153 |
|
double sampleTime = info->sampleTime; |
154 |
|
double statusTime = info->statusTime; |
155 |
|
double thermalTime = info->thermalTime; |
156 |
+ |
double resetTime = info->resetTime; |
157 |
|
|
158 |
+ |
|
159 |
|
double currSample; |
160 |
|
double currThermal; |
161 |
|
double currStatus; |
162 |
< |
|
162 |
> |
double currReset; |
163 |
> |
|
164 |
|
int calcPot, calcStress; |
165 |
|
int isError; |
166 |
|
|
177 |
|
// initialize the forces before the first step |
178 |
|
|
179 |
|
calcForce(1, 1); |
180 |
+ |
|
181 |
+ |
if (nConstrained){ |
182 |
+ |
preMove(); |
183 |
+ |
constrainA(); |
184 |
+ |
calcForce(1, 1); |
185 |
+ |
constrainB(); |
186 |
+ |
} |
187 |
|
|
188 |
|
if (info->setTemp){ |
189 |
|
thermalize(); |
190 |
|
} |
191 |
|
|
182 |
– |
calcPot = 0; |
183 |
– |
calcStress = 0; |
184 |
– |
currSample = sampleTime; |
185 |
– |
currThermal = thermalTime; |
186 |
– |
currStatus = statusTime; |
187 |
– |
|
192 |
|
calcPot = 0; |
193 |
|
calcStress = 0; |
194 |
|
currSample = sampleTime + info->getTime(); |
195 |
|
currThermal = thermalTime+ info->getTime(); |
196 |
|
currStatus = statusTime + info->getTime(); |
197 |
+ |
currReset = resetTime + info->getTime(); |
198 |
|
|
199 |
|
dumpOut->writeDump(info->getTime()); |
200 |
|
statOut->writeStat(info->getTime()); |
235 |
|
currStatus += statusTime; |
236 |
|
} |
237 |
|
|
238 |
+ |
if (info->resetIntegrator){ |
239 |
+ |
if (info->getTime() >= currReset){ |
240 |
+ |
this->resetIntegrator(); |
241 |
+ |
currReset += resetTime; |
242 |
+ |
} |
243 |
+ |
} |
244 |
+ |
|
245 |
|
#ifdef IS_MPI |
246 |
|
strcpy(checkPointMsg, "successfully took a time step."); |
247 |
|
MPIcheckPoint(); |
261 |
|
|
262 |
|
moveA(); |
263 |
|
|
252 |
– |
if (nConstrained){ |
253 |
– |
constrainA(); |
254 |
– |
} |
264 |
|
|
265 |
|
|
266 |
+ |
|
267 |
|
#ifdef IS_MPI |
268 |
|
strcpy(checkPointMsg, "Succesful moveA\n"); |
269 |
|
MPIcheckPoint(); |
284 |
|
|
285 |
|
moveB(); |
286 |
|
|
277 |
– |
if (nConstrained){ |
278 |
– |
constrainB(); |
279 |
– |
} |
287 |
|
|
288 |
+ |
|
289 |
|
#ifdef IS_MPI |
290 |
|
strcpy(checkPointMsg, "Succesful moveB\n"); |
291 |
|
MPIcheckPoint(); |
297 |
|
int i, j; |
298 |
|
DirectionalAtom* dAtom; |
299 |
|
double Tb[3], ji[3]; |
292 |
– |
double A[3][3], I[3][3]; |
293 |
– |
double angle; |
300 |
|
double vel[3], pos[3], frc[3]; |
301 |
|
double mass; |
302 |
|
|
332 |
|
for (j = 0; j < 3; j++) |
333 |
|
ji[j] += (dt2 * Tb[j]) * eConvert; |
334 |
|
|
335 |
< |
// use the angular velocities to propagate the rotation matrix a |
330 |
< |
// full time step |
335 |
> |
this->rotationPropagation( dAtom, ji ); |
336 |
|
|
337 |
< |
dAtom->getA(A); |
333 |
< |
dAtom->getI(I); |
334 |
< |
|
335 |
< |
// rotate about the x-axis |
336 |
< |
angle = dt2 * ji[0] / I[0][0]; |
337 |
< |
this->rotate(1, 2, angle, ji, A); |
338 |
< |
|
339 |
< |
// rotate about the y-axis |
340 |
< |
angle = dt2 * ji[1] / I[1][1]; |
341 |
< |
this->rotate(2, 0, angle, ji, A); |
342 |
< |
|
343 |
< |
// rotate about the z-axis |
344 |
< |
angle = dt * ji[2] / I[2][2]; |
345 |
< |
this->rotate(0, 1, angle, ji, A); |
346 |
< |
|
347 |
< |
// rotate about the y-axis |
348 |
< |
angle = dt2 * ji[1] / I[1][1]; |
349 |
< |
this->rotate(2, 0, angle, ji, A); |
350 |
< |
|
351 |
< |
// rotate about the x-axis |
352 |
< |
angle = dt2 * ji[0] / I[0][0]; |
353 |
< |
this->rotate(1, 2, angle, ji, A); |
354 |
< |
|
355 |
< |
|
356 |
< |
dAtom->setJ(ji); |
357 |
< |
dAtom->setA(A); |
337 |
> |
dAtom->setJ(ji); |
338 |
|
} |
339 |
|
} |
340 |
+ |
|
341 |
+ |
if (nConstrained){ |
342 |
+ |
constrainA(); |
343 |
+ |
} |
344 |
|
} |
345 |
|
|
346 |
|
|
381 |
|
|
382 |
|
dAtom->setJ(ji); |
383 |
|
} |
384 |
+ |
} |
385 |
+ |
|
386 |
+ |
if (nConstrained){ |
387 |
+ |
constrainB(); |
388 |
|
} |
389 |
|
} |
390 |
|
|
544 |
|
painCave.isFatal = 1; |
545 |
|
simError(); |
546 |
|
} |
547 |
+ |
|
548 |
|
} |
549 |
|
|
550 |
|
template<typename T> void Integrator<T>::constrainB(void){ |
646 |
|
painCave.isFatal = 1; |
647 |
|
simError(); |
648 |
|
} |
649 |
+ |
} |
650 |
+ |
|
651 |
+ |
template<typename T> void Integrator<T>::rotationPropagation |
652 |
+ |
( DirectionalAtom* dAtom, double ji[3] ){ |
653 |
+ |
|
654 |
+ |
double angle; |
655 |
+ |
double A[3][3], I[3][3]; |
656 |
+ |
|
657 |
+ |
// use the angular velocities to propagate the rotation matrix a |
658 |
+ |
// full time step |
659 |
+ |
|
660 |
+ |
dAtom->getA(A); |
661 |
+ |
dAtom->getI(I); |
662 |
+ |
|
663 |
+ |
// rotate about the x-axis |
664 |
+ |
angle = dt2 * ji[0] / I[0][0]; |
665 |
+ |
this->rotate( 1, 2, angle, ji, A ); |
666 |
+ |
|
667 |
+ |
// rotate about the y-axis |
668 |
+ |
angle = dt2 * ji[1] / I[1][1]; |
669 |
+ |
this->rotate( 2, 0, angle, ji, A ); |
670 |
+ |
|
671 |
+ |
// rotate about the z-axis |
672 |
+ |
angle = dt * ji[2] / I[2][2]; |
673 |
+ |
this->rotate( 0, 1, angle, ji, A); |
674 |
+ |
|
675 |
+ |
// rotate about the y-axis |
676 |
+ |
angle = dt2 * ji[1] / I[1][1]; |
677 |
+ |
this->rotate( 2, 0, angle, ji, A ); |
678 |
+ |
|
679 |
+ |
// rotate about the x-axis |
680 |
+ |
angle = dt2 * ji[0] / I[0][0]; |
681 |
+ |
this->rotate( 1, 2, angle, ji, A ); |
682 |
+ |
|
683 |
+ |
dAtom->setA( A ); |
684 |
|
} |
685 |
|
|
686 |
|
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
773 |
|
template<typename T> void Integrator<T>::thermalize(){ |
774 |
|
tStats->velocitize(); |
775 |
|
} |
776 |
+ |
|
777 |
+ |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
778 |
+ |
return tStats->getTotalE(); |
779 |
+ |
} |