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 |
integrableObjects = info->integrableObjects; |
35 |
|
36 |
// check for constraints |
37 |
|
38 |
constrainedA = NULL; |
39 |
constrainedB = NULL; |
40 |
constrainedDsqr = NULL; |
41 |
moving = NULL; |
42 |
moved = NULL; |
43 |
oldPos = NULL; |
44 |
|
45 |
nConstrained = 0; |
46 |
|
47 |
checkConstraints(); |
48 |
|
49 |
} |
50 |
|
51 |
template<typename T> Integrator<T>::~Integrator(){ |
52 |
if (nConstrained){ |
53 |
delete[] constrainedA; |
54 |
delete[] constrainedB; |
55 |
delete[] constrainedDsqr; |
56 |
delete[] moving; |
57 |
delete[] moved; |
58 |
delete[] oldPos; |
59 |
} |
60 |
} |
61 |
|
62 |
template<typename T> void Integrator<T>::checkConstraints(void){ |
63 |
isConstrained = 0; |
64 |
|
65 |
Constraint* temp_con; |
66 |
Constraint* dummy_plug; |
67 |
temp_con = new Constraint[info->n_SRI]; |
68 |
nConstrained = 0; |
69 |
int constrained = 0; |
70 |
|
71 |
SRI** theArray; |
72 |
for (int i = 0; i < nMols; i++){ |
73 |
|
74 |
theArray = (SRI * *) molecules[i].getMyBonds(); |
75 |
for (int j = 0; j < molecules[i].getNBonds(); j++){ |
76 |
constrained = theArray[j]->is_constrained(); |
77 |
|
78 |
if (constrained){ |
79 |
dummy_plug = theArray[j]->get_constraint(); |
80 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
81 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
82 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
83 |
|
84 |
nConstrained++; |
85 |
constrained = 0; |
86 |
} |
87 |
} |
88 |
|
89 |
theArray = (SRI * *) molecules[i].getMyBends(); |
90 |
for (int j = 0; j < molecules[i].getNBends(); j++){ |
91 |
constrained = theArray[j]->is_constrained(); |
92 |
|
93 |
if (constrained){ |
94 |
dummy_plug = theArray[j]->get_constraint(); |
95 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
96 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
97 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
98 |
|
99 |
nConstrained++; |
100 |
constrained = 0; |
101 |
} |
102 |
} |
103 |
|
104 |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
105 |
for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
106 |
constrained = theArray[j]->is_constrained(); |
107 |
|
108 |
if (constrained){ |
109 |
dummy_plug = theArray[j]->get_constraint(); |
110 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
111 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
112 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
113 |
|
114 |
nConstrained++; |
115 |
constrained = 0; |
116 |
} |
117 |
} |
118 |
} |
119 |
|
120 |
|
121 |
if (nConstrained > 0){ |
122 |
isConstrained = 1; |
123 |
|
124 |
if (constrainedA != NULL) |
125 |
delete[] constrainedA; |
126 |
if (constrainedB != NULL) |
127 |
delete[] constrainedB; |
128 |
if (constrainedDsqr != NULL) |
129 |
delete[] constrainedDsqr; |
130 |
|
131 |
constrainedA = new int[nConstrained]; |
132 |
constrainedB = new int[nConstrained]; |
133 |
constrainedDsqr = new double[nConstrained]; |
134 |
|
135 |
for (int i = 0; i < nConstrained; i++){ |
136 |
constrainedA[i] = temp_con[i].get_a(); |
137 |
constrainedB[i] = temp_con[i].get_b(); |
138 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
139 |
} |
140 |
|
141 |
|
142 |
// save oldAtoms to check for lode balancing later on. |
143 |
|
144 |
oldAtoms = nAtoms; |
145 |
|
146 |
moving = new int[nAtoms]; |
147 |
moved = new int[nAtoms]; |
148 |
|
149 |
oldPos = new double[nAtoms * 3]; |
150 |
} |
151 |
|
152 |
delete[] temp_con; |
153 |
} |
154 |
|
155 |
|
156 |
template<typename T> void Integrator<T>::integrate(void){ |
157 |
|
158 |
double runTime = info->run_time; |
159 |
double sampleTime = info->sampleTime; |
160 |
double statusTime = info->statusTime; |
161 |
double thermalTime = info->thermalTime; |
162 |
double resetTime = info->resetTime; |
163 |
|
164 |
double difference; |
165 |
double currSample; |
166 |
double currThermal; |
167 |
double currStatus; |
168 |
double currReset; |
169 |
|
170 |
int calcPot, calcStress; |
171 |
|
172 |
tStats = new Thermo(info); |
173 |
statOut = new StatWriter(info); |
174 |
dumpOut = new DumpWriter(info); |
175 |
|
176 |
atoms = info->atoms; |
177 |
|
178 |
dt = info->dt; |
179 |
dt2 = 0.5 * dt; |
180 |
|
181 |
readyCheck(); |
182 |
|
183 |
// remove center of mass drift velocity (in case we passed in a configuration |
184 |
// that was drifting |
185 |
tStats->removeCOMdrift(); |
186 |
|
187 |
// initialize the retraints if necessary |
188 |
if (info->useThermInt) { |
189 |
myFF->initRestraints(); |
190 |
} |
191 |
|
192 |
// initialize the forces before the first step |
193 |
|
194 |
calcForce(1, 1); |
195 |
|
196 |
if (nConstrained){ |
197 |
preMove(); |
198 |
constrainA(); |
199 |
calcForce(1, 1); |
200 |
constrainB(); |
201 |
} |
202 |
|
203 |
if (info->setTemp){ |
204 |
thermalize(); |
205 |
} |
206 |
|
207 |
calcPot = 0; |
208 |
calcStress = 0; |
209 |
currSample = sampleTime + info->getTime(); |
210 |
currThermal = thermalTime+ info->getTime(); |
211 |
currStatus = statusTime + info->getTime(); |
212 |
currReset = resetTime + info->getTime(); |
213 |
|
214 |
dumpOut->writeDump(info->getTime()); |
215 |
statOut->writeStat(info->getTime()); |
216 |
|
217 |
|
218 |
#ifdef IS_MPI |
219 |
strcpy(checkPointMsg, "The integrator is ready to go."); |
220 |
MPIcheckPoint(); |
221 |
#endif // is_mpi |
222 |
|
223 |
while (info->getTime() < runTime && !stopIntegrator()){ |
224 |
difference = info->getTime() + dt - currStatus; |
225 |
if (difference > 0 || fabs(difference) < 1e-4 ){ |
226 |
calcPot = 1; |
227 |
calcStress = 1; |
228 |
} |
229 |
|
230 |
#ifdef PROFILE |
231 |
startProfile( pro1 ); |
232 |
#endif |
233 |
|
234 |
integrateStep(calcPot, calcStress); |
235 |
|
236 |
#ifdef PROFILE |
237 |
endProfile( pro1 ); |
238 |
|
239 |
startProfile( pro2 ); |
240 |
#endif // profile |
241 |
|
242 |
info->incrTime(dt); |
243 |
|
244 |
if (info->setTemp){ |
245 |
if (info->getTime() >= currThermal){ |
246 |
thermalize(); |
247 |
currThermal += thermalTime; |
248 |
} |
249 |
} |
250 |
|
251 |
if (info->getTime() >= currSample){ |
252 |
dumpOut->writeDump(info->getTime()); |
253 |
currSample += sampleTime; |
254 |
} |
255 |
|
256 |
if (info->getTime() >= currStatus){ |
257 |
statOut->writeStat(info->getTime()); |
258 |
statOut->writeRaw(info->getTime()); |
259 |
calcPot = 0; |
260 |
calcStress = 0; |
261 |
currStatus += statusTime; |
262 |
} |
263 |
|
264 |
if (info->resetIntegrator){ |
265 |
if (info->getTime() >= currReset){ |
266 |
this->resetIntegrator(); |
267 |
currReset += resetTime; |
268 |
} |
269 |
} |
270 |
|
271 |
#ifdef PROFILE |
272 |
endProfile( pro2 ); |
273 |
#endif //profile |
274 |
|
275 |
#ifdef IS_MPI |
276 |
strcpy(checkPointMsg, "successfully took a time step."); |
277 |
MPIcheckPoint(); |
278 |
#endif // is_mpi |
279 |
} |
280 |
|
281 |
// dump out a file containing the omega values for the final configuration |
282 |
if (info->useThermInt) |
283 |
myFF->dumpzAngle(); |
284 |
|
285 |
|
286 |
delete dumpOut; |
287 |
delete statOut; |
288 |
} |
289 |
|
290 |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
291 |
int calcStress){ |
292 |
// Position full step, and velocity half step |
293 |
|
294 |
#ifdef PROFILE |
295 |
startProfile(pro3); |
296 |
#endif //profile |
297 |
|
298 |
preMove(); |
299 |
|
300 |
#ifdef PROFILE |
301 |
endProfile(pro3); |
302 |
|
303 |
startProfile(pro4); |
304 |
#endif // profile |
305 |
|
306 |
moveA(); |
307 |
|
308 |
#ifdef PROFILE |
309 |
endProfile(pro4); |
310 |
|
311 |
startProfile(pro5); |
312 |
#endif//profile |
313 |
|
314 |
|
315 |
#ifdef IS_MPI |
316 |
strcpy(checkPointMsg, "Succesful moveA\n"); |
317 |
MPIcheckPoint(); |
318 |
#endif // is_mpi |
319 |
|
320 |
// calc forces |
321 |
calcForce(calcPot, calcStress); |
322 |
|
323 |
#ifdef IS_MPI |
324 |
strcpy(checkPointMsg, "Succesful doForces\n"); |
325 |
MPIcheckPoint(); |
326 |
#endif // is_mpi |
327 |
|
328 |
#ifdef PROFILE |
329 |
endProfile( pro5 ); |
330 |
|
331 |
startProfile( pro6 ); |
332 |
#endif //profile |
333 |
|
334 |
// finish the velocity half step |
335 |
|
336 |
moveB(); |
337 |
|
338 |
#ifdef PROFILE |
339 |
endProfile(pro6); |
340 |
#endif // profile |
341 |
|
342 |
#ifdef IS_MPI |
343 |
strcpy(checkPointMsg, "Succesful moveB\n"); |
344 |
MPIcheckPoint(); |
345 |
#endif // is_mpi |
346 |
} |
347 |
|
348 |
|
349 |
template<typename T> void Integrator<T>::moveA(void){ |
350 |
size_t i, j; |
351 |
DirectionalAtom* dAtom; |
352 |
double Tb[3], ji[3]; |
353 |
double vel[3], pos[3], frc[3]; |
354 |
double mass; |
355 |
double omega; |
356 |
|
357 |
for (i = 0; i < integrableObjects.size() ; i++){ |
358 |
integrableObjects[i]->getVel(vel); |
359 |
integrableObjects[i]->getPos(pos); |
360 |
integrableObjects[i]->getFrc(frc); |
361 |
|
362 |
mass = integrableObjects[i]->getMass(); |
363 |
|
364 |
for (j = 0; j < 3; j++){ |
365 |
// velocity half step |
366 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
367 |
// position whole step |
368 |
pos[j] += dt * vel[j]; |
369 |
} |
370 |
|
371 |
integrableObjects[i]->setVel(vel); |
372 |
integrableObjects[i]->setPos(pos); |
373 |
|
374 |
if (integrableObjects[i]->isDirectional()){ |
375 |
|
376 |
// get and convert the torque to body frame |
377 |
|
378 |
integrableObjects[i]->getTrq(Tb); |
379 |
integrableObjects[i]->lab2Body(Tb); |
380 |
|
381 |
// get the angular momentum, and propagate a half step |
382 |
|
383 |
integrableObjects[i]->getJ(ji); |
384 |
|
385 |
for (j = 0; j < 3; j++) |
386 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
387 |
|
388 |
this->rotationPropagation( integrableObjects[i], ji ); |
389 |
|
390 |
integrableObjects[i]->setJ(ji); |
391 |
} |
392 |
} |
393 |
|
394 |
if (nConstrained){ |
395 |
constrainA(); |
396 |
} |
397 |
} |
398 |
|
399 |
|
400 |
template<typename T> void Integrator<T>::moveB(void){ |
401 |
int i, j; |
402 |
double Tb[3], ji[3]; |
403 |
double vel[3], frc[3]; |
404 |
double mass; |
405 |
|
406 |
for (i = 0; i < integrableObjects.size(); i++){ |
407 |
integrableObjects[i]->getVel(vel); |
408 |
integrableObjects[i]->getFrc(frc); |
409 |
|
410 |
mass = integrableObjects[i]->getMass(); |
411 |
|
412 |
// velocity half step |
413 |
for (j = 0; j < 3; j++) |
414 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
415 |
|
416 |
integrableObjects[i]->setVel(vel); |
417 |
|
418 |
if (integrableObjects[i]->isDirectional()){ |
419 |
|
420 |
// get and convert the torque to body frame |
421 |
|
422 |
integrableObjects[i]->getTrq(Tb); |
423 |
integrableObjects[i]->lab2Body(Tb); |
424 |
|
425 |
// get the angular momentum, and propagate a half step |
426 |
|
427 |
integrableObjects[i]->getJ(ji); |
428 |
|
429 |
for (j = 0; j < 3; j++) |
430 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
431 |
|
432 |
|
433 |
integrableObjects[i]->setJ(ji); |
434 |
} |
435 |
} |
436 |
|
437 |
if (nConstrained){ |
438 |
constrainB(); |
439 |
} |
440 |
} |
441 |
|
442 |
template<typename T> void Integrator<T>::preMove(void){ |
443 |
int i, j; |
444 |
double pos[3]; |
445 |
|
446 |
if (nConstrained){ |
447 |
for (i = 0; i < nAtoms; i++){ |
448 |
atoms[i]->getPos(pos); |
449 |
|
450 |
for (j = 0; j < 3; j++){ |
451 |
oldPos[3 * i + j] = pos[j]; |
452 |
} |
453 |
} |
454 |
} |
455 |
} |
456 |
|
457 |
template<typename T> void Integrator<T>::constrainA(){ |
458 |
int i, j; |
459 |
int done; |
460 |
double posA[3], posB[3]; |
461 |
double velA[3], velB[3]; |
462 |
double pab[3]; |
463 |
double rab[3]; |
464 |
int a, b, ax, ay, az, bx, by, bz; |
465 |
double rma, rmb; |
466 |
double dx, dy, dz; |
467 |
double rpab; |
468 |
double rabsq, pabsq, rpabsq; |
469 |
double diffsq; |
470 |
double gab; |
471 |
int iteration; |
472 |
|
473 |
for (i = 0; i < nAtoms; i++){ |
474 |
moving[i] = 0; |
475 |
moved[i] = 1; |
476 |
} |
477 |
|
478 |
iteration = 0; |
479 |
done = 0; |
480 |
while (!done && (iteration < maxIteration)){ |
481 |
done = 1; |
482 |
for (i = 0; i < nConstrained; i++){ |
483 |
a = constrainedA[i]; |
484 |
b = constrainedB[i]; |
485 |
|
486 |
ax = (a * 3) + 0; |
487 |
ay = (a * 3) + 1; |
488 |
az = (a * 3) + 2; |
489 |
|
490 |
bx = (b * 3) + 0; |
491 |
by = (b * 3) + 1; |
492 |
bz = (b * 3) + 2; |
493 |
|
494 |
if (moved[a] || moved[b]){ |
495 |
atoms[a]->getPos(posA); |
496 |
atoms[b]->getPos(posB); |
497 |
|
498 |
for (j = 0; j < 3; j++) |
499 |
pab[j] = posA[j] - posB[j]; |
500 |
|
501 |
//periodic boundary condition |
502 |
|
503 |
info->wrapVector(pab); |
504 |
|
505 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
506 |
|
507 |
rabsq = constrainedDsqr[i]; |
508 |
diffsq = rabsq - pabsq; |
509 |
|
510 |
// the original rattle code from alan tidesley |
511 |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
512 |
rab[0] = oldPos[ax] - oldPos[bx]; |
513 |
rab[1] = oldPos[ay] - oldPos[by]; |
514 |
rab[2] = oldPos[az] - oldPos[bz]; |
515 |
|
516 |
info->wrapVector(rab); |
517 |
|
518 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
519 |
|
520 |
rpabsq = rpab * rpab; |
521 |
|
522 |
|
523 |
if (rpabsq < (rabsq * -diffsq)){ |
524 |
#ifdef IS_MPI |
525 |
a = atoms[a]->getGlobalIndex(); |
526 |
b = atoms[b]->getGlobalIndex(); |
527 |
#endif //is_mpi |
528 |
sprintf(painCave.errMsg, |
529 |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
530 |
b); |
531 |
painCave.isFatal = 1; |
532 |
simError(); |
533 |
} |
534 |
|
535 |
rma = 1.0 / atoms[a]->getMass(); |
536 |
rmb = 1.0 / atoms[b]->getMass(); |
537 |
|
538 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
539 |
|
540 |
dx = rab[0] * gab; |
541 |
dy = rab[1] * gab; |
542 |
dz = rab[2] * gab; |
543 |
|
544 |
posA[0] += rma * dx; |
545 |
posA[1] += rma * dy; |
546 |
posA[2] += rma * dz; |
547 |
|
548 |
atoms[a]->setPos(posA); |
549 |
|
550 |
posB[0] -= rmb * dx; |
551 |
posB[1] -= rmb * dy; |
552 |
posB[2] -= rmb * dz; |
553 |
|
554 |
atoms[b]->setPos(posB); |
555 |
|
556 |
dx = dx / dt; |
557 |
dy = dy / dt; |
558 |
dz = dz / dt; |
559 |
|
560 |
atoms[a]->getVel(velA); |
561 |
|
562 |
velA[0] += rma * dx; |
563 |
velA[1] += rma * dy; |
564 |
velA[2] += rma * dz; |
565 |
|
566 |
atoms[a]->setVel(velA); |
567 |
|
568 |
atoms[b]->getVel(velB); |
569 |
|
570 |
velB[0] -= rmb * dx; |
571 |
velB[1] -= rmb * dy; |
572 |
velB[2] -= rmb * dz; |
573 |
|
574 |
atoms[b]->setVel(velB); |
575 |
|
576 |
moving[a] = 1; |
577 |
moving[b] = 1; |
578 |
done = 0; |
579 |
} |
580 |
} |
581 |
} |
582 |
|
583 |
for (i = 0; i < nAtoms; i++){ |
584 |
moved[i] = moving[i]; |
585 |
moving[i] = 0; |
586 |
} |
587 |
|
588 |
iteration++; |
589 |
} |
590 |
|
591 |
if (!done){ |
592 |
sprintf(painCave.errMsg, |
593 |
"Constraint failure in constrainA, too many iterations: %d\n", |
594 |
iteration); |
595 |
painCave.isFatal = 1; |
596 |
simError(); |
597 |
} |
598 |
|
599 |
} |
600 |
|
601 |
template<typename T> void Integrator<T>::constrainB(void){ |
602 |
int i, j; |
603 |
int done; |
604 |
double posA[3], posB[3]; |
605 |
double velA[3], velB[3]; |
606 |
double vxab, vyab, vzab; |
607 |
double rab[3]; |
608 |
int a, b, ax, ay, az, bx, by, bz; |
609 |
double rma, rmb; |
610 |
double dx, dy, dz; |
611 |
double rvab; |
612 |
double gab; |
613 |
int iteration; |
614 |
|
615 |
for (i = 0; i < nAtoms; i++){ |
616 |
moving[i] = 0; |
617 |
moved[i] = 1; |
618 |
} |
619 |
|
620 |
done = 0; |
621 |
iteration = 0; |
622 |
while (!done && (iteration < maxIteration)){ |
623 |
done = 1; |
624 |
|
625 |
for (i = 0; i < nConstrained; i++){ |
626 |
a = constrainedA[i]; |
627 |
b = constrainedB[i]; |
628 |
|
629 |
ax = (a * 3) + 0; |
630 |
ay = (a * 3) + 1; |
631 |
az = (a * 3) + 2; |
632 |
|
633 |
bx = (b * 3) + 0; |
634 |
by = (b * 3) + 1; |
635 |
bz = (b * 3) + 2; |
636 |
|
637 |
if (moved[a] || moved[b]){ |
638 |
atoms[a]->getVel(velA); |
639 |
atoms[b]->getVel(velB); |
640 |
|
641 |
vxab = velA[0] - velB[0]; |
642 |
vyab = velA[1] - velB[1]; |
643 |
vzab = velA[2] - velB[2]; |
644 |
|
645 |
atoms[a]->getPos(posA); |
646 |
atoms[b]->getPos(posB); |
647 |
|
648 |
for (j = 0; j < 3; j++) |
649 |
rab[j] = posA[j] - posB[j]; |
650 |
|
651 |
info->wrapVector(rab); |
652 |
|
653 |
rma = 1.0 / atoms[a]->getMass(); |
654 |
rmb = 1.0 / atoms[b]->getMass(); |
655 |
|
656 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
657 |
|
658 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
659 |
|
660 |
if (fabs(gab) > tol){ |
661 |
dx = rab[0] * gab; |
662 |
dy = rab[1] * gab; |
663 |
dz = rab[2] * gab; |
664 |
|
665 |
velA[0] += rma * dx; |
666 |
velA[1] += rma * dy; |
667 |
velA[2] += rma * dz; |
668 |
|
669 |
atoms[a]->setVel(velA); |
670 |
|
671 |
velB[0] -= rmb * dx; |
672 |
velB[1] -= rmb * dy; |
673 |
velB[2] -= rmb * dz; |
674 |
|
675 |
atoms[b]->setVel(velB); |
676 |
|
677 |
moving[a] = 1; |
678 |
moving[b] = 1; |
679 |
done = 0; |
680 |
} |
681 |
} |
682 |
} |
683 |
|
684 |
for (i = 0; i < nAtoms; i++){ |
685 |
moved[i] = moving[i]; |
686 |
moving[i] = 0; |
687 |
} |
688 |
|
689 |
iteration++; |
690 |
} |
691 |
|
692 |
if (!done){ |
693 |
sprintf(painCave.errMsg, |
694 |
"Constraint failure in constrainB, too many iterations: %d\n", |
695 |
iteration); |
696 |
painCave.isFatal = 1; |
697 |
simError(); |
698 |
} |
699 |
} |
700 |
|
701 |
template<typename T> void Integrator<T>::rotationPropagation |
702 |
( StuntDouble* sd, double ji[3] ){ |
703 |
|
704 |
double angle; |
705 |
double A[3][3], I[3][3]; |
706 |
int i, j, k; |
707 |
|
708 |
// use the angular velocities to propagate the rotation matrix a |
709 |
// full time step |
710 |
|
711 |
sd->getA(A); |
712 |
sd->getI(I); |
713 |
|
714 |
if (sd->isLinear()) { |
715 |
i = sd->linearAxis(); |
716 |
j = (i+1)%3; |
717 |
k = (i+2)%3; |
718 |
|
719 |
angle = dt2 * ji[j] / I[j][j]; |
720 |
this->rotate( k, i, angle, ji, A ); |
721 |
|
722 |
angle = dt * ji[k] / I[k][k]; |
723 |
this->rotate( i, j, angle, ji, A); |
724 |
|
725 |
angle = dt2 * ji[j] / I[j][j]; |
726 |
this->rotate( k, i, angle, ji, A ); |
727 |
|
728 |
} else { |
729 |
// rotate about the x-axis |
730 |
angle = dt2 * ji[0] / I[0][0]; |
731 |
this->rotate( 1, 2, angle, ji, A ); |
732 |
|
733 |
// rotate about the y-axis |
734 |
angle = dt2 * ji[1] / I[1][1]; |
735 |
this->rotate( 2, 0, angle, ji, A ); |
736 |
|
737 |
// rotate about the z-axis |
738 |
angle = dt * ji[2] / I[2][2]; |
739 |
sd->addZangle(angle); |
740 |
this->rotate( 0, 1, angle, ji, A); |
741 |
|
742 |
// rotate about the y-axis |
743 |
angle = dt2 * ji[1] / I[1][1]; |
744 |
this->rotate( 2, 0, angle, ji, A ); |
745 |
|
746 |
// rotate about the x-axis |
747 |
angle = dt2 * ji[0] / I[0][0]; |
748 |
this->rotate( 1, 2, angle, ji, A ); |
749 |
|
750 |
} |
751 |
sd->setA( A ); |
752 |
} |
753 |
|
754 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
755 |
double angle, double ji[3], |
756 |
double A[3][3]){ |
757 |
int i, j, k; |
758 |
double sinAngle; |
759 |
double cosAngle; |
760 |
double angleSqr; |
761 |
double angleSqrOver4; |
762 |
double top, bottom; |
763 |
double rot[3][3]; |
764 |
double tempA[3][3]; |
765 |
double tempJ[3]; |
766 |
|
767 |
// initialize the tempA |
768 |
|
769 |
for (i = 0; i < 3; i++){ |
770 |
for (j = 0; j < 3; j++){ |
771 |
tempA[j][i] = A[i][j]; |
772 |
} |
773 |
} |
774 |
|
775 |
// initialize the tempJ |
776 |
|
777 |
for (i = 0; i < 3; i++) |
778 |
tempJ[i] = ji[i]; |
779 |
|
780 |
// initalize rot as a unit matrix |
781 |
|
782 |
rot[0][0] = 1.0; |
783 |
rot[0][1] = 0.0; |
784 |
rot[0][2] = 0.0; |
785 |
|
786 |
rot[1][0] = 0.0; |
787 |
rot[1][1] = 1.0; |
788 |
rot[1][2] = 0.0; |
789 |
|
790 |
rot[2][0] = 0.0; |
791 |
rot[2][1] = 0.0; |
792 |
rot[2][2] = 1.0; |
793 |
|
794 |
// use a small angle aproximation for sin and cosine |
795 |
|
796 |
angleSqr = angle * angle; |
797 |
angleSqrOver4 = angleSqr / 4.0; |
798 |
top = 1.0 - angleSqrOver4; |
799 |
bottom = 1.0 + angleSqrOver4; |
800 |
|
801 |
cosAngle = top / bottom; |
802 |
sinAngle = angle / bottom; |
803 |
|
804 |
rot[axes1][axes1] = cosAngle; |
805 |
rot[axes2][axes2] = cosAngle; |
806 |
|
807 |
rot[axes1][axes2] = sinAngle; |
808 |
rot[axes2][axes1] = -sinAngle; |
809 |
|
810 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
811 |
|
812 |
for (i = 0; i < 3; i++){ |
813 |
ji[i] = 0.0; |
814 |
for (k = 0; k < 3; k++){ |
815 |
ji[i] += rot[i][k] * tempJ[k]; |
816 |
} |
817 |
} |
818 |
|
819 |
// rotate the Rotation matrix acording to: |
820 |
// A[][] = A[][] * transpose(rot[][]) |
821 |
|
822 |
|
823 |
// NOte for as yet unknown reason, we are performing the |
824 |
// calculation as: |
825 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
826 |
|
827 |
for (i = 0; i < 3; i++){ |
828 |
for (j = 0; j < 3; j++){ |
829 |
A[j][i] = 0.0; |
830 |
for (k = 0; k < 3; k++){ |
831 |
A[j][i] += tempA[i][k] * rot[j][k]; |
832 |
} |
833 |
} |
834 |
} |
835 |
} |
836 |
|
837 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
838 |
myFF->doForces(calcPot, calcStress); |
839 |
} |
840 |
|
841 |
template<typename T> void Integrator<T>::thermalize(){ |
842 |
tStats->velocitize(); |
843 |
} |
844 |
|
845 |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
846 |
return tStats->getTotalE(); |
847 |
} |
848 |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
849 |
//By default, return a null string |
850 |
//The reason we use string instead of char* is that if we use char*, we will |
851 |
//return a pointer point to local variable which might cause problem |
852 |
return string(); |
853 |
} |