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 |
146 |
|
|
147 |
|
|
148 |
|
template<typename T> void Integrator<T>::integrate(void){ |
150 |
– |
int i, j; // loop counters |
149 |
|
|
150 |
|
double runTime = info->run_time; |
151 |
|
double sampleTime = info->sampleTime; |
160 |
|
double currReset; |
161 |
|
|
162 |
|
int calcPot, calcStress; |
165 |
– |
int isError; |
163 |
|
|
164 |
|
tStats = new Thermo(info); |
165 |
|
statOut = new StatWriter(info); |
166 |
|
dumpOut = new DumpWriter(info); |
167 |
|
|
168 |
|
atoms = info->atoms; |
172 |
– |
DirectionalAtom* dAtom; |
169 |
|
|
170 |
|
dt = info->dt; |
171 |
|
dt2 = 0.5 * dt; |
172 |
|
|
173 |
+ |
readyCheck(); |
174 |
+ |
|
175 |
|
// initialize the forces before the first step |
176 |
|
|
177 |
|
calcForce(1, 1); |
178 |
+ |
|
179 |
+ |
if (nConstrained){ |
180 |
+ |
preMove(); |
181 |
+ |
constrainA(); |
182 |
+ |
calcForce(1, 1); |
183 |
+ |
constrainB(); |
184 |
+ |
} |
185 |
|
|
186 |
|
if (info->setTemp){ |
187 |
|
thermalize(); |
197 |
|
dumpOut->writeDump(info->getTime()); |
198 |
|
statOut->writeStat(info->getTime()); |
199 |
|
|
195 |
– |
readyCheck(); |
200 |
|
|
201 |
+ |
|
202 |
|
#ifdef IS_MPI |
203 |
|
strcpy(checkPointMsg, "The integrator is ready to go."); |
204 |
|
MPIcheckPoint(); |
259 |
|
|
260 |
|
moveA(); |
261 |
|
|
257 |
– |
if (nConstrained){ |
258 |
– |
constrainA(); |
259 |
– |
} |
262 |
|
|
263 |
|
|
264 |
+ |
|
265 |
|
#ifdef IS_MPI |
266 |
|
strcpy(checkPointMsg, "Succesful moveA\n"); |
267 |
|
MPIcheckPoint(); |
282 |
|
|
283 |
|
moveB(); |
284 |
|
|
282 |
– |
if (nConstrained){ |
283 |
– |
constrainB(); |
284 |
– |
} |
285 |
|
|
286 |
+ |
|
287 |
|
#ifdef IS_MPI |
288 |
|
strcpy(checkPointMsg, "Succesful moveB\n"); |
289 |
|
MPIcheckPoint(); |
295 |
|
int i, j; |
296 |
|
DirectionalAtom* dAtom; |
297 |
|
double Tb[3], ji[3]; |
297 |
– |
double A[3][3], I[3][3]; |
298 |
– |
double angle; |
298 |
|
double vel[3], pos[3], frc[3]; |
299 |
|
double mass; |
300 |
|
|
330 |
|
for (j = 0; j < 3; j++) |
331 |
|
ji[j] += (dt2 * Tb[j]) * eConvert; |
332 |
|
|
333 |
< |
// use the angular velocities to propagate the rotation matrix a |
335 |
< |
// full time step |
333 |
> |
this->rotationPropagation( dAtom, ji ); |
334 |
|
|
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 |
– |
|
360 |
– |
|
335 |
|
dAtom->setJ(ji); |
362 |
– |
dAtom->setA(A); |
336 |
|
} |
337 |
|
} |
338 |
+ |
|
339 |
+ |
if (nConstrained){ |
340 |
+ |
constrainA(); |
341 |
+ |
} |
342 |
|
} |
343 |
|
|
344 |
|
|
380 |
|
dAtom->setJ(ji); |
381 |
|
} |
382 |
|
} |
383 |
+ |
|
384 |
+ |
if (nConstrained){ |
385 |
+ |
constrainB(); |
386 |
+ |
} |
387 |
|
} |
388 |
|
|
389 |
|
template<typename T> void Integrator<T>::preMove(void){ |
402 |
|
} |
403 |
|
|
404 |
|
template<typename T> void Integrator<T>::constrainA(){ |
405 |
< |
int i, j, k; |
405 |
> |
int i, j; |
406 |
|
int done; |
407 |
|
double posA[3], posB[3]; |
408 |
|
double velA[3], velB[3]; |
542 |
|
painCave.isFatal = 1; |
543 |
|
simError(); |
544 |
|
} |
545 |
+ |
|
546 |
|
} |
547 |
|
|
548 |
|
template<typename T> void Integrator<T>::constrainB(void){ |
549 |
< |
int i, j, k; |
549 |
> |
int i, j; |
550 |
|
int done; |
551 |
|
double posA[3], posB[3]; |
552 |
|
double velA[3], velB[3]; |
555 |
|
int a, b, ax, ay, az, bx, by, bz; |
556 |
|
double rma, rmb; |
557 |
|
double dx, dy, dz; |
558 |
< |
double rabsq, pabsq, rvab; |
577 |
< |
double diffsq; |
558 |
> |
double rvab; |
559 |
|
double gab; |
560 |
|
int iteration; |
561 |
|
|
645 |
|
} |
646 |
|
} |
647 |
|
|
648 |
+ |
template<typename T> void Integrator<T>::rotationPropagation |
649 |
+ |
( DirectionalAtom* dAtom, double ji[3] ){ |
650 |
+ |
|
651 |
+ |
double angle; |
652 |
+ |
double A[3][3], I[3][3]; |
653 |
+ |
|
654 |
+ |
// use the angular velocities to propagate the rotation matrix a |
655 |
+ |
// full time step |
656 |
+ |
|
657 |
+ |
dAtom->getA(A); |
658 |
+ |
dAtom->getI(I); |
659 |
+ |
|
660 |
+ |
// rotate about the x-axis |
661 |
+ |
angle = dt2 * ji[0] / I[0][0]; |
662 |
+ |
this->rotate( 1, 2, angle, ji, A ); |
663 |
+ |
|
664 |
+ |
// rotate about the y-axis |
665 |
+ |
angle = dt2 * ji[1] / I[1][1]; |
666 |
+ |
this->rotate( 2, 0, angle, ji, A ); |
667 |
+ |
|
668 |
+ |
// rotate about the z-axis |
669 |
+ |
angle = dt * ji[2] / I[2][2]; |
670 |
+ |
this->rotate( 0, 1, angle, ji, A); |
671 |
+ |
|
672 |
+ |
// rotate about the y-axis |
673 |
+ |
angle = dt2 * ji[1] / I[1][1]; |
674 |
+ |
this->rotate( 2, 0, angle, ji, A ); |
675 |
+ |
|
676 |
+ |
// rotate about the x-axis |
677 |
+ |
angle = dt2 * ji[0] / I[0][0]; |
678 |
+ |
this->rotate( 1, 2, angle, ji, A ); |
679 |
+ |
|
680 |
+ |
dAtom->setA( A ); |
681 |
+ |
} |
682 |
+ |
|
683 |
|
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
684 |
|
double angle, double ji[3], |
685 |
|
double A[3][3]){ |
770 |
|
template<typename T> void Integrator<T>::thermalize(){ |
771 |
|
tStats->velocitize(); |
772 |
|
} |
773 |
+ |
|
774 |
+ |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
775 |
+ |
return tStats->getTotalE(); |
776 |
+ |
} |