1 |
gezelter |
617 |
#include <cmath> |
2 |
gezelter |
576 |
#include "Atom.hpp" |
3 |
|
|
#include "SRI.hpp" |
4 |
|
|
#include "AbstractClasses.hpp" |
5 |
|
|
#include "SimInfo.hpp" |
6 |
|
|
#include "ForceFields.hpp" |
7 |
|
|
#include "Thermo.hpp" |
8 |
|
|
#include "ReadWrite.hpp" |
9 |
|
|
#include "Integrator.hpp" |
10 |
|
|
#include "simError.h" |
11 |
|
|
|
12 |
|
|
|
13 |
gezelter |
578 |
// Basic non-isotropic thermostating and barostating via the Melchionna |
14 |
gezelter |
576 |
// modification of the Hoover algorithm: |
15 |
|
|
// |
16 |
|
|
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
17 |
|
|
// Molec. Phys., 78, 533. |
18 |
|
|
// |
19 |
|
|
// and |
20 |
|
|
// |
21 |
|
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
22 |
|
|
|
23 |
tim |
645 |
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
24 |
|
|
T( theInfo, the_ff ) |
25 |
gezelter |
576 |
{ |
26 |
gezelter |
588 |
int i, j; |
27 |
gezelter |
576 |
chi = 0.0; |
28 |
tim |
763 |
integralOfChidt = 0.0; |
29 |
gezelter |
588 |
|
30 |
|
|
for(i = 0; i < 3; i++) |
31 |
mmeineke |
590 |
for (j = 0; j < 3; j++) |
32 |
gezelter |
588 |
eta[i][j] = 0.0; |
33 |
|
|
|
34 |
gezelter |
576 |
have_tau_thermostat = 0; |
35 |
|
|
have_tau_barostat = 0; |
36 |
|
|
have_target_temp = 0; |
37 |
|
|
have_target_pressure = 0; |
38 |
tim |
767 |
|
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 |
gezelter |
576 |
} |
52 |
|
|
|
53 |
tim |
767 |
template<typename T> NPTf<T>::~NPTf() { |
54 |
|
|
delete[] oldPos; |
55 |
|
|
delete[] oldVel; |
56 |
|
|
delete[] oldJi; |
57 |
|
|
} |
58 |
|
|
|
59 |
tim |
645 |
template<typename T> void NPTf<T>::moveA() { |
60 |
gezelter |
576 |
|
61 |
gezelter |
600 |
int i, j, k; |
62 |
gezelter |
576 |
DirectionalAtom* dAtom; |
63 |
gezelter |
600 |
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; |
71 |
|
|
double sc[3]; |
72 |
|
|
double eta2ij; |
73 |
gezelter |
588 |
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
74 |
gezelter |
617 |
double bigScale, smallScale, offDiagMax; |
75 |
tim |
767 |
double COM[3]; |
76 |
gezelter |
576 |
|
77 |
|
|
tt2 = tauThermostat * tauThermostat; |
78 |
|
|
tb2 = tauBarostat * tauBarostat; |
79 |
|
|
|
80 |
|
|
instaTemp = tStats->getTemperature(); |
81 |
gezelter |
577 |
tStats->getPressureTensor(press); |
82 |
gezelter |
576 |
instaVol = tStats->getVolume(); |
83 |
|
|
|
84 |
tim |
767 |
tStats->getCOM(COM); |
85 |
gezelter |
588 |
|
86 |
tim |
767 |
//calculate scale factor of veloity |
87 |
gezelter |
588 |
for (i = 0; i < 3; i++ ) { |
88 |
|
|
for (j = 0; j < 3; j++ ) { |
89 |
tim |
767 |
vScale[i][j] = eta[i][j]; |
90 |
|
|
|
91 |
gezelter |
588 |
if (i == j) { |
92 |
tim |
767 |
vScale[i][j] += chi; |
93 |
|
|
} |
94 |
gezelter |
588 |
} |
95 |
|
|
} |
96 |
tim |
767 |
|
97 |
|
|
//evolve velocity half step |
98 |
gezelter |
576 |
for( i=0; i<nAtoms; i++ ){ |
99 |
gezelter |
600 |
|
100 |
|
|
atoms[i]->getVel( vel ); |
101 |
|
|
atoms[i]->getFrc( frc ); |
102 |
|
|
|
103 |
|
|
mass = atoms[i]->getMass(); |
104 |
gezelter |
576 |
|
105 |
gezelter |
600 |
info->matVecMul3( vScale, vel, sc ); |
106 |
tim |
767 |
|
107 |
|
|
for (j=0; j < 3; j++) { |
108 |
|
|
// velocity half step (use chi from previous step here): |
109 |
gezelter |
600 |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
110 |
tim |
767 |
|
111 |
gezelter |
600 |
} |
112 |
gezelter |
576 |
|
113 |
gezelter |
600 |
atoms[i]->setVel( vel ); |
114 |
gezelter |
576 |
|
115 |
|
|
if( atoms[i]->isDirectional() ){ |
116 |
|
|
|
117 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
118 |
tim |
767 |
|
119 |
gezelter |
576 |
// get and convert the torque to body frame |
120 |
|
|
|
121 |
gezelter |
600 |
dAtom->getTrq( Tb ); |
122 |
gezelter |
576 |
dAtom->lab2Body( Tb ); |
123 |
|
|
|
124 |
|
|
// get the angular momentum, and propagate a half step |
125 |
|
|
|
126 |
gezelter |
600 |
dAtom->getJ( ji ); |
127 |
|
|
|
128 |
|
|
for (j=0; j < 3; j++) |
129 |
|
|
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
130 |
gezelter |
576 |
|
131 |
|
|
// use the angular velocities to propagate the rotation matrix a |
132 |
|
|
// full time step |
133 |
gezelter |
600 |
|
134 |
|
|
dAtom->getA(A); |
135 |
|
|
dAtom->getI(I); |
136 |
|
|
|
137 |
gezelter |
576 |
// rotate about the x-axis |
138 |
gezelter |
600 |
angle = dt2 * ji[0] / I[0][0]; |
139 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
140 |
|
|
|
141 |
gezelter |
576 |
// rotate about the y-axis |
142 |
gezelter |
600 |
angle = dt2 * ji[1] / I[1][1]; |
143 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
144 |
gezelter |
576 |
|
145 |
|
|
// rotate about the z-axis |
146 |
gezelter |
600 |
angle = dt * ji[2] / I[2][2]; |
147 |
|
|
this->rotate( 0, 1, angle, ji, A); |
148 |
gezelter |
576 |
|
149 |
|
|
// rotate about the y-axis |
150 |
gezelter |
600 |
angle = dt2 * ji[1] / I[1][1]; |
151 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
152 |
gezelter |
576 |
|
153 |
|
|
// rotate about the x-axis |
154 |
gezelter |
600 |
angle = dt2 * ji[0] / I[0][0]; |
155 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
156 |
gezelter |
576 |
|
157 |
gezelter |
600 |
dAtom->setJ( ji ); |
158 |
|
|
dAtom->setA( A ); |
159 |
tim |
767 |
} |
160 |
gezelter |
576 |
} |
161 |
tim |
767 |
|
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 |
gezelter |
600 |
|
185 |
tim |
767 |
//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 |
gezelter |
577 |
// Scale the box after all the positions have been moved: |
210 |
gezelter |
600 |
|
211 |
gezelter |
578 |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
212 |
|
|
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
213 |
gezelter |
600 |
|
214 |
gezelter |
617 |
bigScale = 1.0; |
215 |
|
|
smallScale = 1.0; |
216 |
|
|
offDiagMax = 0.0; |
217 |
gezelter |
600 |
|
218 |
gezelter |
578 |
for(i=0; i<3; i++){ |
219 |
|
|
for(j=0; j<3; j++){ |
220 |
gezelter |
600 |
|
221 |
gezelter |
588 |
// Calculate the matrix Product of the eta array (we only need |
222 |
|
|
// the ij element right now): |
223 |
gezelter |
600 |
|
224 |
gezelter |
588 |
eta2ij = 0.0; |
225 |
gezelter |
578 |
for(k=0; k<3; k++){ |
226 |
gezelter |
588 |
eta2ij += eta[i][k] * eta[k][j]; |
227 |
gezelter |
578 |
} |
228 |
gezelter |
588 |
|
229 |
|
|
scaleMat[i][j] = 0.0; |
230 |
|
|
// identity matrix (see above): |
231 |
|
|
if (i == j) scaleMat[i][j] = 1.0; |
232 |
|
|
// Taylor expansion for the exponential truncated at second order: |
233 |
|
|
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
234 |
gezelter |
617 |
|
235 |
|
|
if (i != j) |
236 |
|
|
if (fabs(scaleMat[i][j]) > offDiagMax) |
237 |
|
|
offDiagMax = fabs(scaleMat[i][j]); |
238 |
gezelter |
578 |
} |
239 |
gezelter |
617 |
|
240 |
|
|
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
241 |
|
|
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
242 |
gezelter |
578 |
} |
243 |
gezelter |
600 |
|
244 |
gezelter |
617 |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
245 |
|
|
sprintf( painCave.errMsg, |
246 |
|
|
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
247 |
|
|
" Check your tauBarostat, as it is probably too small!\n\n" |
248 |
|
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
249 |
|
|
" [%lf\t%lf\t%lf]\n" |
250 |
|
|
" [%lf\t%lf\t%lf]\n", |
251 |
|
|
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
252 |
|
|
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
253 |
|
|
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
254 |
|
|
painCave.isFatal = 1; |
255 |
|
|
simError(); |
256 |
|
|
} else if (offDiagMax > 0.1) { |
257 |
|
|
sprintf( painCave.errMsg, |
258 |
|
|
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
259 |
|
|
" Check your tauBarostat, as it is probably too small!\n\n" |
260 |
|
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
261 |
|
|
" [%lf\t%lf\t%lf]\n" |
262 |
|
|
" [%lf\t%lf\t%lf]\n", |
263 |
|
|
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
264 |
|
|
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
265 |
|
|
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
266 |
|
|
painCave.isFatal = 1; |
267 |
|
|
simError(); |
268 |
|
|
} else { |
269 |
|
|
info->getBoxM(hm); |
270 |
|
|
info->matMul3(hm, scaleMat, hmnew); |
271 |
|
|
info->setBoxM(hmnew); |
272 |
|
|
} |
273 |
gezelter |
577 |
|
274 |
gezelter |
576 |
} |
275 |
|
|
|
276 |
tim |
645 |
template<typename T> void NPTf<T>::moveB( void ){ |
277 |
gezelter |
600 |
|
278 |
tim |
767 |
int i, j, k; |
279 |
gezelter |
576 |
DirectionalAtom* dAtom; |
280 |
gezelter |
600 |
double Tb[3], ji[3]; |
281 |
|
|
double vel[3], frc[3]; |
282 |
|
|
double mass; |
283 |
|
|
|
284 |
|
|
double instaTemp, instaPress, instaVol; |
285 |
gezelter |
576 |
double tt2, tb2; |
286 |
gezelter |
600 |
double sc[3]; |
287 |
gezelter |
588 |
double press[3][3], vScale[3][3]; |
288 |
tim |
767 |
double oldChi, prevChi; |
289 |
|
|
double oldEta[3][3], preEta[3][3], diffEta; |
290 |
gezelter |
576 |
|
291 |
|
|
tt2 = tauThermostat * tauThermostat; |
292 |
|
|
tb2 = tauBarostat * tauBarostat; |
293 |
|
|
|
294 |
tim |
767 |
|
295 |
|
|
// Set things up for the iteration: |
296 |
|
|
|
297 |
|
|
oldChi = chi; |
298 |
gezelter |
578 |
|
299 |
tim |
767 |
for(i = 0; i < 3; i++) |
300 |
|
|
for(j = 0; j < 3; j++) |
301 |
|
|
oldEta[i][j] = eta[i][j]; |
302 |
gezelter |
578 |
|
303 |
tim |
767 |
for( i=0; i<nAtoms; i++ ){ |
304 |
gezelter |
588 |
|
305 |
tim |
767 |
atoms[i]->getVel( vel ); |
306 |
gezelter |
588 |
|
307 |
tim |
767 |
for (j=0; j < 3; j++) |
308 |
|
|
oldVel[3*i + j] = vel[j]; |
309 |
|
|
|
310 |
|
|
if( atoms[i]->isDirectional() ){ |
311 |
|
|
|
312 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
313 |
|
|
|
314 |
|
|
dAtom->getJ( ji ); |
315 |
|
|
|
316 |
|
|
for (j=0; j < 3; j++) |
317 |
|
|
oldJi[3*i + j] = ji[j]; |
318 |
|
|
|
319 |
gezelter |
588 |
} |
320 |
|
|
} |
321 |
|
|
|
322 |
tim |
767 |
// do the iteration: |
323 |
gezelter |
578 |
|
324 |
tim |
767 |
instaVol = tStats->getVolume(); |
325 |
|
|
|
326 |
|
|
for (k=0; k < 4; k++) { |
327 |
gezelter |
600 |
|
328 |
tim |
767 |
instaTemp = tStats->getTemperature(); |
329 |
|
|
tStats->getPressureTensor(press); |
330 |
gezelter |
578 |
|
331 |
tim |
767 |
// 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 |
gezelter |
578 |
|
336 |
tim |
767 |
for(i = 0; i < 3; i++) |
337 |
|
|
for(j = 0; j < 3; j++) |
338 |
|
|
preEta[i][j] = eta[i][j]; |
339 |
gezelter |
600 |
|
340 |
tim |
767 |
//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 |
gezelter |
576 |
|
361 |
tim |
767 |
mass = atoms[i]->getMass(); |
362 |
gezelter |
576 |
|
363 |
tim |
767 |
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 |
gezelter |
576 |
|
370 |
tim |
767 |
atoms[i]->setVel( vel ); |
371 |
gezelter |
576 |
|
372 |
tim |
767 |
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 |
gezelter |
576 |
|
384 |
tim |
767 |
dAtom->setJ( ji ); |
385 |
|
|
} |
386 |
|
|
} |
387 |
gezelter |
600 |
|
388 |
tim |
767 |
|
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 |
gezelter |
576 |
} |
396 |
tim |
767 |
|
397 |
|
|
//calculate integral of chida |
398 |
|
|
integralOfChidt += dt2*chi; |
399 |
|
|
|
400 |
|
|
|
401 |
gezelter |
576 |
} |
402 |
|
|
|
403 |
mmeineke |
746 |
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 |
tim |
645 |
template<typename T> int NPTf<T>::readyCheck() { |
415 |
tim |
658 |
|
416 |
|
|
//check parent's readyCheck() first |
417 |
|
|
if (T::readyCheck() == -1) |
418 |
|
|
return -1; |
419 |
gezelter |
576 |
|
420 |
|
|
// First check to see if we have a target temperature. |
421 |
|
|
// Not having one is fatal. |
422 |
|
|
|
423 |
|
|
if (!have_target_temp) { |
424 |
|
|
sprintf( painCave.errMsg, |
425 |
gezelter |
580 |
"NPTf error: You can't use the NPTf integrator\n" |
426 |
gezelter |
576 |
" without a targetTemp!\n" |
427 |
|
|
); |
428 |
|
|
painCave.isFatal = 1; |
429 |
|
|
simError(); |
430 |
|
|
return -1; |
431 |
|
|
} |
432 |
|
|
|
433 |
|
|
if (!have_target_pressure) { |
434 |
|
|
sprintf( painCave.errMsg, |
435 |
gezelter |
580 |
"NPTf error: You can't use the NPTf integrator\n" |
436 |
gezelter |
576 |
" without a targetPressure!\n" |
437 |
|
|
); |
438 |
|
|
painCave.isFatal = 1; |
439 |
|
|
simError(); |
440 |
|
|
return -1; |
441 |
|
|
} |
442 |
|
|
|
443 |
|
|
// We must set tauThermostat. |
444 |
|
|
|
445 |
|
|
if (!have_tau_thermostat) { |
446 |
|
|
sprintf( painCave.errMsg, |
447 |
gezelter |
580 |
"NPTf error: If you use the NPTf\n" |
448 |
gezelter |
576 |
" integrator, you must set tauThermostat.\n"); |
449 |
|
|
painCave.isFatal = 1; |
450 |
|
|
simError(); |
451 |
|
|
return -1; |
452 |
|
|
} |
453 |
|
|
|
454 |
|
|
// We must set tauBarostat. |
455 |
|
|
|
456 |
|
|
if (!have_tau_barostat) { |
457 |
|
|
sprintf( painCave.errMsg, |
458 |
gezelter |
580 |
"NPTf error: If you use the NPTf\n" |
459 |
gezelter |
576 |
" integrator, you must set tauBarostat.\n"); |
460 |
|
|
painCave.isFatal = 1; |
461 |
|
|
simError(); |
462 |
|
|
return -1; |
463 |
|
|
} |
464 |
|
|
|
465 |
|
|
// We need NkBT a lot, so just set it here: |
466 |
|
|
|
467 |
tim |
767 |
NkBT = (double)Nparticles * kB * targetTemp; |
468 |
|
|
fkBT = (double)info->ndf * kB * targetTemp; |
469 |
gezelter |
576 |
|
470 |
|
|
return 1; |
471 |
|
|
} |
472 |
tim |
763 |
|
473 |
|
|
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
474 |
|
|
|
475 |
|
|
double conservedQuantity; |
476 |
|
|
double tb2; |
477 |
tim |
767 |
double trEta; |
478 |
|
|
double U; |
479 |
|
|
double thermo; |
480 |
|
|
double integral; |
481 |
|
|
double baro; |
482 |
|
|
double PV; |
483 |
tim |
763 |
|
484 |
tim |
767 |
U = tStats->getTotalE(); |
485 |
|
|
thermo = (fkBT * tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
486 |
tim |
763 |
|
487 |
tim |
767 |
tb2 = tauBarostat * tauBarostat; |
488 |
|
|
trEta = info->matTrace3(eta); |
489 |
|
|
baro = ((double)info->ndfTrans * kB * targetTemp * tb2 * trEta * trEta / 2.0) / eConvert; |
490 |
tim |
763 |
|
491 |
tim |
767 |
integral = ((double)(info->ndf + 1) * kB * targetTemp * integralOfChidt) /eConvert; |
492 |
tim |
763 |
|
493 |
tim |
767 |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
494 |
|
|
|
495 |
|
|
|
496 |
|
|
cout.width(8); |
497 |
|
|
cout.precision(8); |
498 |
tim |
763 |
|
499 |
tim |
767 |
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 |
tim |
763 |
|
512 |
|
|
} |