25 |
|
if (info->the_integrator != NULL){ |
26 |
|
delete info->the_integrator; |
27 |
|
} |
28 |
< |
info->the_integrator = this; |
29 |
< |
|
28 |
> |
|
29 |
|
nAtoms = info->n_atoms; |
30 |
|
|
31 |
|
// check for constraints |
173 |
|
dt = info->dt; |
174 |
|
dt2 = 0.5 * dt; |
175 |
|
|
176 |
+ |
readyCheck(); |
177 |
+ |
|
178 |
|
// initialize the forces before the first step |
179 |
|
|
180 |
|
calcForce(1, 1); |
181 |
+ |
|
182 |
+ |
if (nConstrained){ |
183 |
+ |
preMove(); |
184 |
+ |
constrainA(); |
185 |
+ |
calcForce(1, 1); |
186 |
+ |
constrainB(); |
187 |
+ |
} |
188 |
|
|
189 |
|
if (info->setTemp){ |
190 |
|
thermalize(); |
200 |
|
dumpOut->writeDump(info->getTime()); |
201 |
|
statOut->writeStat(info->getTime()); |
202 |
|
|
195 |
– |
readyCheck(); |
203 |
|
|
204 |
+ |
|
205 |
|
#ifdef IS_MPI |
206 |
|
strcpy(checkPointMsg, "The integrator is ready to go."); |
207 |
|
MPIcheckPoint(); |
262 |
|
|
263 |
|
moveA(); |
264 |
|
|
257 |
– |
if (nConstrained){ |
258 |
– |
constrainA(); |
259 |
– |
} |
265 |
|
|
266 |
|
|
267 |
+ |
|
268 |
|
#ifdef IS_MPI |
269 |
|
strcpy(checkPointMsg, "Succesful moveA\n"); |
270 |
|
MPIcheckPoint(); |
285 |
|
|
286 |
|
moveB(); |
287 |
|
|
282 |
– |
if (nConstrained){ |
283 |
– |
constrainB(); |
284 |
– |
} |
288 |
|
|
289 |
+ |
|
290 |
|
#ifdef IS_MPI |
291 |
|
strcpy(checkPointMsg, "Succesful moveB\n"); |
292 |
|
MPIcheckPoint(); |
298 |
|
int i, j; |
299 |
|
DirectionalAtom* dAtom; |
300 |
|
double Tb[3], ji[3]; |
297 |
– |
double A[3][3], I[3][3]; |
298 |
– |
double angle; |
301 |
|
double vel[3], pos[3], frc[3]; |
302 |
|
double mass; |
303 |
|
|
333 |
|
for (j = 0; j < 3; j++) |
334 |
|
ji[j] += (dt2 * Tb[j]) * eConvert; |
335 |
|
|
336 |
< |
// use the angular velocities to propagate the rotation matrix a |
335 |
< |
// full time step |
336 |
< |
|
337 |
< |
dAtom->getA(A); |
338 |
< |
dAtom->getI(I); |
339 |
< |
|
340 |
< |
// rotate about the x-axis |
341 |
< |
angle = dt2 * ji[0] / I[0][0]; |
342 |
< |
this->rotate(1, 2, angle, ji, A); |
343 |
< |
|
344 |
< |
// rotate about the y-axis |
345 |
< |
angle = dt2 * ji[1] / I[1][1]; |
346 |
< |
this->rotate(2, 0, angle, ji, A); |
347 |
< |
|
348 |
< |
// rotate about the z-axis |
349 |
< |
angle = dt * ji[2] / I[2][2]; |
350 |
< |
this->rotate(0, 1, angle, ji, A); |
351 |
< |
|
352 |
< |
// rotate about the y-axis |
353 |
< |
angle = dt2 * ji[1] / I[1][1]; |
354 |
< |
this->rotate(2, 0, angle, ji, A); |
355 |
< |
|
356 |
< |
// rotate about the x-axis |
357 |
< |
angle = dt2 * ji[0] / I[0][0]; |
358 |
< |
this->rotate(1, 2, angle, ji, A); |
359 |
< |
|
336 |
> |
this->rotationPropagation( dAtom, ji ); |
337 |
|
|
338 |
|
dAtom->setJ(ji); |
362 |
– |
dAtom->setA(A); |
339 |
|
} |
340 |
|
} |
341 |
+ |
|
342 |
+ |
if (nConstrained){ |
343 |
+ |
constrainA(); |
344 |
+ |
} |
345 |
|
} |
346 |
|
|
347 |
|
|
382 |
|
|
383 |
|
dAtom->setJ(ji); |
384 |
|
} |
385 |
+ |
} |
386 |
+ |
|
387 |
+ |
if (nConstrained){ |
388 |
+ |
constrainB(); |
389 |
|
} |
390 |
|
} |
391 |
|
|
545 |
|
painCave.isFatal = 1; |
546 |
|
simError(); |
547 |
|
} |
548 |
+ |
|
549 |
|
} |
550 |
|
|
551 |
|
template<typename T> void Integrator<T>::constrainB(void){ |
648 |
|
simError(); |
649 |
|
} |
650 |
|
} |
651 |
+ |
|
652 |
+ |
template<typename T> void Integrator<T>::rotationPropagation |
653 |
+ |
( DirectionalAtom* dAtom, double ji[3] ){ |
654 |
|
|
655 |
+ |
double angle; |
656 |
+ |
double A[3][3], I[3][3]; |
657 |
+ |
|
658 |
+ |
// use the angular velocities to propagate the rotation matrix a |
659 |
+ |
// full time step |
660 |
+ |
|
661 |
+ |
dAtom->getA(A); |
662 |
+ |
dAtom->getI(I); |
663 |
+ |
|
664 |
+ |
// rotate about the x-axis |
665 |
+ |
angle = dt2 * ji[0] / I[0][0]; |
666 |
+ |
this->rotate( 1, 2, angle, ji, A ); |
667 |
+ |
|
668 |
+ |
// rotate about the y-axis |
669 |
+ |
angle = dt2 * ji[1] / I[1][1]; |
670 |
+ |
this->rotate( 2, 0, angle, ji, A ); |
671 |
+ |
|
672 |
+ |
// rotate about the z-axis |
673 |
+ |
angle = dt * ji[2] / I[2][2]; |
674 |
+ |
this->rotate( 0, 1, angle, ji, A); |
675 |
+ |
|
676 |
+ |
// rotate about the y-axis |
677 |
+ |
angle = dt2 * ji[1] / I[1][1]; |
678 |
+ |
this->rotate( 2, 0, angle, ji, A ); |
679 |
+ |
|
680 |
+ |
// rotate about the x-axis |
681 |
+ |
angle = dt2 * ji[0] / I[0][0]; |
682 |
+ |
this->rotate( 1, 2, angle, ji, A ); |
683 |
+ |
|
684 |
+ |
dAtom->setA( A ); |
685 |
+ |
} |
686 |
+ |
|
687 |
|
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
688 |
|
double angle, double ji[3], |
689 |
|
double A[3][3]){ |
774 |
|
template<typename T> void Integrator<T>::thermalize(){ |
775 |
|
tStats->velocitize(); |
776 |
|
} |
777 |
+ |
|
778 |
+ |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
779 |
+ |
return tStats->getTotalE(); |
780 |
+ |
} |