axis |
123 |
< |
angle = dt2 * ji[1] / I[1][1]; |
124 |
< |
this->rotate( 2, 0, angle, ji, A ); |
125 |
< |
|
126 |
< |
// rotate about the z-axis |
127 |
< |
angle = dt * ji[2] / I[2][2]; |
128 |
< |
this->rotate( 0, 1, angle, ji, A); |
129 |
< |
|
130 |
< |
// rotate about the y-axis |
131 |
< |
angle = dt2 * ji[1] / I[1][1]; |
132 |
< |
this->rotate( 2, 0, angle, ji, A ); |
133 |
< |
|
134 |
< |
// rotate about the x-axis |
135 |
< |
angle = dt2 * ji[0] / I[0][0]; |
136 |
< |
this->rotate( 1, 2, angle, ji, A ); |
137 |
< |
|
138 |
< |
dAtom->setJ( ji ); |
139 |
< |
dAtom->setA( A ); |
140 |
< |
} |
141 |
< |
} |
81 |
> |
double scaleFactor; |
82 |
|
|
143 |
– |
// advance chi half step |
144 |
– |
|
145 |
– |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
146 |
– |
|
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); |
158 |
– |
for(j = 0; j < 3; j++) |
159 |
– |
oldPos[i*3 + j] = pos[j]; |
160 |
– |
} |
161 |
– |
|
162 |
– |
//the first estimation of r(t+dt) is equal to r(t) |
163 |
– |
|
164 |
– |
for(k = 0; k < 4; k ++){ |
165 |
– |
|
166 |
– |
for(i =0 ; i < nAtoms; i++){ |
167 |
– |
|
168 |
– |
atoms[i]->getVel(vel); |
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]; |
173 |
– |
|
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 ); |
178 |
– |
} |
179 |
– |
|
180 |
– |
if (nConstrained){ |
181 |
– |
constrainA(); |
182 |
– |
} |
183 |
– |
} |
184 |
– |
|
185 |
– |
|
186 |
– |
// Scale the box after all the positions have been moved: |
187 |
– |
|
83 |
|
scaleFactor = exp(dt*eta); |
84 |
|
|
85 |
|
if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
96 |
|
|
97 |
|
} |
98 |
|
|
99 |
< |
template<typename T> void NPTi<T>::moveB( void ){ |
205 |
< |
|
206 |
< |
//new version of NPTi |
207 |
< |
int i, j, k; |
208 |
< |
DirectionalAtom* dAtom; |
209 |
< |
double Tb[3], ji[3]; |
210 |
< |
double vel[3], frc[3]; |
211 |
< |
double mass; |
212 |
< |
|
213 |
< |
double instaTemp, instaPress, instaVol; |
214 |
< |
double tt2, tb2; |
215 |
< |
double oldChi, prevChi; |
216 |
< |
double oldEta, prevEta; |
217 |
< |
|
218 |
< |
tt2 = tauThermostat * tauThermostat; |
219 |
< |
tb2 = tauBarostat * tauBarostat; |
220 |
< |
|
221 |
< |
// Set things up for the iteration: |
99 |
> |
template<typename T> bool NPTi<T>::etaConverged() { |
100 |
|
|
101 |
< |
oldChi = chi; |
224 |
< |
oldEta = eta; |
225 |
< |
|
226 |
< |
for( i=0; i<nAtoms; i++ ){ |
227 |
< |
|
228 |
< |
atoms[i]->getVel( vel ); |
229 |
< |
|
230 |
< |
for (j=0; j < 3; j++) |
231 |
< |
oldVel[3*i + j] = vel[j]; |
232 |
< |
|
233 |
< |
if( atoms[i]->isDirectional() ){ |
234 |
< |
|
235 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
236 |
< |
|
237 |
< |
dAtom->getJ( ji ); |
238 |
< |
|
239 |
< |
for (j=0; j < 3; j++) |
240 |
< |
oldJi[3*i + j] = ji[j]; |
241 |
< |
|
242 |
< |
} |
243 |
< |
} |
244 |
< |
|
245 |
< |
// do the iteration: |
246 |
< |
|
247 |
< |
instaVol = tStats->getVolume(); |
248 |
< |
|
249 |
< |
for (k=0; k < 4; k++) { |
250 |
< |
|
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 * ( instaTemp / targetTemp - 1.0) / tt2; |
258 |
< |
|
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 |
< |
|
267 |
< |
for( i=0; i<nAtoms; i++ ){ |
268 |
< |
|
269 |
< |
atoms[i]->getFrc( frc ); |
270 |
< |
atoms[i]->getVel(vel); |
271 |
< |
|
272 |
< |
mass = atoms[i]->getMass(); |
273 |
< |
|
274 |
< |
// velocity half step |
275 |
< |
for (j=0; j < 3; j++) |
276 |
< |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*(chi + eta)); |
277 |
< |
|
278 |
< |
atoms[i]->setVel( vel ); |
279 |
< |
|
280 |
< |
if( atoms[i]->isDirectional() ){ |
281 |
< |
|
282 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
283 |
< |
|
284 |
< |
// get and convert the torque to body frame |
285 |
< |
|
286 |
< |
dAtom->getTrq( Tb ); |
287 |
< |
dAtom->lab2Body( Tb ); |
288 |
< |
|
289 |
< |
for (j=0; j < 3; j++) |
290 |
< |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
291 |
< |
|
292 |
< |
dAtom->setJ( ji ); |
293 |
< |
} |
294 |
< |
} |
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 chidt |
306 |
< |
integralOfChidt += dt2*chi; |
307 |
< |
|
101 |
> |
return ( fabs(prevEta - eta) <= etaTolerance ); |
102 |
|
} |
103 |
|
|
310 |
– |
template<typename T> void NPTi<T>::resetIntegrator() { |
311 |
– |
chi = 0.0; |
312 |
– |
eta = 0.0; |
313 |
– |
} |
314 |
– |
|
315 |
– |
template<typename T> int NPTi<T>::readyCheck() { |
316 |
– |
|
317 |
– |
//check parent's readyCheck() first |
318 |
– |
if (T::readyCheck() == -1) |
319 |
– |
return -1; |
320 |
– |
|
321 |
– |
// First check to see if we have a target temperature. |
322 |
– |
// Not having one is fatal. |
323 |
– |
|
324 |
– |
if (!have_target_temp) { |
325 |
– |
sprintf( painCave.errMsg, |
326 |
– |
"NPTi error: You can't use the NPTi integrator\n" |
327 |
– |
" without a targetTemp!\n" |
328 |
– |
); |
329 |
– |
painCave.isFatal = 1; |
330 |
– |
simError(); |
331 |
– |
return -1; |
332 |
– |
} |
333 |
– |
|
334 |
– |
if (!have_target_pressure) { |
335 |
– |
sprintf( painCave.errMsg, |
336 |
– |
"NPTi error: You can't use the NPTi integrator\n" |
337 |
– |
" without a targetPressure!\n" |
338 |
– |
); |
339 |
– |
painCave.isFatal = 1; |
340 |
– |
simError(); |
341 |
– |
return -1; |
342 |
– |
} |
343 |
– |
|
344 |
– |
// We must set tauThermostat. |
345 |
– |
|
346 |
– |
if (!have_tau_thermostat) { |
347 |
– |
sprintf( painCave.errMsg, |
348 |
– |
"NPTi error: If you use the NPTi\n" |
349 |
– |
" integrator, you must set tauThermostat.\n"); |
350 |
– |
painCave.isFatal = 1; |
351 |
– |
simError(); |
352 |
– |
return -1; |
353 |
– |
} |
354 |
– |
|
355 |
– |
// We must set tauBarostat. |
356 |
– |
|
357 |
– |
if (!have_tau_barostat) { |
358 |
– |
sprintf( painCave.errMsg, |
359 |
– |
"NPTi error: If you use the NPTi\n" |
360 |
– |
" integrator, you must set tauBarostat.\n"); |
361 |
– |
painCave.isFatal = 1; |
362 |
– |
simError(); |
363 |
– |
return -1; |
364 |
– |
} |
365 |
– |
|
366 |
– |
if (!have_chi_tolerance) { |
367 |
– |
sprintf( painCave.errMsg, |
368 |
– |
"NPTi warning: setting chi tolerance to 1e-6\n"); |
369 |
– |
chiTolerance = 1e-6; |
370 |
– |
have_chi_tolerance = 1; |
371 |
– |
painCave.isFatal = 0; |
372 |
– |
simError(); |
373 |
– |
} |
374 |
– |
|
375 |
– |
if (!have_eta_tolerance) { |
376 |
– |
sprintf( painCave.errMsg, |
377 |
– |
"NPTi warning: setting eta tolerance to 1e-6\n"); |
378 |
– |
etaTolerance = 1e-6; |
379 |
– |
have_eta_tolerance = 1; |
380 |
– |
painCave.isFatal = 0; |
381 |
– |
simError(); |
382 |
– |
} |
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; |
398 |
– |
} |
399 |
– |
|
104 |
|
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
105 |
|
|
106 |
|
double conservedQuantity; |
130 |
|
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
131 |
|
barostat_kinetic + barostat_potential; |
132 |
|
|
133 |
< |
cout.width(8); |
134 |
< |
cout.precision(8); |
133 |
> |
// cout.width(8); |
134 |
> |
// cout.precision(8); |
135 |
|
|
136 |
< |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
137 |
< |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
138 |
< |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
435 |
< |
|
136 |
> |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
137 |
> |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
138 |
> |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
139 |
|
return conservedQuantity; |
140 |
|
} |