1 |
#include <iostream> |
2 |
#include <stdlib.h> |
3 |
#include <math.h> |
4 |
|
5 |
#ifdef IS_MPI |
6 |
#include "mpiSimulation.hpp" |
7 |
#include <unistd.h> |
8 |
#endif //is_mpi |
9 |
|
10 |
#ifdef PROFILE |
11 |
#include "mdProfile.hpp" |
12 |
#endif // profile |
13 |
|
14 |
#include "Integrator.hpp" |
15 |
#include "simError.h" |
16 |
|
17 |
|
18 |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
19 |
ForceFields* the_ff){ |
20 |
info = theInfo; |
21 |
myFF = the_ff; |
22 |
isFirst = 1; |
23 |
|
24 |
molecules = info->molecules; |
25 |
nMols = info->n_mol; |
26 |
|
27 |
// give a little love back to the SimInfo object |
28 |
|
29 |
if (info->the_integrator != NULL){ |
30 |
delete info->the_integrator; |
31 |
} |
32 |
|
33 |
nAtoms = info->n_atoms; |
34 |
|
35 |
// check for constraints |
36 |
|
37 |
constrainedA = NULL; |
38 |
constrainedB = NULL; |
39 |
constrainedDsqr = NULL; |
40 |
moving = NULL; |
41 |
moved = NULL; |
42 |
oldPos = NULL; |
43 |
|
44 |
nConstrained = 0; |
45 |
|
46 |
checkConstraints(); |
47 |
} |
48 |
|
49 |
template<typename T> Integrator<T>::~Integrator(){ |
50 |
if (nConstrained){ |
51 |
delete[] constrainedA; |
52 |
delete[] constrainedB; |
53 |
delete[] constrainedDsqr; |
54 |
delete[] moving; |
55 |
delete[] moved; |
56 |
delete[] oldPos; |
57 |
} |
58 |
} |
59 |
|
60 |
template<typename T> void Integrator<T>::checkConstraints(void){ |
61 |
isConstrained = 0; |
62 |
|
63 |
Constraint* temp_con; |
64 |
Constraint* dummy_plug; |
65 |
temp_con = new Constraint[info->n_SRI]; |
66 |
nConstrained = 0; |
67 |
int constrained = 0; |
68 |
|
69 |
SRI** theArray; |
70 |
for (int i = 0; i < nMols; i++){ |
71 |
|
72 |
theArray = (SRI * *) molecules[i].getMyBonds(); |
73 |
for (int j = 0; j < molecules[i].getNBonds(); j++){ |
74 |
constrained = theArray[j]->is_constrained(); |
75 |
|
76 |
if (constrained){ |
77 |
dummy_plug = theArray[j]->get_constraint(); |
78 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
79 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
80 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
81 |
|
82 |
nConstrained++; |
83 |
constrained = 0; |
84 |
} |
85 |
} |
86 |
|
87 |
theArray = (SRI * *) molecules[i].getMyBends(); |
88 |
for (int j = 0; j < molecules[i].getNBends(); j++){ |
89 |
constrained = theArray[j]->is_constrained(); |
90 |
|
91 |
if (constrained){ |
92 |
dummy_plug = theArray[j]->get_constraint(); |
93 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
94 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
95 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
96 |
|
97 |
nConstrained++; |
98 |
constrained = 0; |
99 |
} |
100 |
} |
101 |
|
102 |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
103 |
for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
104 |
constrained = theArray[j]->is_constrained(); |
105 |
|
106 |
if (constrained){ |
107 |
dummy_plug = theArray[j]->get_constraint(); |
108 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
109 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
110 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
111 |
|
112 |
nConstrained++; |
113 |
constrained = 0; |
114 |
} |
115 |
} |
116 |
} |
117 |
|
118 |
|
119 |
if (nConstrained > 0){ |
120 |
isConstrained = 1; |
121 |
|
122 |
if (constrainedA != NULL) |
123 |
delete[] constrainedA; |
124 |
if (constrainedB != NULL) |
125 |
delete[] constrainedB; |
126 |
if (constrainedDsqr != NULL) |
127 |
delete[] constrainedDsqr; |
128 |
|
129 |
constrainedA = new int[nConstrained]; |
130 |
constrainedB = new int[nConstrained]; |
131 |
constrainedDsqr = new double[nConstrained]; |
132 |
|
133 |
for (int i = 0; i < nConstrained; i++){ |
134 |
constrainedA[i] = temp_con[i].get_a(); |
135 |
constrainedB[i] = temp_con[i].get_b(); |
136 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
137 |
} |
138 |
|
139 |
|
140 |
// save oldAtoms to check for lode balancing later on. |
141 |
|
142 |
oldAtoms = nAtoms; |
143 |
|
144 |
moving = new int[nAtoms]; |
145 |
moved = new int[nAtoms]; |
146 |
|
147 |
oldPos = new double[nAtoms * 3]; |
148 |
} |
149 |
|
150 |
delete[] temp_con; |
151 |
} |
152 |
|
153 |
|
154 |
template<typename T> void Integrator<T>::integrate(void){ |
155 |
|
156 |
double runTime = info->run_time; |
157 |
double sampleTime = info->sampleTime; |
158 |
double statusTime = info->statusTime; |
159 |
double thermalTime = info->thermalTime; |
160 |
double resetTime = info->resetTime; |
161 |
|
162 |
|
163 |
double currSample; |
164 |
double currThermal; |
165 |
double currStatus; |
166 |
double currReset; |
167 |
|
168 |
int calcPot, calcStress; |
169 |
|
170 |
tStats = new Thermo(info); |
171 |
statOut = new StatWriter(info); |
172 |
dumpOut = new DumpWriter(info); |
173 |
|
174 |
atoms = info->atoms; |
175 |
|
176 |
dt = info->dt; |
177 |
dt2 = 0.5 * dt; |
178 |
|
179 |
readyCheck(); |
180 |
|
181 |
// initialize the forces before the first step |
182 |
|
183 |
calcForce(1, 1); |
184 |
|
185 |
//temp test |
186 |
tStats->getPotential(); |
187 |
|
188 |
if (nConstrained){ |
189 |
preMove(); |
190 |
constrainA(); |
191 |
calcForce(1, 1); |
192 |
constrainB(); |
193 |
} |
194 |
|
195 |
if (info->setTemp){ |
196 |
thermalize(); |
197 |
} |
198 |
|
199 |
calcPot = 0; |
200 |
calcStress = 0; |
201 |
currSample = sampleTime + info->getTime(); |
202 |
currThermal = thermalTime+ info->getTime(); |
203 |
currStatus = statusTime + info->getTime(); |
204 |
currReset = resetTime + info->getTime(); |
205 |
|
206 |
dumpOut->writeDump(info->getTime()); |
207 |
statOut->writeStat(info->getTime()); |
208 |
|
209 |
|
210 |
#ifdef IS_MPI |
211 |
strcpy(checkPointMsg, "The integrator is ready to go."); |
212 |
MPIcheckPoint(); |
213 |
#endif // is_mpi |
214 |
|
215 |
while (info->getTime() < runTime){ |
216 |
if ((info->getTime() + dt) >= currStatus){ |
217 |
calcPot = 1; |
218 |
calcStress = 1; |
219 |
} |
220 |
|
221 |
#ifdef PROFILE |
222 |
startProfile( pro1 ); |
223 |
#endif |
224 |
|
225 |
integrateStep(calcPot, calcStress); |
226 |
|
227 |
#ifdef PROFILE |
228 |
endProfile( pro1 ); |
229 |
|
230 |
startProfile( pro2 ); |
231 |
#endif // profile |
232 |
|
233 |
info->incrTime(dt); |
234 |
|
235 |
if (info->setTemp){ |
236 |
if (info->getTime() >= currThermal){ |
237 |
thermalize(); |
238 |
currThermal += thermalTime; |
239 |
} |
240 |
} |
241 |
|
242 |
if (info->getTime() >= currSample){ |
243 |
dumpOut->writeDump(info->getTime()); |
244 |
currSample += sampleTime; |
245 |
} |
246 |
|
247 |
if (info->getTime() >= currStatus){ |
248 |
statOut->writeStat(info->getTime()); |
249 |
calcPot = 0; |
250 |
calcStress = 0; |
251 |
currStatus += statusTime; |
252 |
} |
253 |
|
254 |
if (info->resetIntegrator){ |
255 |
if (info->getTime() >= currReset){ |
256 |
this->resetIntegrator(); |
257 |
currReset += resetTime; |
258 |
} |
259 |
} |
260 |
|
261 |
#ifdef PROFILE |
262 |
endProfile( pro2 ); |
263 |
#endif //profile |
264 |
|
265 |
#ifdef IS_MPI |
266 |
strcpy(checkPointMsg, "successfully took a time step."); |
267 |
MPIcheckPoint(); |
268 |
#endif // is_mpi |
269 |
} |
270 |
|
271 |
delete dumpOut; |
272 |
delete statOut; |
273 |
} |
274 |
|
275 |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
276 |
int calcStress){ |
277 |
// Position full step, and velocity half step |
278 |
|
279 |
#ifdef PROFILE |
280 |
startProfile(pro3); |
281 |
#endif //profile |
282 |
|
283 |
preMove(); |
284 |
|
285 |
#ifdef PROFILE |
286 |
endProfile(pro3); |
287 |
|
288 |
startProfile(pro4); |
289 |
#endif // profile |
290 |
|
291 |
moveA(); |
292 |
|
293 |
#ifdef PROFILE |
294 |
endProfile(pro4); |
295 |
|
296 |
startProfile(pro5); |
297 |
#endif//profile |
298 |
|
299 |
|
300 |
#ifdef IS_MPI |
301 |
strcpy(checkPointMsg, "Succesful moveA\n"); |
302 |
MPIcheckPoint(); |
303 |
#endif // is_mpi |
304 |
|
305 |
|
306 |
// calc forces |
307 |
|
308 |
calcForce(calcPot, calcStress); |
309 |
|
310 |
#ifdef IS_MPI |
311 |
strcpy(checkPointMsg, "Succesful doForces\n"); |
312 |
MPIcheckPoint(); |
313 |
#endif // is_mpi |
314 |
|
315 |
#ifdef PROFILE |
316 |
endProfile( pro5 ); |
317 |
|
318 |
startProfile( pro6 ); |
319 |
#endif //profile |
320 |
|
321 |
// finish the velocity half step |
322 |
|
323 |
moveB(); |
324 |
|
325 |
#ifdef PROFILE |
326 |
endProfile(pro6); |
327 |
#endif // profile |
328 |
|
329 |
#ifdef IS_MPI |
330 |
strcpy(checkPointMsg, "Succesful moveB\n"); |
331 |
MPIcheckPoint(); |
332 |
#endif // is_mpi |
333 |
} |
334 |
|
335 |
|
336 |
template<typename T> void Integrator<T>::moveA(void){ |
337 |
int i, j; |
338 |
DirectionalAtom* dAtom; |
339 |
double Tb[3], ji[3]; |
340 |
double vel[3], pos[3], frc[3]; |
341 |
double mass; |
342 |
|
343 |
for (i = 0; i < nAtoms; i++){ |
344 |
atoms[i]->getVel(vel); |
345 |
atoms[i]->getPos(pos); |
346 |
atoms[i]->getFrc(frc); |
347 |
|
348 |
mass = atoms[i]->getMass(); |
349 |
|
350 |
for (j = 0; j < 3; j++){ |
351 |
// velocity half step |
352 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
353 |
// position whole step |
354 |
pos[j] += dt * vel[j]; |
355 |
} |
356 |
|
357 |
atoms[i]->setVel(vel); |
358 |
atoms[i]->setPos(pos); |
359 |
|
360 |
if (atoms[i]->isDirectional()){ |
361 |
dAtom = (DirectionalAtom *) atoms[i]; |
362 |
|
363 |
// get and convert the torque to body frame |
364 |
|
365 |
dAtom->getTrq(Tb); |
366 |
dAtom->lab2Body(Tb); |
367 |
|
368 |
// get the angular momentum, and propagate a half step |
369 |
|
370 |
dAtom->getJ(ji); |
371 |
|
372 |
for (j = 0; j < 3; j++) |
373 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
374 |
|
375 |
this->rotationPropagation( dAtom, ji ); |
376 |
|
377 |
dAtom->setJ(ji); |
378 |
} |
379 |
} |
380 |
|
381 |
if (nConstrained){ |
382 |
constrainA(); |
383 |
} |
384 |
} |
385 |
|
386 |
|
387 |
template<typename T> void Integrator<T>::moveB(void){ |
388 |
int i, j; |
389 |
DirectionalAtom* dAtom; |
390 |
double Tb[3], ji[3]; |
391 |
double vel[3], frc[3]; |
392 |
double mass; |
393 |
|
394 |
for (i = 0; i < nAtoms; i++){ |
395 |
atoms[i]->getVel(vel); |
396 |
atoms[i]->getFrc(frc); |
397 |
|
398 |
mass = atoms[i]->getMass(); |
399 |
|
400 |
// velocity half step |
401 |
for (j = 0; j < 3; j++) |
402 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
403 |
|
404 |
atoms[i]->setVel(vel); |
405 |
|
406 |
if (atoms[i]->isDirectional()){ |
407 |
dAtom = (DirectionalAtom *) atoms[i]; |
408 |
|
409 |
// get and convert the torque to body frame |
410 |
|
411 |
dAtom->getTrq(Tb); |
412 |
dAtom->lab2Body(Tb); |
413 |
|
414 |
// get the angular momentum, and propagate a half step |
415 |
|
416 |
dAtom->getJ(ji); |
417 |
|
418 |
for (j = 0; j < 3; j++) |
419 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
420 |
|
421 |
|
422 |
dAtom->setJ(ji); |
423 |
} |
424 |
} |
425 |
|
426 |
if (nConstrained){ |
427 |
constrainB(); |
428 |
} |
429 |
} |
430 |
|
431 |
template<typename T> void Integrator<T>::preMove(void){ |
432 |
int i, j; |
433 |
double pos[3]; |
434 |
|
435 |
if (nConstrained){ |
436 |
for (i = 0; i < nAtoms; i++){ |
437 |
atoms[i]->getPos(pos); |
438 |
|
439 |
for (j = 0; j < 3; j++){ |
440 |
oldPos[3 * i + j] = pos[j]; |
441 |
} |
442 |
} |
443 |
} |
444 |
} |
445 |
|
446 |
template<typename T> void Integrator<T>::constrainA(){ |
447 |
int i, j; |
448 |
int done; |
449 |
double posA[3], posB[3]; |
450 |
double velA[3], velB[3]; |
451 |
double pab[3]; |
452 |
double rab[3]; |
453 |
int a, b, ax, ay, az, bx, by, bz; |
454 |
double rma, rmb; |
455 |
double dx, dy, dz; |
456 |
double rpab; |
457 |
double rabsq, pabsq, rpabsq; |
458 |
double diffsq; |
459 |
double gab; |
460 |
int iteration; |
461 |
|
462 |
for (i = 0; i < nAtoms; i++){ |
463 |
moving[i] = 0; |
464 |
moved[i] = 1; |
465 |
} |
466 |
|
467 |
iteration = 0; |
468 |
done = 0; |
469 |
while (!done && (iteration < maxIteration)){ |
470 |
done = 1; |
471 |
for (i = 0; i < nConstrained; i++){ |
472 |
a = constrainedA[i]; |
473 |
b = constrainedB[i]; |
474 |
|
475 |
ax = (a * 3) + 0; |
476 |
ay = (a * 3) + 1; |
477 |
az = (a * 3) + 2; |
478 |
|
479 |
bx = (b * 3) + 0; |
480 |
by = (b * 3) + 1; |
481 |
bz = (b * 3) + 2; |
482 |
|
483 |
if (moved[a] || moved[b]){ |
484 |
atoms[a]->getPos(posA); |
485 |
atoms[b]->getPos(posB); |
486 |
|
487 |
for (j = 0; j < 3; j++) |
488 |
pab[j] = posA[j] - posB[j]; |
489 |
|
490 |
//periodic boundary condition |
491 |
|
492 |
info->wrapVector(pab); |
493 |
|
494 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
495 |
|
496 |
rabsq = constrainedDsqr[i]; |
497 |
diffsq = rabsq - pabsq; |
498 |
|
499 |
// the original rattle code from alan tidesley |
500 |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
501 |
rab[0] = oldPos[ax] - oldPos[bx]; |
502 |
rab[1] = oldPos[ay] - oldPos[by]; |
503 |
rab[2] = oldPos[az] - oldPos[bz]; |
504 |
|
505 |
info->wrapVector(rab); |
506 |
|
507 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
508 |
|
509 |
rpabsq = rpab * rpab; |
510 |
|
511 |
|
512 |
if (rpabsq < (rabsq * -diffsq)){ |
513 |
#ifdef IS_MPI |
514 |
a = atoms[a]->getGlobalIndex(); |
515 |
b = atoms[b]->getGlobalIndex(); |
516 |
#endif //is_mpi |
517 |
sprintf(painCave.errMsg, |
518 |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
519 |
b); |
520 |
painCave.isFatal = 1; |
521 |
simError(); |
522 |
} |
523 |
|
524 |
rma = 1.0 / atoms[a]->getMass(); |
525 |
rmb = 1.0 / atoms[b]->getMass(); |
526 |
|
527 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
528 |
|
529 |
dx = rab[0] * gab; |
530 |
dy = rab[1] * gab; |
531 |
dz = rab[2] * gab; |
532 |
|
533 |
posA[0] += rma * dx; |
534 |
posA[1] += rma * dy; |
535 |
posA[2] += rma * dz; |
536 |
|
537 |
atoms[a]->setPos(posA); |
538 |
|
539 |
posB[0] -= rmb * dx; |
540 |
posB[1] -= rmb * dy; |
541 |
posB[2] -= rmb * dz; |
542 |
|
543 |
atoms[b]->setPos(posB); |
544 |
|
545 |
dx = dx / dt; |
546 |
dy = dy / dt; |
547 |
dz = dz / dt; |
548 |
|
549 |
atoms[a]->getVel(velA); |
550 |
|
551 |
velA[0] += rma * dx; |
552 |
velA[1] += rma * dy; |
553 |
velA[2] += rma * dz; |
554 |
|
555 |
atoms[a]->setVel(velA); |
556 |
|
557 |
atoms[b]->getVel(velB); |
558 |
|
559 |
velB[0] -= rmb * dx; |
560 |
velB[1] -= rmb * dy; |
561 |
velB[2] -= rmb * dz; |
562 |
|
563 |
atoms[b]->setVel(velB); |
564 |
|
565 |
moving[a] = 1; |
566 |
moving[b] = 1; |
567 |
done = 0; |
568 |
} |
569 |
} |
570 |
} |
571 |
|
572 |
for (i = 0; i < nAtoms; i++){ |
573 |
moved[i] = moving[i]; |
574 |
moving[i] = 0; |
575 |
} |
576 |
|
577 |
iteration++; |
578 |
} |
579 |
|
580 |
if (!done){ |
581 |
sprintf(painCave.errMsg, |
582 |
"Constraint failure in constrainA, too many iterations: %d\n", |
583 |
iteration); |
584 |
painCave.isFatal = 1; |
585 |
simError(); |
586 |
} |
587 |
|
588 |
} |
589 |
|
590 |
template<typename T> void Integrator<T>::constrainB(void){ |
591 |
int i, j; |
592 |
int done; |
593 |
double posA[3], posB[3]; |
594 |
double velA[3], velB[3]; |
595 |
double vxab, vyab, vzab; |
596 |
double rab[3]; |
597 |
int a, b, ax, ay, az, bx, by, bz; |
598 |
double rma, rmb; |
599 |
double dx, dy, dz; |
600 |
double rvab; |
601 |
double gab; |
602 |
int iteration; |
603 |
|
604 |
for (i = 0; i < nAtoms; i++){ |
605 |
moving[i] = 0; |
606 |
moved[i] = 1; |
607 |
} |
608 |
|
609 |
done = 0; |
610 |
iteration = 0; |
611 |
while (!done && (iteration < maxIteration)){ |
612 |
done = 1; |
613 |
|
614 |
for (i = 0; i < nConstrained; i++){ |
615 |
a = constrainedA[i]; |
616 |
b = constrainedB[i]; |
617 |
|
618 |
ax = (a * 3) + 0; |
619 |
ay = (a * 3) + 1; |
620 |
az = (a * 3) + 2; |
621 |
|
622 |
bx = (b * 3) + 0; |
623 |
by = (b * 3) + 1; |
624 |
bz = (b * 3) + 2; |
625 |
|
626 |
if (moved[a] || moved[b]){ |
627 |
atoms[a]->getVel(velA); |
628 |
atoms[b]->getVel(velB); |
629 |
|
630 |
vxab = velA[0] - velB[0]; |
631 |
vyab = velA[1] - velB[1]; |
632 |
vzab = velA[2] - velB[2]; |
633 |
|
634 |
atoms[a]->getPos(posA); |
635 |
atoms[b]->getPos(posB); |
636 |
|
637 |
for (j = 0; j < 3; j++) |
638 |
rab[j] = posA[j] - posB[j]; |
639 |
|
640 |
info->wrapVector(rab); |
641 |
|
642 |
rma = 1.0 / atoms[a]->getMass(); |
643 |
rmb = 1.0 / atoms[b]->getMass(); |
644 |
|
645 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
646 |
|
647 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
648 |
|
649 |
if (fabs(gab) > tol){ |
650 |
dx = rab[0] * gab; |
651 |
dy = rab[1] * gab; |
652 |
dz = rab[2] * gab; |
653 |
|
654 |
velA[0] += rma * dx; |
655 |
velA[1] += rma * dy; |
656 |
velA[2] += rma * dz; |
657 |
|
658 |
atoms[a]->setVel(velA); |
659 |
|
660 |
velB[0] -= rmb * dx; |
661 |
velB[1] -= rmb * dy; |
662 |
velB[2] -= rmb * dz; |
663 |
|
664 |
atoms[b]->setVel(velB); |
665 |
|
666 |
moving[a] = 1; |
667 |
moving[b] = 1; |
668 |
done = 0; |
669 |
} |
670 |
} |
671 |
} |
672 |
|
673 |
for (i = 0; i < nAtoms; i++){ |
674 |
moved[i] = moving[i]; |
675 |
moving[i] = 0; |
676 |
} |
677 |
|
678 |
iteration++; |
679 |
} |
680 |
|
681 |
if (!done){ |
682 |
sprintf(painCave.errMsg, |
683 |
"Constraint failure in constrainB, too many iterations: %d\n", |
684 |
iteration); |
685 |
painCave.isFatal = 1; |
686 |
simError(); |
687 |
} |
688 |
} |
689 |
|
690 |
template<typename T> void Integrator<T>::rotationPropagation |
691 |
( DirectionalAtom* dAtom, double ji[3] ){ |
692 |
|
693 |
double angle; |
694 |
double A[3][3], I[3][3]; |
695 |
|
696 |
// use the angular velocities to propagate the rotation matrix a |
697 |
// full time step |
698 |
|
699 |
dAtom->getA(A); |
700 |
dAtom->getI(I); |
701 |
|
702 |
// rotate about the x-axis |
703 |
angle = dt2 * ji[0] / I[0][0]; |
704 |
this->rotate( 1, 2, angle, ji, A ); |
705 |
|
706 |
// rotate about the y-axis |
707 |
angle = dt2 * ji[1] / I[1][1]; |
708 |
this->rotate( 2, 0, angle, ji, A ); |
709 |
|
710 |
// rotate about the z-axis |
711 |
angle = dt * ji[2] / I[2][2]; |
712 |
this->rotate( 0, 1, angle, ji, A); |
713 |
|
714 |
// rotate about the y-axis |
715 |
angle = dt2 * ji[1] / I[1][1]; |
716 |
this->rotate( 2, 0, angle, ji, A ); |
717 |
|
718 |
// rotate about the x-axis |
719 |
angle = dt2 * ji[0] / I[0][0]; |
720 |
this->rotate( 1, 2, angle, ji, A ); |
721 |
|
722 |
dAtom->setA( A ); |
723 |
} |
724 |
|
725 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
726 |
double angle, double ji[3], |
727 |
double A[3][3]){ |
728 |
int i, j, k; |
729 |
double sinAngle; |
730 |
double cosAngle; |
731 |
double angleSqr; |
732 |
double angleSqrOver4; |
733 |
double top, bottom; |
734 |
double rot[3][3]; |
735 |
double tempA[3][3]; |
736 |
double tempJ[3]; |
737 |
|
738 |
// initialize the tempA |
739 |
|
740 |
for (i = 0; i < 3; i++){ |
741 |
for (j = 0; j < 3; j++){ |
742 |
tempA[j][i] = A[i][j]; |
743 |
} |
744 |
} |
745 |
|
746 |
// initialize the tempJ |
747 |
|
748 |
for (i = 0; i < 3; i++) |
749 |
tempJ[i] = ji[i]; |
750 |
|
751 |
// initalize rot as a unit matrix |
752 |
|
753 |
rot[0][0] = 1.0; |
754 |
rot[0][1] = 0.0; |
755 |
rot[0][2] = 0.0; |
756 |
|
757 |
rot[1][0] = 0.0; |
758 |
rot[1][1] = 1.0; |
759 |
rot[1][2] = 0.0; |
760 |
|
761 |
rot[2][0] = 0.0; |
762 |
rot[2][1] = 0.0; |
763 |
rot[2][2] = 1.0; |
764 |
|
765 |
// use a small angle aproximation for sin and cosine |
766 |
|
767 |
angleSqr = angle * angle; |
768 |
angleSqrOver4 = angleSqr / 4.0; |
769 |
top = 1.0 - angleSqrOver4; |
770 |
bottom = 1.0 + angleSqrOver4; |
771 |
|
772 |
cosAngle = top / bottom; |
773 |
sinAngle = angle / bottom; |
774 |
|
775 |
rot[axes1][axes1] = cosAngle; |
776 |
rot[axes2][axes2] = cosAngle; |
777 |
|
778 |
rot[axes1][axes2] = sinAngle; |
779 |
rot[axes2][axes1] = -sinAngle; |
780 |
|
781 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
782 |
|
783 |
for (i = 0; i < 3; i++){ |
784 |
ji[i] = 0.0; |
785 |
for (k = 0; k < 3; k++){ |
786 |
ji[i] += rot[i][k] * tempJ[k]; |
787 |
} |
788 |
} |
789 |
|
790 |
// rotate the Rotation matrix acording to: |
791 |
// A[][] = A[][] * transpose(rot[][]) |
792 |
|
793 |
|
794 |
// NOte for as yet unknown reason, we are performing the |
795 |
// calculation as: |
796 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
797 |
|
798 |
for (i = 0; i < 3; i++){ |
799 |
for (j = 0; j < 3; j++){ |
800 |
A[j][i] = 0.0; |
801 |
for (k = 0; k < 3; k++){ |
802 |
A[j][i] += tempA[i][k] * rot[j][k]; |
803 |
} |
804 |
} |
805 |
} |
806 |
} |
807 |
|
808 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
809 |
myFF->doForces(calcPot, calcStress); |
810 |
} |
811 |
|
812 |
template<typename T> void Integrator<T>::thermalize(){ |
813 |
tStats->velocitize(); |
814 |
} |
815 |
|
816 |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
817 |
return tStats->getTotalE(); |
818 |
} |
819 |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
820 |
//By default, return a null string |
821 |
//The reason we use string instead of char* is that if we use char*, we will |
822 |
//return a pointer point to local variable which might cause problem |
823 |
return string(); |
824 |
} |