1 |
#include <iostream> |
2 |
#include <stdlib.h> |
3 |
#include <math.h> |
4 |
#ifdef IS_MPI |
5 |
#include "mpiSimulation.hpp" |
6 |
#include <unistd.h> |
7 |
#endif //is_mpi |
8 |
|
9 |
#ifdef PROFILE |
10 |
#include "mdProfile.hpp" |
11 |
#endif // profile |
12 |
|
13 |
#include "Integrator.hpp" |
14 |
#include "simError.h" |
15 |
|
16 |
|
17 |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
18 |
ForceFields* the_ff){ |
19 |
info = theInfo; |
20 |
myFF = the_ff; |
21 |
isFirst = 1; |
22 |
|
23 |
molecules = info->molecules; |
24 |
nMols = info->n_mol; |
25 |
|
26 |
// give a little love back to the SimInfo object |
27 |
|
28 |
if (info->the_integrator != NULL){ |
29 |
delete info->the_integrator; |
30 |
} |
31 |
|
32 |
nAtoms = info->n_atoms; |
33 |
integrableObjects = info->integrableObjects; |
34 |
|
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 |
|
53 |
if (nConstrained){ |
54 |
delete[] constrainedA; |
55 |
delete[] constrainedB; |
56 |
delete[] constrainedDsqr; |
57 |
delete[] moving; |
58 |
delete[] moved; |
59 |
delete[] oldPos; |
60 |
} |
61 |
|
62 |
} |
63 |
|
64 |
|
65 |
template<typename T> void Integrator<T>::checkConstraints(void){ |
66 |
isConstrained = 0; |
67 |
|
68 |
Constraint* temp_con; |
69 |
Constraint* dummy_plug; |
70 |
temp_con = new Constraint[info->n_SRI]; |
71 |
nConstrained = 0; |
72 |
int constrained = 0; |
73 |
|
74 |
SRI** theArray; |
75 |
for (int i = 0; i < nMols; i++){ |
76 |
|
77 |
theArray = (SRI * *) molecules[i].getMyBonds(); |
78 |
for (int j = 0; j < molecules[i].getNBonds(); j++){ |
79 |
constrained = theArray[j]->is_constrained(); |
80 |
|
81 |
if (constrained){ |
82 |
dummy_plug = theArray[j]->get_constraint(); |
83 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
84 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
85 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
86 |
|
87 |
nConstrained++; |
88 |
constrained = 0; |
89 |
} |
90 |
} |
91 |
|
92 |
theArray = (SRI * *) molecules[i].getMyBends(); |
93 |
for (int j = 0; j < molecules[i].getNBends(); j++){ |
94 |
constrained = theArray[j]->is_constrained(); |
95 |
|
96 |
if (constrained){ |
97 |
dummy_plug = theArray[j]->get_constraint(); |
98 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
99 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
100 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
101 |
|
102 |
nConstrained++; |
103 |
constrained = 0; |
104 |
} |
105 |
} |
106 |
|
107 |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
108 |
for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
109 |
constrained = theArray[j]->is_constrained(); |
110 |
|
111 |
if (constrained){ |
112 |
dummy_plug = theArray[j]->get_constraint(); |
113 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
114 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
115 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
116 |
|
117 |
nConstrained++; |
118 |
constrained = 0; |
119 |
} |
120 |
} |
121 |
} |
122 |
|
123 |
|
124 |
if (nConstrained > 0){ |
125 |
isConstrained = 1; |
126 |
|
127 |
if (constrainedA != NULL) |
128 |
delete[] constrainedA; |
129 |
if (constrainedB != NULL) |
130 |
delete[] constrainedB; |
131 |
if (constrainedDsqr != NULL) |
132 |
delete[] constrainedDsqr; |
133 |
|
134 |
constrainedA = new int[nConstrained]; |
135 |
constrainedB = new int[nConstrained]; |
136 |
constrainedDsqr = new double[nConstrained]; |
137 |
|
138 |
for (int i = 0; i < nConstrained; i++){ |
139 |
constrainedA[i] = temp_con[i].get_a(); |
140 |
constrainedB[i] = temp_con[i].get_b(); |
141 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
142 |
} |
143 |
|
144 |
|
145 |
// save oldAtoms to check for lode balancing later on. |
146 |
|
147 |
oldAtoms = nAtoms; |
148 |
|
149 |
moving = new int[nAtoms]; |
150 |
moved = new int[nAtoms]; |
151 |
|
152 |
oldPos = new double[nAtoms * 3]; |
153 |
} |
154 |
|
155 |
delete[] temp_con; |
156 |
} |
157 |
|
158 |
|
159 |
template<typename T> void Integrator<T>::integrate(void){ |
160 |
|
161 |
double runTime = info->run_time; |
162 |
double sampleTime = info->sampleTime; |
163 |
double statusTime = info->statusTime; |
164 |
double thermalTime = info->thermalTime; |
165 |
double resetTime = info->resetTime; |
166 |
|
167 |
double difference; |
168 |
double currSample; |
169 |
double currThermal; |
170 |
double currStatus; |
171 |
double currReset; |
172 |
|
173 |
int calcPot, calcStress; |
174 |
|
175 |
tStats = new Thermo(info); |
176 |
statOut = new StatWriter(info); |
177 |
dumpOut = new DumpWriter(info); |
178 |
|
179 |
atoms = info->atoms; |
180 |
|
181 |
dt = info->dt; |
182 |
dt2 = 0.5 * dt; |
183 |
|
184 |
readyCheck(); |
185 |
|
186 |
// remove center of mass drift velocity (in case we passed in a configuration |
187 |
// that was drifting |
188 |
tStats->removeCOMdrift(); |
189 |
|
190 |
// initialize the retraints if necessary |
191 |
if (info->useSolidThermInt && !info->useLiquidThermInt) { |
192 |
myFF->initRestraints(); |
193 |
} |
194 |
|
195 |
// initialize the forces before the first step |
196 |
|
197 |
calcForce(1, 1); |
198 |
|
199 |
//execute constraint algorithm to make sure at the very beginning the system is constrained |
200 |
if(nConstrained){ |
201 |
preMove(); |
202 |
constrainA(); |
203 |
calcForce(1, 1); |
204 |
constrainB(); |
205 |
} |
206 |
|
207 |
if (info->setTemp){ |
208 |
thermalize(); |
209 |
} |
210 |
|
211 |
calcPot = 0; |
212 |
calcStress = 0; |
213 |
currSample = sampleTime + info->getTime(); |
214 |
currThermal = thermalTime+ info->getTime(); |
215 |
currStatus = statusTime + info->getTime(); |
216 |
currReset = resetTime + info->getTime(); |
217 |
|
218 |
dumpOut->writeDump(info->getTime()); |
219 |
statOut->writeStat(info->getTime()); |
220 |
|
221 |
|
222 |
#ifdef IS_MPI |
223 |
strcpy(checkPointMsg, "The integrator is ready to go."); |
224 |
MPIcheckPoint(); |
225 |
#endif // is_mpi |
226 |
|
227 |
while (info->getTime() < runTime && !stopIntegrator()){ |
228 |
difference = info->getTime() + dt - currStatus; |
229 |
if (difference > 0 || fabs(difference) < 1e-4 ){ |
230 |
calcPot = 1; |
231 |
calcStress = 1; |
232 |
} |
233 |
|
234 |
#ifdef PROFILE |
235 |
startProfile( pro1 ); |
236 |
#endif |
237 |
|
238 |
integrateStep(calcPot, calcStress); |
239 |
|
240 |
#ifdef PROFILE |
241 |
endProfile( pro1 ); |
242 |
|
243 |
startProfile( pro2 ); |
244 |
#endif // profile |
245 |
|
246 |
info->incrTime(dt); |
247 |
|
248 |
if (info->setTemp){ |
249 |
if (info->getTime() >= currThermal){ |
250 |
thermalize(); |
251 |
currThermal += thermalTime; |
252 |
} |
253 |
} |
254 |
|
255 |
if (info->getTime() >= currSample){ |
256 |
dumpOut->writeDump(info->getTime()); |
257 |
currSample += sampleTime; |
258 |
} |
259 |
|
260 |
if (info->getTime() >= currStatus){ |
261 |
statOut->writeStat(info->getTime()); |
262 |
calcPot = 0; |
263 |
calcStress = 0; |
264 |
currStatus += statusTime; |
265 |
} |
266 |
|
267 |
if (info->resetIntegrator){ |
268 |
if (info->getTime() >= currReset){ |
269 |
this->resetIntegrator(); |
270 |
currReset += resetTime; |
271 |
} |
272 |
} |
273 |
|
274 |
#ifdef PROFILE |
275 |
endProfile( pro2 ); |
276 |
#endif //profile |
277 |
|
278 |
#ifdef IS_MPI |
279 |
strcpy(checkPointMsg, "successfully took a time step."); |
280 |
MPIcheckPoint(); |
281 |
#endif // is_mpi |
282 |
} |
283 |
|
284 |
// dump out a file containing the omega values for the final configuration |
285 |
if (info->useSolidThermInt && !info->useLiquidThermInt) |
286 |
myFF->dumpzAngle(); |
287 |
|
288 |
|
289 |
delete dumpOut; |
290 |
delete statOut; |
291 |
} |
292 |
|
293 |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
294 |
int calcStress){ |
295 |
// Position full step, and velocity half step |
296 |
|
297 |
#ifdef PROFILE |
298 |
startProfile(pro3); |
299 |
#endif //profile |
300 |
|
301 |
//save old state (position, velocity etc) |
302 |
preMove(); |
303 |
#ifdef PROFILE |
304 |
endProfile(pro3); |
305 |
|
306 |
startProfile(pro4); |
307 |
#endif // profile |
308 |
|
309 |
moveA(); |
310 |
|
311 |
#ifdef PROFILE |
312 |
endProfile(pro4); |
313 |
|
314 |
startProfile(pro5); |
315 |
#endif//profile |
316 |
|
317 |
|
318 |
#ifdef IS_MPI |
319 |
strcpy(checkPointMsg, "Succesful moveA\n"); |
320 |
MPIcheckPoint(); |
321 |
#endif // is_mpi |
322 |
|
323 |
// calc forces |
324 |
calcForce(calcPot, calcStress); |
325 |
|
326 |
#ifdef IS_MPI |
327 |
strcpy(checkPointMsg, "Succesful doForces\n"); |
328 |
MPIcheckPoint(); |
329 |
#endif // is_mpi |
330 |
|
331 |
#ifdef PROFILE |
332 |
endProfile( pro5 ); |
333 |
|
334 |
startProfile( pro6 ); |
335 |
#endif //profile |
336 |
|
337 |
// finish the velocity half step |
338 |
|
339 |
moveB(); |
340 |
|
341 |
#ifdef PROFILE |
342 |
endProfile(pro6); |
343 |
#endif // profile |
344 |
|
345 |
#ifdef IS_MPI |
346 |
strcpy(checkPointMsg, "Succesful moveB\n"); |
347 |
MPIcheckPoint(); |
348 |
#endif // is_mpi |
349 |
} |
350 |
|
351 |
|
352 |
template<typename T> void Integrator<T>::moveA(void){ |
353 |
size_t i, j; |
354 |
DirectionalAtom* dAtom; |
355 |
double Tb[3], ji[3]; |
356 |
double vel[3], pos[3], frc[3]; |
357 |
double mass; |
358 |
double omega; |
359 |
|
360 |
for (i = 0; i < integrableObjects.size() ; i++){ |
361 |
integrableObjects[i]->getVel(vel); |
362 |
integrableObjects[i]->getPos(pos); |
363 |
integrableObjects[i]->getFrc(frc); |
364 |
|
365 |
mass = integrableObjects[i]->getMass(); |
366 |
|
367 |
for (j = 0; j < 3; j++){ |
368 |
// velocity half step |
369 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
370 |
// position whole step |
371 |
pos[j] += dt * vel[j]; |
372 |
} |
373 |
|
374 |
integrableObjects[i]->setVel(vel); |
375 |
integrableObjects[i]->setPos(pos); |
376 |
|
377 |
if (integrableObjects[i]->isDirectional()){ |
378 |
|
379 |
// get and convert the torque to body frame |
380 |
|
381 |
integrableObjects[i]->getTrq(Tb); |
382 |
integrableObjects[i]->lab2Body(Tb); |
383 |
|
384 |
// get the angular momentum, and propagate a half step |
385 |
|
386 |
integrableObjects[i]->getJ(ji); |
387 |
|
388 |
for (j = 0; j < 3; j++) |
389 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
390 |
|
391 |
this->rotationPropagation( integrableObjects[i], ji ); |
392 |
|
393 |
integrableObjects[i]->setJ(ji); |
394 |
} |
395 |
} |
396 |
|
397 |
if(nConstrained) |
398 |
constrainA(); |
399 |
} |
400 |
|
401 |
|
402 |
template<typename T> void Integrator<T>::moveB(void){ |
403 |
int i, j; |
404 |
double Tb[3], ji[3]; |
405 |
double vel[3], frc[3]; |
406 |
double mass; |
407 |
|
408 |
for (i = 0; i < integrableObjects.size(); i++){ |
409 |
integrableObjects[i]->getVel(vel); |
410 |
integrableObjects[i]->getFrc(frc); |
411 |
|
412 |
mass = integrableObjects[i]->getMass(); |
413 |
|
414 |
// velocity half step |
415 |
for (j = 0; j < 3; j++) |
416 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
417 |
|
418 |
integrableObjects[i]->setVel(vel); |
419 |
|
420 |
if (integrableObjects[i]->isDirectional()){ |
421 |
|
422 |
// get and convert the torque to body frame |
423 |
|
424 |
integrableObjects[i]->getTrq(Tb); |
425 |
integrableObjects[i]->lab2Body(Tb); |
426 |
|
427 |
// get the angular momentum, and propagate a half step |
428 |
|
429 |
integrableObjects[i]->getJ(ji); |
430 |
|
431 |
for (j = 0; j < 3; j++) |
432 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
433 |
|
434 |
|
435 |
integrableObjects[i]->setJ(ji); |
436 |
} |
437 |
} |
438 |
|
439 |
if(nConstrained) |
440 |
constrainB(); |
441 |
} |
442 |
|
443 |
|
444 |
template<typename T> void Integrator<T>::preMove(void){ |
445 |
int i, j; |
446 |
double pos[3]; |
447 |
|
448 |
if (nConstrained){ |
449 |
for (i = 0; i < nAtoms; i++){ |
450 |
atoms[i]->getPos(pos); |
451 |
|
452 |
for (j = 0; j < 3; j++){ |
453 |
oldPos[3 * i + j] = pos[j]; |
454 |
} |
455 |
} |
456 |
} |
457 |
} |
458 |
|
459 |
template<typename T> void Integrator<T>::constrainA(){ |
460 |
int i, j; |
461 |
int done; |
462 |
double posA[3], posB[3]; |
463 |
double velA[3], velB[3]; |
464 |
double pab[3]; |
465 |
double rab[3]; |
466 |
int a, b, ax, ay, az, bx, by, bz; |
467 |
double rma, rmb; |
468 |
double dx, dy, dz; |
469 |
double rpab; |
470 |
double rabsq, pabsq, rpabsq; |
471 |
double diffsq; |
472 |
double gab; |
473 |
int iteration; |
474 |
|
475 |
for (i = 0; i < nAtoms; i++){ |
476 |
moving[i] = 0; |
477 |
moved[i] = 1; |
478 |
} |
479 |
|
480 |
iteration = 0; |
481 |
done = 0; |
482 |
while (!done && (iteration < maxIteration)){ |
483 |
done = 1; |
484 |
for (i = 0; i < nConstrained; i++){ |
485 |
a = constrainedA[i]; |
486 |
b = constrainedB[i]; |
487 |
|
488 |
ax = (a * 3) + 0; |
489 |
ay = (a * 3) + 1; |
490 |
az = (a * 3) + 2; |
491 |
|
492 |
bx = (b * 3) + 0; |
493 |
by = (b * 3) + 1; |
494 |
bz = (b * 3) + 2; |
495 |
|
496 |
if (moved[a] || moved[b]){ |
497 |
atoms[a]->getPos(posA); |
498 |
atoms[b]->getPos(posB); |
499 |
|
500 |
for (j = 0; j < 3; j++) |
501 |
pab[j] = posA[j] - posB[j]; |
502 |
|
503 |
//periodic boundary condition |
504 |
|
505 |
info->wrapVector(pab); |
506 |
|
507 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
508 |
|
509 |
rabsq = constrainedDsqr[i]; |
510 |
diffsq = rabsq - pabsq; |
511 |
|
512 |
// the original rattle code from alan tidesley |
513 |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
514 |
rab[0] = oldPos[ax] - oldPos[bx]; |
515 |
rab[1] = oldPos[ay] - oldPos[by]; |
516 |
rab[2] = oldPos[az] - oldPos[bz]; |
517 |
|
518 |
info->wrapVector(rab); |
519 |
|
520 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
521 |
|
522 |
rpabsq = rpab * rpab; |
523 |
|
524 |
|
525 |
if (rpabsq < (rabsq * -diffsq)){ |
526 |
#ifdef IS_MPI |
527 |
a = atoms[a]->getGlobalIndex(); |
528 |
b = atoms[b]->getGlobalIndex(); |
529 |
#endif //is_mpi |
530 |
sprintf(painCave.errMsg, |
531 |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
532 |
b); |
533 |
painCave.isFatal = 1; |
534 |
simError(); |
535 |
} |
536 |
|
537 |
rma = 1.0 / atoms[a]->getMass(); |
538 |
rmb = 1.0 / atoms[b]->getMass(); |
539 |
|
540 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
541 |
|
542 |
dx = rab[0] * gab; |
543 |
dy = rab[1] * gab; |
544 |
dz = rab[2] * gab; |
545 |
|
546 |
posA[0] += rma * dx; |
547 |
posA[1] += rma * dy; |
548 |
posA[2] += rma * dz; |
549 |
|
550 |
atoms[a]->setPos(posA); |
551 |
|
552 |
posB[0] -= rmb * dx; |
553 |
posB[1] -= rmb * dy; |
554 |
posB[2] -= rmb * dz; |
555 |
|
556 |
atoms[b]->setPos(posB); |
557 |
|
558 |
dx = dx / dt; |
559 |
dy = dy / dt; |
560 |
dz = dz / dt; |
561 |
|
562 |
atoms[a]->getVel(velA); |
563 |
|
564 |
velA[0] += rma * dx; |
565 |
velA[1] += rma * dy; |
566 |
velA[2] += rma * dz; |
567 |
|
568 |
atoms[a]->setVel(velA); |
569 |
|
570 |
atoms[b]->getVel(velB); |
571 |
|
572 |
velB[0] -= rmb * dx; |
573 |
velB[1] -= rmb * dy; |
574 |
velB[2] -= rmb * dz; |
575 |
|
576 |
atoms[b]->setVel(velB); |
577 |
|
578 |
moving[a] = 1; |
579 |
moving[b] = 1; |
580 |
done = 0; |
581 |
} |
582 |
} |
583 |
} |
584 |
|
585 |
for (i = 0; i < nAtoms; i++){ |
586 |
moved[i] = moving[i]; |
587 |
moving[i] = 0; |
588 |
} |
589 |
|
590 |
iteration++; |
591 |
} |
592 |
|
593 |
if (!done){ |
594 |
sprintf(painCave.errMsg, |
595 |
"Constraint failure in constrainA, too many iterations: %d\n", |
596 |
iteration); |
597 |
painCave.isFatal = 1; |
598 |
simError(); |
599 |
} |
600 |
|
601 |
} |
602 |
|
603 |
template<typename T> void Integrator<T>::constrainB(void){ |
604 |
int i, j; |
605 |
int done; |
606 |
double posA[3], posB[3]; |
607 |
double velA[3], velB[3]; |
608 |
double vxab, vyab, vzab; |
609 |
double rab[3]; |
610 |
int a, b, ax, ay, az, bx, by, bz; |
611 |
double rma, rmb; |
612 |
double dx, dy, dz; |
613 |
double rvab; |
614 |
double gab; |
615 |
int iteration; |
616 |
|
617 |
for (i = 0; i < nAtoms; i++){ |
618 |
moving[i] = 0; |
619 |
moved[i] = 1; |
620 |
} |
621 |
|
622 |
done = 0; |
623 |
iteration = 0; |
624 |
while (!done && (iteration < maxIteration)){ |
625 |
done = 1; |
626 |
|
627 |
for (i = 0; i < nConstrained; i++){ |
628 |
a = constrainedA[i]; |
629 |
b = constrainedB[i]; |
630 |
|
631 |
ax = (a * 3) + 0; |
632 |
ay = (a * 3) + 1; |
633 |
az = (a * 3) + 2; |
634 |
|
635 |
bx = (b * 3) + 0; |
636 |
by = (b * 3) + 1; |
637 |
bz = (b * 3) + 2; |
638 |
|
639 |
if (moved[a] || moved[b]){ |
640 |
atoms[a]->getVel(velA); |
641 |
atoms[b]->getVel(velB); |
642 |
|
643 |
vxab = velA[0] - velB[0]; |
644 |
vyab = velA[1] - velB[1]; |
645 |
vzab = velA[2] - velB[2]; |
646 |
|
647 |
atoms[a]->getPos(posA); |
648 |
atoms[b]->getPos(posB); |
649 |
|
650 |
for (j = 0; j < 3; j++) |
651 |
rab[j] = posA[j] - posB[j]; |
652 |
|
653 |
info->wrapVector(rab); |
654 |
|
655 |
rma = 1.0 / atoms[a]->getMass(); |
656 |
rmb = 1.0 / atoms[b]->getMass(); |
657 |
|
658 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
659 |
|
660 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
661 |
|
662 |
if (fabs(gab) > tol){ |
663 |
dx = rab[0] * gab; |
664 |
dy = rab[1] * gab; |
665 |
dz = rab[2] * gab; |
666 |
|
667 |
velA[0] += rma * dx; |
668 |
velA[1] += rma * dy; |
669 |
velA[2] += rma * dz; |
670 |
|
671 |
atoms[a]->setVel(velA); |
672 |
|
673 |
velB[0] -= rmb * dx; |
674 |
velB[1] -= rmb * dy; |
675 |
velB[2] -= rmb * dz; |
676 |
|
677 |
atoms[b]->setVel(velB); |
678 |
|
679 |
moving[a] = 1; |
680 |
moving[b] = 1; |
681 |
done = 0; |
682 |
} |
683 |
} |
684 |
} |
685 |
|
686 |
for (i = 0; i < nAtoms; i++){ |
687 |
moved[i] = moving[i]; |
688 |
moving[i] = 0; |
689 |
} |
690 |
|
691 |
iteration++; |
692 |
} |
693 |
|
694 |
if (!done){ |
695 |
sprintf(painCave.errMsg, |
696 |
"Constraint failure in constrainB, too many iterations: %d\n", |
697 |
iteration); |
698 |
painCave.isFatal = 1; |
699 |
simError(); |
700 |
} |
701 |
} |
702 |
|
703 |
template<typename T> void Integrator<T>::rotationPropagation |
704 |
( StuntDouble* sd, double ji[3] ){ |
705 |
|
706 |
double angle; |
707 |
double A[3][3], I[3][3]; |
708 |
int i, j, k; |
709 |
|
710 |
// use the angular velocities to propagate the rotation matrix a |
711 |
// full time step |
712 |
|
713 |
sd->getA(A); |
714 |
sd->getI(I); |
715 |
|
716 |
if (sd->isLinear()) { |
717 |
i = sd->linearAxis(); |
718 |
j = (i+1)%3; |
719 |
k = (i+2)%3; |
720 |
|
721 |
angle = dt2 * ji[j] / I[j][j]; |
722 |
this->rotate( k, i, angle, ji, A ); |
723 |
|
724 |
angle = dt * ji[k] / I[k][k]; |
725 |
this->rotate( i, j, angle, ji, A); |
726 |
|
727 |
angle = dt2 * ji[j] / I[j][j]; |
728 |
this->rotate( k, i, angle, ji, A ); |
729 |
|
730 |
} else { |
731 |
// rotate about the x-axis |
732 |
angle = dt2 * ji[0] / I[0][0]; |
733 |
this->rotate( 1, 2, angle, ji, A ); |
734 |
|
735 |
// rotate about the y-axis |
736 |
angle = dt2 * ji[1] / I[1][1]; |
737 |
this->rotate( 2, 0, angle, ji, A ); |
738 |
|
739 |
// rotate about the z-axis |
740 |
angle = dt * ji[2] / I[2][2]; |
741 |
sd->addZangle(angle); |
742 |
this->rotate( 0, 1, angle, ji, A); |
743 |
|
744 |
// rotate about the y-axis |
745 |
angle = dt2 * ji[1] / I[1][1]; |
746 |
this->rotate( 2, 0, angle, ji, A ); |
747 |
|
748 |
// rotate about the x-axis |
749 |
angle = dt2 * ji[0] / I[0][0]; |
750 |
this->rotate( 1, 2, angle, ji, A ); |
751 |
|
752 |
} |
753 |
sd->setA( A ); |
754 |
} |
755 |
|
756 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
757 |
double angle, double ji[3], |
758 |
double A[3][3]){ |
759 |
int i, j, k; |
760 |
double sinAngle; |
761 |
double cosAngle; |
762 |
double angleSqr; |
763 |
double angleSqrOver4; |
764 |
double top, bottom; |
765 |
double rot[3][3]; |
766 |
double tempA[3][3]; |
767 |
double tempJ[3]; |
768 |
|
769 |
// initialize the tempA |
770 |
|
771 |
for (i = 0; i < 3; i++){ |
772 |
for (j = 0; j < 3; j++){ |
773 |
tempA[j][i] = A[i][j]; |
774 |
} |
775 |
} |
776 |
|
777 |
// initialize the tempJ |
778 |
|
779 |
for (i = 0; i < 3; i++) |
780 |
tempJ[i] = ji[i]; |
781 |
|
782 |
// initalize rot as a unit matrix |
783 |
|
784 |
rot[0][0] = 1.0; |
785 |
rot[0][1] = 0.0; |
786 |
rot[0][2] = 0.0; |
787 |
|
788 |
rot[1][0] = 0.0; |
789 |
rot[1][1] = 1.0; |
790 |
rot[1][2] = 0.0; |
791 |
|
792 |
rot[2][0] = 0.0; |
793 |
rot[2][1] = 0.0; |
794 |
rot[2][2] = 1.0; |
795 |
|
796 |
// use a small angle aproximation for sin and cosine |
797 |
|
798 |
angleSqr = angle * angle; |
799 |
angleSqrOver4 = angleSqr / 4.0; |
800 |
top = 1.0 - angleSqrOver4; |
801 |
bottom = 1.0 + angleSqrOver4; |
802 |
|
803 |
cosAngle = top / bottom; |
804 |
sinAngle = angle / bottom; |
805 |
|
806 |
rot[axes1][axes1] = cosAngle; |
807 |
rot[axes2][axes2] = cosAngle; |
808 |
|
809 |
rot[axes1][axes2] = sinAngle; |
810 |
rot[axes2][axes1] = -sinAngle; |
811 |
|
812 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
813 |
|
814 |
for (i = 0; i < 3; i++){ |
815 |
ji[i] = 0.0; |
816 |
for (k = 0; k < 3; k++){ |
817 |
ji[i] += rot[i][k] * tempJ[k]; |
818 |
} |
819 |
} |
820 |
|
821 |
// rotate the Rotation matrix acording to: |
822 |
// A[][] = A[][] * transpose(rot[][]) |
823 |
|
824 |
|
825 |
// NOte for as yet unknown reason, we are performing the |
826 |
// calculation as: |
827 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
828 |
|
829 |
for (i = 0; i < 3; i++){ |
830 |
for (j = 0; j < 3; j++){ |
831 |
A[j][i] = 0.0; |
832 |
for (k = 0; k < 3; k++){ |
833 |
A[j][i] += tempA[i][k] * rot[j][k]; |
834 |
} |
835 |
} |
836 |
} |
837 |
} |
838 |
|
839 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
840 |
myFF->doForces(calcPot, calcStress); |
841 |
} |
842 |
|
843 |
template<typename T> void Integrator<T>::thermalize(){ |
844 |
tStats->velocitize(); |
845 |
} |
846 |
|
847 |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
848 |
return tStats->getTotalE(); |
849 |
} |
850 |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
851 |
//By default, return a null string |
852 |
//The reason we use string instead of char* is that if we use char*, we will |
853 |
//return a pointer point to local variable which might cause problem |
854 |
return string(); |
855 |
} |