9 |
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#include "Integrator.hpp" |
10 |
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#include "simError.h" |
11 |
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|
12 |
+ |
#ifdef IS_MPI |
13 |
+ |
#include "mpiSimulation.hpp" |
14 |
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#endif |
15 |
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|
16 |
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|
17 |
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// Basic isotropic thermostating and barostating via the Melchionna |
18 |
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// modification of the Hoover algorithm: |
19 |
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// |
24 |
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// |
25 |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
26 |
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|
27 |
< |
NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
28 |
< |
Integrator( theInfo, the_ff ) |
27 |
> |
template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
28 |
> |
T( theInfo, the_ff ) |
29 |
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{ |
30 |
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chi = 0.0; |
31 |
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eta = 0.0; |
32 |
+ |
integralOfChidt = 0.0; |
33 |
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have_tau_thermostat = 0; |
34 |
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have_tau_barostat = 0; |
35 |
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have_target_temp = 0; |
36 |
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have_target_pressure = 0; |
37 |
+ |
have_chi_tolerance = 0; |
38 |
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have_eta_tolerance = 0; |
39 |
+ |
have_pos_iter_tolerance = 0; |
40 |
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|
41 |
+ |
oldPos = new double[3*nAtoms]; |
42 |
+ |
oldVel = new double[3*nAtoms]; |
43 |
+ |
oldJi = new double[3*nAtoms]; |
44 |
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#ifdef IS_MPI |
45 |
+ |
Nparticles = mpiSim->getTotAtoms(); |
46 |
+ |
#else |
47 |
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Nparticles = theInfo->n_atoms; |
48 |
+ |
#endif |
49 |
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|
50 |
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} |
51 |
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|
52 |
< |
void NPTi::moveA() { |
52 |
> |
template<typename T> NPTi<T>::~NPTi() { |
53 |
> |
delete[] oldPos; |
54 |
> |
delete[] oldVel; |
55 |
> |
delete[] oldJi; |
56 |
> |
} |
57 |
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|
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 |
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|
81 |
< |
int i, j; |
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 |
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|
103 |
> |
// for (j = 0; j < 3; j++) |
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> |
// pos[j] += dt * (vel[j] + eta*rj[j]); |
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|
106 |
> |
// atoms[i]->setPos( pos ); |
107 |
> |
|
108 |
> |
// if( atoms[i]->isDirectional() ){ |
109 |
> |
|
110 |
> |
// dAtom = (DirectionalAtom *)atoms[i]; |
111 |
> |
|
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> |
// // get and convert the torque to body frame |
113 |
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|
114 |
> |
// dAtom->getTrq( Tb ); |
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> |
// dAtom->lab2Body( Tb ); |
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> |
|
117 |
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// // get the angular momentum, and propagate a half step |
118 |
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|
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// dAtom->getJ( ji ); |
120 |
> |
|
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// for (j=0; j < 3; j++) |
122 |
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// ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
123 |
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|
124 |
> |
// // use the angular velocities to propagate the rotation matrix a |
125 |
> |
// // full time step |
126 |
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|
127 |
> |
// dAtom->getA(A); |
128 |
> |
// dAtom->getI(I); |
129 |
> |
|
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> |
// // rotate about the x-axis |
131 |
> |
// angle = dt2 * ji[0] / I[0][0]; |
132 |
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// this->rotate( 1, 2, angle, ji, A ); |
133 |
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|
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// // 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 |
> |
|
172 |
> |
|
173 |
> |
//new version of NPTi |
174 |
> |
int i, j, k; |
175 |
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DirectionalAtom* dAtom; |
176 |
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double Tb[3], ji[3]; |
177 |
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double A[3][3], I[3][3]; |
181 |
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double rj[3]; |
182 |
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double instaTemp, instaPress, instaVol; |
183 |
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double tt2, tb2, scaleFactor; |
184 |
+ |
double COM[3]; |
185 |
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|
186 |
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tt2 = tauThermostat * tauThermostat; |
187 |
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tb2 = tauBarostat * tauBarostat; |
189 |
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instaTemp = tStats->getTemperature(); |
190 |
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instaPress = tStats->getPressure(); |
191 |
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instaVol = tStats->getVolume(); |
53 |
– |
|
54 |
– |
// first evolve chi a half step |
192 |
|
|
193 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
194 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
195 |
< |
(p_convert*NkBT*tb2)); |
59 |
< |
|
193 |
> |
tStats->getCOM(COM); |
194 |
> |
|
195 |
> |
//evolve velocity half step |
196 |
|
for( i=0; i<nAtoms; i++ ){ |
197 |
+ |
|
198 |
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atoms[i]->getVel( vel ); |
62 |
– |
atoms[i]->getPos( pos ); |
199 |
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atoms[i]->getFrc( frc ); |
200 |
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|
201 |
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mass = atoms[i]->getMass(); |
202 |
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|
203 |
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for (j=0; j < 3; j++) { |
204 |
< |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
205 |
< |
rj[j] = pos[j]; |
204 |
> |
// velocity half step (use chi from previous step here): |
205 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta)); |
206 |
> |
|
207 |
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} |
208 |
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|
209 |
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atoms[i]->setVel( vel ); |
210 |
< |
|
74 |
< |
info->wrapVector(rj); |
75 |
< |
|
76 |
< |
for (j = 0; j < 3; j++) |
77 |
< |
pos[j] += dt * (vel[j] + eta*rj[j]); |
78 |
< |
|
79 |
< |
atoms[i]->setPos( pos ); |
80 |
< |
|
210 |
> |
|
211 |
|
if( atoms[i]->isDirectional() ){ |
212 |
|
|
213 |
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dAtom = (DirectionalAtom *)atoms[i]; |
214 |
< |
|
214 |
> |
|
215 |
|
// get and convert the torque to body frame |
216 |
|
|
217 |
|
dAtom->getTrq( Tb ); |
252 |
|
|
253 |
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dAtom->setJ( ji ); |
254 |
|
dAtom->setA( A ); |
255 |
< |
} |
255 |
> |
} |
256 |
> |
} |
257 |
|
|
258 |
+ |
// evolve chi and eta half step |
259 |
+ |
|
260 |
+ |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
261 |
+ |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
262 |
+ |
|
263 |
+ |
//calculate the integral of chidt |
264 |
+ |
integralOfChidt += dt2*chi; |
265 |
+ |
|
266 |
+ |
//save the old positions |
267 |
+ |
for(i = 0; i < nAtoms; i++){ |
268 |
+ |
atoms[i]->getPos(pos); |
269 |
+ |
for(j = 0; j < 3; j++) |
270 |
+ |
oldPos[i*3 + j] = pos[j]; |
271 |
|
} |
272 |
+ |
|
273 |
+ |
//the first estimation of r(t+dt) is equal to r(t) |
274 |
+ |
|
275 |
+ |
for(k = 0; k < 4; k ++){ |
276 |
|
|
277 |
+ |
for(i =0 ; i < nAtoms; i++){ |
278 |
+ |
|
279 |
+ |
atoms[i]->getVel(vel); |
280 |
+ |
atoms[i]->getPos(pos); |
281 |
+ |
|
282 |
+ |
for(j = 0; j < 3; j++) |
283 |
+ |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
284 |
+ |
|
285 |
+ |
|
286 |
+ |
//wrapVector(r(t)) = r(t)-R0 |
287 |
+ |
//info->wrapVector(rj); |
288 |
+ |
|
289 |
+ |
for(j = 0; j < 3; j++) |
290 |
+ |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
291 |
+ |
|
292 |
+ |
atoms[i]->setPos( pos ); |
293 |
+ |
|
294 |
+ |
} |
295 |
+ |
|
296 |
+ |
} |
297 |
+ |
|
298 |
+ |
|
299 |
|
// Scale the box after all the positions have been moved: |
300 |
|
|
301 |
|
scaleFactor = exp(dt*eta); |
309 |
|
painCave.isFatal = 1; |
310 |
|
simError(); |
311 |
|
} else { |
312 |
< |
info->scaleBox(exp(dt*eta)); |
313 |
< |
} |
312 |
> |
info->scaleBox(scaleFactor); |
313 |
> |
} |
314 |
|
|
315 |
+ |
//advance volume; |
316 |
+ |
volume = volume * exp(dt*eta); |
317 |
|
} |
318 |
|
|
319 |
< |
void NPTi::moveB( void ){ |
319 |
> |
template<typename T> void NPTi<T>::moveB( void ){ |
320 |
|
|
321 |
+ |
/* |
322 |
|
int i, j; |
323 |
|
DirectionalAtom* dAtom; |
324 |
|
double Tb[3], ji[3]; |
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 |
|
|
372 |
|
dAtom->setJ( ji ); |
373 |
|
} |
374 |
|
} |
375 |
+ |
|
376 |
+ |
*/ |
377 |
+ |
|
378 |
+ |
//new version of NPTi |
379 |
+ |
int i, j, k; |
380 |
+ |
DirectionalAtom* dAtom; |
381 |
+ |
double Tb[3], ji[3]; |
382 |
+ |
double vel[3], frc[3]; |
383 |
+ |
double mass; |
384 |
+ |
|
385 |
+ |
double instTemp, instPress, instVol; |
386 |
+ |
double tt2, tb2; |
387 |
+ |
double oldChi, prevChi; |
388 |
+ |
double oldEta, preEta; |
389 |
+ |
|
390 |
+ |
tt2 = tauThermostat * tauThermostat; |
391 |
+ |
tb2 = tauBarostat * tauBarostat; |
392 |
+ |
|
393 |
+ |
|
394 |
+ |
// Set things up for the iteration: |
395 |
+ |
|
396 |
+ |
oldChi = chi; |
397 |
+ |
oldEta = eta; |
398 |
+ |
|
399 |
+ |
for( i=0; i<nAtoms; i++ ){ |
400 |
+ |
|
401 |
+ |
atoms[i]->getVel( vel ); |
402 |
+ |
|
403 |
+ |
for (j=0; j < 3; j++) |
404 |
+ |
oldVel[3*i + j] = vel[j]; |
405 |
+ |
|
406 |
+ |
if( atoms[i]->isDirectional() ){ |
407 |
+ |
|
408 |
+ |
dAtom = (DirectionalAtom *)atoms[i]; |
409 |
+ |
|
410 |
+ |
dAtom->getJ( ji ); |
411 |
+ |
|
412 |
+ |
for (j=0; j < 3; j++) |
413 |
+ |
oldJi[3*i + j] = ji[j]; |
414 |
+ |
|
415 |
+ |
} |
416 |
+ |
} |
417 |
+ |
|
418 |
+ |
// do the iteration: |
419 |
+ |
|
420 |
+ |
instVol = tStats->getVolume(); |
421 |
+ |
|
422 |
+ |
for (k=0; k < 4; k++) { |
423 |
+ |
|
424 |
+ |
instTemp = tStats->getTemperature(); |
425 |
+ |
instPress = tStats->getPressure(); |
426 |
+ |
|
427 |
+ |
// evolve chi another half step using the temperature at t + dt/2 |
428 |
+ |
|
429 |
+ |
prevChi = chi; |
430 |
+ |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
431 |
+ |
(tauThermostat*tauThermostat); |
432 |
+ |
|
433 |
+ |
preEta = eta; |
434 |
+ |
eta = oldEta + dt2 * ( instVol * (instPress - targetPressure) / |
435 |
+ |
(p_convert*NkBT*tb2)); |
436 |
+ |
|
437 |
+ |
|
438 |
+ |
for( i=0; i<nAtoms; i++ ){ |
439 |
+ |
|
440 |
+ |
atoms[i]->getFrc( frc ); |
441 |
+ |
atoms[i]->getVel(vel); |
442 |
+ |
|
443 |
+ |
mass = atoms[i]->getMass(); |
444 |
+ |
|
445 |
+ |
// velocity half step |
446 |
+ |
for (j=0; j < 3; j++) |
447 |
+ |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*(chi + eta)); |
448 |
+ |
|
449 |
+ |
atoms[i]->setVel( vel ); |
450 |
+ |
|
451 |
+ |
if( atoms[i]->isDirectional() ){ |
452 |
+ |
|
453 |
+ |
dAtom = (DirectionalAtom *)atoms[i]; |
454 |
+ |
|
455 |
+ |
// get and convert the torque to body frame |
456 |
+ |
|
457 |
+ |
dAtom->getTrq( Tb ); |
458 |
+ |
dAtom->lab2Body( Tb ); |
459 |
+ |
|
460 |
+ |
for (j=0; j < 3; j++) |
461 |
+ |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
462 |
+ |
|
463 |
+ |
dAtom->setJ( ji ); |
464 |
+ |
} |
465 |
+ |
} |
466 |
+ |
|
467 |
+ |
if (fabs(prevChi - chi) <= chiTolerance && fabs(preEta -eta) <= etaTolerance) |
468 |
+ |
break; |
469 |
+ |
} |
470 |
+ |
|
471 |
+ |
//calculate integral of chida |
472 |
+ |
integralOfChidt += dt2*chi; |
473 |
+ |
|
474 |
+ |
|
475 |
|
} |
476 |
|
|
477 |
< |
int NPTi::readyCheck() { |
477 |
> |
template<typename T> void NPTi<T>::resetIntegrator() { |
478 |
> |
chi = 0.0; |
479 |
> |
eta = 0.0; |
480 |
> |
} |
481 |
> |
|
482 |
> |
template<typename T> int NPTi<T>::readyCheck() { |
483 |
> |
|
484 |
> |
//check parent's readyCheck() first |
485 |
> |
if (T::readyCheck() == -1) |
486 |
> |
return -1; |
487 |
|
|
488 |
|
// First check to see if we have a target temperature. |
489 |
|
// Not having one is fatal. |
530 |
|
return -1; |
531 |
|
} |
532 |
|
|
533 |
+ |
if (!have_chi_tolerance) { |
534 |
+ |
sprintf( painCave.errMsg, |
535 |
+ |
"NPTi warning: setting chi tolerance to 1e-6\n"); |
536 |
+ |
chiTolerance = 1e-6; |
537 |
+ |
have_chi_tolerance = 1; |
538 |
+ |
painCave.isFatal = 0; |
539 |
+ |
simError(); |
540 |
+ |
} |
541 |
+ |
|
542 |
+ |
if (!have_eta_tolerance) { |
543 |
+ |
sprintf( painCave.errMsg, |
544 |
+ |
"NPTi warning: setting eta tolerance to 1e-6\n"); |
545 |
+ |
etaTolerance = 1e-6; |
546 |
+ |
have_eta_tolerance = 1; |
547 |
+ |
painCave.isFatal = 0; |
548 |
+ |
simError(); |
549 |
+ |
} |
550 |
|
// We need NkBT a lot, so just set it here: |
551 |
|
|
552 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
552 |
> |
NkBT = (double)Nparticles * kB * targetTemp; |
553 |
> |
fkBT = (double)info->ndf * kB * targetTemp; |
554 |
|
|
555 |
|
return 1; |
556 |
|
} |
557 |
+ |
|
558 |
+ |
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
559 |
+ |
|
560 |
+ |
double conservedQuantity; |
561 |
+ |
double tb2; |
562 |
+ |
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; |
574 |
+ |
|
575 |
+ |
double delta_U; |
576 |
+ |
double delta_TS; |
577 |
+ |
double delta_PV; |
578 |
+ |
double delta_extra; |
579 |
+ |
|
580 |
+ |
U = tStats->getTotalE(); |
581 |
+ |
|
582 |
+ |
TS = fkBT * |
583 |
+ |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
584 |
+ |
|
585 |
+ |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
586 |
+ |
|
587 |
+ |
tb2 = tauBarostat * tauBarostat; |
588 |
+ |
eta2 = eta * eta; |
589 |
+ |
|
590 |
+ |
extra = (fkBT * tb2 * eta2 / 2.0 ) / eConvert; |
591 |
+ |
/* |
592 |
+ |
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 |
+ |
*/ |
605 |
+ |
cout.width(8); |
606 |
+ |
cout.precision(8); |
607 |
+ |
|
608 |
+ |
|
609 |
+ |
cout << info->getTime() << "\t" |
610 |
+ |
<< chi << "\t" |
611 |
+ |
<< eta << "\t" |
612 |
+ |
<< U << "\t" |
613 |
+ |
<< TS << "\t" |
614 |
+ |
<< PV << "\t" |
615 |
+ |
<< extra << "\t" |
616 |
+ |
<< U+TS+PV+extra << endl; |
617 |
+ |
|
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; |
632 |
+ |
return conservedQuantity; |
633 |
+ |
} |