1 |
#include <iostream> |
2 |
#include <stdlib.h> |
3 |
#include <math.h> |
4 |
#include "Rattle.hpp" |
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 |
rattle = new RattleFramework(info); |
37 |
|
38 |
if(rattle == NULL){ |
39 |
sprintf(painCave.errMsg, |
40 |
"Integrator::Intergrator() Error: Memory allocation error for RattleFramework" ); |
41 |
painCave.isFatal = 1; |
42 |
simError(); |
43 |
} |
44 |
|
45 |
/* |
46 |
// check for constraints |
47 |
|
48 |
constrainedA = NULL; |
49 |
constrainedB = NULL; |
50 |
constrainedDsqr = NULL; |
51 |
moving = NULL; |
52 |
moved = NULL; |
53 |
oldPos = NULL; |
54 |
|
55 |
nConstrained = 0; |
56 |
|
57 |
checkConstraints(); |
58 |
*/ |
59 |
} |
60 |
|
61 |
template<typename T> Integrator<T>::~Integrator(){ |
62 |
if (rattle != NULL) |
63 |
delete rattle; |
64 |
/* |
65 |
if (nConstrained){ |
66 |
delete[] constrainedA; |
67 |
delete[] constrainedB; |
68 |
delete[] constrainedDsqr; |
69 |
delete[] moving; |
70 |
delete[] moved; |
71 |
delete[] oldPos; |
72 |
} |
73 |
*/ |
74 |
} |
75 |
|
76 |
/* |
77 |
template<typename T> void Integrator<T>::checkConstraints(void){ |
78 |
isConstrained = 0; |
79 |
|
80 |
Constraint* temp_con; |
81 |
Constraint* dummy_plug; |
82 |
temp_con = new Constraint[info->n_SRI]; |
83 |
nConstrained = 0; |
84 |
int constrained = 0; |
85 |
|
86 |
SRI** theArray; |
87 |
for (int i = 0; i < nMols; i++){ |
88 |
|
89 |
theArray = (SRI * *) molecules[i].getMyBonds(); |
90 |
for (int j = 0; j < molecules[i].getNBonds(); 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].getMyBends(); |
105 |
for (int j = 0; j < molecules[i].getNBends(); 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 |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
120 |
for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
121 |
constrained = theArray[j]->is_constrained(); |
122 |
|
123 |
if (constrained){ |
124 |
dummy_plug = theArray[j]->get_constraint(); |
125 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
126 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
127 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
128 |
|
129 |
nConstrained++; |
130 |
constrained = 0; |
131 |
} |
132 |
} |
133 |
} |
134 |
|
135 |
|
136 |
if (nConstrained > 0){ |
137 |
isConstrained = 1; |
138 |
|
139 |
if (constrainedA != NULL) |
140 |
delete[] constrainedA; |
141 |
if (constrainedB != NULL) |
142 |
delete[] constrainedB; |
143 |
if (constrainedDsqr != NULL) |
144 |
delete[] constrainedDsqr; |
145 |
|
146 |
constrainedA = new int[nConstrained]; |
147 |
constrainedB = new int[nConstrained]; |
148 |
constrainedDsqr = new double[nConstrained]; |
149 |
|
150 |
for (int i = 0; i < nConstrained; i++){ |
151 |
constrainedA[i] = temp_con[i].get_a(); |
152 |
constrainedB[i] = temp_con[i].get_b(); |
153 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
154 |
} |
155 |
|
156 |
|
157 |
// save oldAtoms to check for lode balancing later on. |
158 |
|
159 |
oldAtoms = nAtoms; |
160 |
|
161 |
moving = new int[nAtoms]; |
162 |
moved = new int[nAtoms]; |
163 |
|
164 |
oldPos = new double[nAtoms * 3]; |
165 |
} |
166 |
|
167 |
delete[] temp_con; |
168 |
} |
169 |
*/ |
170 |
|
171 |
template<typename T> void Integrator<T>::integrate(void){ |
172 |
|
173 |
double runTime = info->run_time; |
174 |
double sampleTime = info->sampleTime; |
175 |
double statusTime = info->statusTime; |
176 |
double thermalTime = info->thermalTime; |
177 |
double resetTime = info->resetTime; |
178 |
|
179 |
double difference; |
180 |
double currSample; |
181 |
double currThermal; |
182 |
double currStatus; |
183 |
double currReset; |
184 |
|
185 |
int calcPot, calcStress; |
186 |
|
187 |
tStats = new Thermo(info); |
188 |
statOut = new StatWriter(info); |
189 |
dumpOut = new DumpWriter(info); |
190 |
|
191 |
atoms = info->atoms; |
192 |
|
193 |
dt = info->dt; |
194 |
dt2 = 0.5 * dt; |
195 |
|
196 |
readyCheck(); |
197 |
|
198 |
// remove center of mass drift velocity (in case we passed in a configuration |
199 |
// that was drifting |
200 |
tStats->removeCOMdrift(); |
201 |
|
202 |
// initialize the retraints if necessary |
203 |
if (info->useSolidThermInt && !info->useLiquidThermInt) { |
204 |
myFF->initRestraints(); |
205 |
} |
206 |
|
207 |
// initialize the forces before the first step |
208 |
|
209 |
calcForce(1, 1); |
210 |
|
211 |
//execute constraint algorithm to make sure at the very beginning the system is constrained |
212 |
rattle->doPreConstraint(); |
213 |
rattle->doRattleA(); |
214 |
calcForce(1, 1); |
215 |
rattle->doRattleB(); |
216 |
|
217 |
if (info->setTemp){ |
218 |
thermalize(); |
219 |
} |
220 |
|
221 |
calcPot = 0; |
222 |
calcStress = 0; |
223 |
currSample = sampleTime + info->getTime(); |
224 |
currThermal = thermalTime+ info->getTime(); |
225 |
currStatus = statusTime + info->getTime(); |
226 |
currReset = resetTime + info->getTime(); |
227 |
|
228 |
dumpOut->writeDump(info->getTime()); |
229 |
statOut->writeStat(info->getTime()); |
230 |
|
231 |
|
232 |
#ifdef IS_MPI |
233 |
strcpy(checkPointMsg, "The integrator is ready to go."); |
234 |
MPIcheckPoint(); |
235 |
#endif // is_mpi |
236 |
|
237 |
while (info->getTime() < runTime && !stopIntegrator()){ |
238 |
difference = info->getTime() + dt - currStatus; |
239 |
if (difference > 0 || fabs(difference) < 1e-4 ){ |
240 |
calcPot = 1; |
241 |
calcStress = 1; |
242 |
} |
243 |
|
244 |
#ifdef PROFILE |
245 |
startProfile( pro1 ); |
246 |
#endif |
247 |
|
248 |
integrateStep(calcPot, calcStress); |
249 |
|
250 |
#ifdef PROFILE |
251 |
endProfile( pro1 ); |
252 |
|
253 |
startProfile( pro2 ); |
254 |
#endif // profile |
255 |
|
256 |
info->incrTime(dt); |
257 |
|
258 |
if (info->setTemp){ |
259 |
if (info->getTime() >= currThermal){ |
260 |
thermalize(); |
261 |
currThermal += thermalTime; |
262 |
} |
263 |
} |
264 |
|
265 |
if (info->getTime() >= currSample){ |
266 |
dumpOut->writeDump(info->getTime()); |
267 |
currSample += sampleTime; |
268 |
} |
269 |
|
270 |
if (info->getTime() >= currStatus){ |
271 |
statOut->writeStat(info->getTime()); |
272 |
calcPot = 0; |
273 |
calcStress = 0; |
274 |
currStatus += statusTime; |
275 |
} |
276 |
|
277 |
if (info->resetIntegrator){ |
278 |
if (info->getTime() >= currReset){ |
279 |
this->resetIntegrator(); |
280 |
currReset += resetTime; |
281 |
} |
282 |
} |
283 |
|
284 |
#ifdef PROFILE |
285 |
endProfile( pro2 ); |
286 |
#endif //profile |
287 |
|
288 |
#ifdef IS_MPI |
289 |
strcpy(checkPointMsg, "successfully took a time step."); |
290 |
MPIcheckPoint(); |
291 |
#endif // is_mpi |
292 |
} |
293 |
|
294 |
// dump out a file containing the omega values for the final configuration |
295 |
if (info->useSolidThermInt && !info->useLiquidThermInt) |
296 |
myFF->dumpzAngle(); |
297 |
|
298 |
|
299 |
delete dumpOut; |
300 |
delete statOut; |
301 |
} |
302 |
|
303 |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
304 |
int calcStress){ |
305 |
// Position full step, and velocity half step |
306 |
|
307 |
#ifdef PROFILE |
308 |
startProfile(pro3); |
309 |
#endif //profile |
310 |
|
311 |
//save old state (position, velocity etc) |
312 |
rattle->doPreConstraint(); |
313 |
|
314 |
#ifdef PROFILE |
315 |
endProfile(pro3); |
316 |
|
317 |
startProfile(pro4); |
318 |
#endif // profile |
319 |
|
320 |
moveA(); |
321 |
|
322 |
#ifdef PROFILE |
323 |
endProfile(pro4); |
324 |
|
325 |
startProfile(pro5); |
326 |
#endif//profile |
327 |
|
328 |
|
329 |
#ifdef IS_MPI |
330 |
strcpy(checkPointMsg, "Succesful moveA\n"); |
331 |
MPIcheckPoint(); |
332 |
#endif // is_mpi |
333 |
|
334 |
// calc forces |
335 |
calcForce(calcPot, calcStress); |
336 |
|
337 |
#ifdef IS_MPI |
338 |
strcpy(checkPointMsg, "Succesful doForces\n"); |
339 |
MPIcheckPoint(); |
340 |
#endif // is_mpi |
341 |
|
342 |
#ifdef PROFILE |
343 |
endProfile( pro5 ); |
344 |
|
345 |
startProfile( pro6 ); |
346 |
#endif //profile |
347 |
|
348 |
// finish the velocity half step |
349 |
|
350 |
moveB(); |
351 |
|
352 |
#ifdef PROFILE |
353 |
endProfile(pro6); |
354 |
#endif // profile |
355 |
|
356 |
#ifdef IS_MPI |
357 |
strcpy(checkPointMsg, "Succesful moveB\n"); |
358 |
MPIcheckPoint(); |
359 |
#endif // is_mpi |
360 |
} |
361 |
|
362 |
|
363 |
template<typename T> void Integrator<T>::moveA(void){ |
364 |
size_t i, j; |
365 |
DirectionalAtom* dAtom; |
366 |
double Tb[3], ji[3]; |
367 |
double vel[3], pos[3], frc[3]; |
368 |
double mass; |
369 |
double omega; |
370 |
|
371 |
for (i = 0; i < integrableObjects.size() ; i++){ |
372 |
integrableObjects[i]->getVel(vel); |
373 |
integrableObjects[i]->getPos(pos); |
374 |
integrableObjects[i]->getFrc(frc); |
375 |
|
376 |
mass = integrableObjects[i]->getMass(); |
377 |
|
378 |
for (j = 0; j < 3; j++){ |
379 |
// velocity half step |
380 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
381 |
// position whole step |
382 |
pos[j] += dt * vel[j]; |
383 |
} |
384 |
|
385 |
integrableObjects[i]->setVel(vel); |
386 |
integrableObjects[i]->setPos(pos); |
387 |
|
388 |
if (integrableObjects[i]->isDirectional()){ |
389 |
|
390 |
// get and convert the torque to body frame |
391 |
|
392 |
integrableObjects[i]->getTrq(Tb); |
393 |
integrableObjects[i]->lab2Body(Tb); |
394 |
|
395 |
// get the angular momentum, and propagate a half step |
396 |
|
397 |
integrableObjects[i]->getJ(ji); |
398 |
|
399 |
for (j = 0; j < 3; j++) |
400 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
401 |
|
402 |
this->rotationPropagation( integrableObjects[i], ji ); |
403 |
|
404 |
integrableObjects[i]->setJ(ji); |
405 |
} |
406 |
} |
407 |
|
408 |
rattle->doRattleA(); |
409 |
} |
410 |
|
411 |
|
412 |
template<typename T> void Integrator<T>::moveB(void){ |
413 |
int i, j; |
414 |
double Tb[3], ji[3]; |
415 |
double vel[3], frc[3]; |
416 |
double mass; |
417 |
|
418 |
for (i = 0; i < integrableObjects.size(); i++){ |
419 |
integrableObjects[i]->getVel(vel); |
420 |
integrableObjects[i]->getFrc(frc); |
421 |
|
422 |
mass = integrableObjects[i]->getMass(); |
423 |
|
424 |
// velocity half step |
425 |
for (j = 0; j < 3; j++) |
426 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
427 |
|
428 |
integrableObjects[i]->setVel(vel); |
429 |
|
430 |
if (integrableObjects[i]->isDirectional()){ |
431 |
|
432 |
// get and convert the torque to body frame |
433 |
|
434 |
integrableObjects[i]->getTrq(Tb); |
435 |
integrableObjects[i]->lab2Body(Tb); |
436 |
|
437 |
// get the angular momentum, and propagate a half step |
438 |
|
439 |
integrableObjects[i]->getJ(ji); |
440 |
|
441 |
for (j = 0; j < 3; j++) |
442 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
443 |
|
444 |
|
445 |
integrableObjects[i]->setJ(ji); |
446 |
} |
447 |
} |
448 |
|
449 |
rattle->doRattleB(); |
450 |
} |
451 |
|
452 |
/* |
453 |
template<typename T> void Integrator<T>::preMove(void){ |
454 |
int i, j; |
455 |
double pos[3]; |
456 |
|
457 |
if (nConstrained){ |
458 |
for (i = 0; i < nAtoms; i++){ |
459 |
atoms[i]->getPos(pos); |
460 |
|
461 |
for (j = 0; j < 3; j++){ |
462 |
oldPos[3 * i + j] = pos[j]; |
463 |
} |
464 |
} |
465 |
} |
466 |
} |
467 |
|
468 |
template<typename T> void Integrator<T>::constrainA(){ |
469 |
int i, j; |
470 |
int done; |
471 |
double posA[3], posB[3]; |
472 |
double velA[3], velB[3]; |
473 |
double pab[3]; |
474 |
double rab[3]; |
475 |
int a, b, ax, ay, az, bx, by, bz; |
476 |
double rma, rmb; |
477 |
double dx, dy, dz; |
478 |
double rpab; |
479 |
double rabsq, pabsq, rpabsq; |
480 |
double diffsq; |
481 |
double gab; |
482 |
int iteration; |
483 |
|
484 |
for (i = 0; i < nAtoms; i++){ |
485 |
moving[i] = 0; |
486 |
moved[i] = 1; |
487 |
} |
488 |
|
489 |
iteration = 0; |
490 |
done = 0; |
491 |
while (!done && (iteration < maxIteration)){ |
492 |
done = 1; |
493 |
for (i = 0; i < nConstrained; i++){ |
494 |
a = constrainedA[i]; |
495 |
b = constrainedB[i]; |
496 |
|
497 |
ax = (a * 3) + 0; |
498 |
ay = (a * 3) + 1; |
499 |
az = (a * 3) + 2; |
500 |
|
501 |
bx = (b * 3) + 0; |
502 |
by = (b * 3) + 1; |
503 |
bz = (b * 3) + 2; |
504 |
|
505 |
if (moved[a] || moved[b]){ |
506 |
atoms[a]->getPos(posA); |
507 |
atoms[b]->getPos(posB); |
508 |
|
509 |
for (j = 0; j < 3; j++) |
510 |
pab[j] = posA[j] - posB[j]; |
511 |
|
512 |
//periodic boundary condition |
513 |
|
514 |
info->wrapVector(pab); |
515 |
|
516 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
517 |
|
518 |
rabsq = constrainedDsqr[i]; |
519 |
diffsq = rabsq - pabsq; |
520 |
|
521 |
// the original rattle code from alan tidesley |
522 |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
523 |
rab[0] = oldPos[ax] - oldPos[bx]; |
524 |
rab[1] = oldPos[ay] - oldPos[by]; |
525 |
rab[2] = oldPos[az] - oldPos[bz]; |
526 |
|
527 |
info->wrapVector(rab); |
528 |
|
529 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
530 |
|
531 |
rpabsq = rpab * rpab; |
532 |
|
533 |
|
534 |
if (rpabsq < (rabsq * -diffsq)){ |
535 |
#ifdef IS_MPI |
536 |
a = atoms[a]->getGlobalIndex(); |
537 |
b = atoms[b]->getGlobalIndex(); |
538 |
#endif //is_mpi |
539 |
sprintf(painCave.errMsg, |
540 |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
541 |
b); |
542 |
painCave.isFatal = 1; |
543 |
simError(); |
544 |
} |
545 |
|
546 |
rma = 1.0 / atoms[a]->getMass(); |
547 |
rmb = 1.0 / atoms[b]->getMass(); |
548 |
|
549 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
550 |
|
551 |
dx = rab[0] * gab; |
552 |
dy = rab[1] * gab; |
553 |
dz = rab[2] * gab; |
554 |
|
555 |
posA[0] += rma * dx; |
556 |
posA[1] += rma * dy; |
557 |
posA[2] += rma * dz; |
558 |
|
559 |
atoms[a]->setPos(posA); |
560 |
|
561 |
posB[0] -= rmb * dx; |
562 |
posB[1] -= rmb * dy; |
563 |
posB[2] -= rmb * dz; |
564 |
|
565 |
atoms[b]->setPos(posB); |
566 |
|
567 |
dx = dx / dt; |
568 |
dy = dy / dt; |
569 |
dz = dz / dt; |
570 |
|
571 |
atoms[a]->getVel(velA); |
572 |
|
573 |
velA[0] += rma * dx; |
574 |
velA[1] += rma * dy; |
575 |
velA[2] += rma * dz; |
576 |
|
577 |
atoms[a]->setVel(velA); |
578 |
|
579 |
atoms[b]->getVel(velB); |
580 |
|
581 |
velB[0] -= rmb * dx; |
582 |
velB[1] -= rmb * dy; |
583 |
velB[2] -= rmb * dz; |
584 |
|
585 |
atoms[b]->setVel(velB); |
586 |
|
587 |
moving[a] = 1; |
588 |
moving[b] = 1; |
589 |
done = 0; |
590 |
} |
591 |
} |
592 |
} |
593 |
|
594 |
for (i = 0; i < nAtoms; i++){ |
595 |
moved[i] = moving[i]; |
596 |
moving[i] = 0; |
597 |
} |
598 |
|
599 |
iteration++; |
600 |
} |
601 |
|
602 |
if (!done){ |
603 |
sprintf(painCave.errMsg, |
604 |
"Constraint failure in constrainA, too many iterations: %d\n", |
605 |
iteration); |
606 |
painCave.isFatal = 1; |
607 |
simError(); |
608 |
} |
609 |
|
610 |
} |
611 |
|
612 |
template<typename T> void Integrator<T>::constrainB(void){ |
613 |
int i, j; |
614 |
int done; |
615 |
double posA[3], posB[3]; |
616 |
double velA[3], velB[3]; |
617 |
double vxab, vyab, vzab; |
618 |
double rab[3]; |
619 |
int a, b, ax, ay, az, bx, by, bz; |
620 |
double rma, rmb; |
621 |
double dx, dy, dz; |
622 |
double rvab; |
623 |
double gab; |
624 |
int iteration; |
625 |
|
626 |
for (i = 0; i < nAtoms; i++){ |
627 |
moving[i] = 0; |
628 |
moved[i] = 1; |
629 |
} |
630 |
|
631 |
done = 0; |
632 |
iteration = 0; |
633 |
while (!done && (iteration < maxIteration)){ |
634 |
done = 1; |
635 |
|
636 |
for (i = 0; i < nConstrained; i++){ |
637 |
a = constrainedA[i]; |
638 |
b = constrainedB[i]; |
639 |
|
640 |
ax = (a * 3) + 0; |
641 |
ay = (a * 3) + 1; |
642 |
az = (a * 3) + 2; |
643 |
|
644 |
bx = (b * 3) + 0; |
645 |
by = (b * 3) + 1; |
646 |
bz = (b * 3) + 2; |
647 |
|
648 |
if (moved[a] || moved[b]){ |
649 |
atoms[a]->getVel(velA); |
650 |
atoms[b]->getVel(velB); |
651 |
|
652 |
vxab = velA[0] - velB[0]; |
653 |
vyab = velA[1] - velB[1]; |
654 |
vzab = velA[2] - velB[2]; |
655 |
|
656 |
atoms[a]->getPos(posA); |
657 |
atoms[b]->getPos(posB); |
658 |
|
659 |
for (j = 0; j < 3; j++) |
660 |
rab[j] = posA[j] - posB[j]; |
661 |
|
662 |
info->wrapVector(rab); |
663 |
|
664 |
rma = 1.0 / atoms[a]->getMass(); |
665 |
rmb = 1.0 / atoms[b]->getMass(); |
666 |
|
667 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
668 |
|
669 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
670 |
|
671 |
if (fabs(gab) > tol){ |
672 |
dx = rab[0] * gab; |
673 |
dy = rab[1] * gab; |
674 |
dz = rab[2] * gab; |
675 |
|
676 |
velA[0] += rma * dx; |
677 |
velA[1] += rma * dy; |
678 |
velA[2] += rma * dz; |
679 |
|
680 |
atoms[a]->setVel(velA); |
681 |
|
682 |
velB[0] -= rmb * dx; |
683 |
velB[1] -= rmb * dy; |
684 |
velB[2] -= rmb * dz; |
685 |
|
686 |
atoms[b]->setVel(velB); |
687 |
|
688 |
moving[a] = 1; |
689 |
moving[b] = 1; |
690 |
done = 0; |
691 |
} |
692 |
} |
693 |
} |
694 |
|
695 |
for (i = 0; i < nAtoms; i++){ |
696 |
moved[i] = moving[i]; |
697 |
moving[i] = 0; |
698 |
} |
699 |
|
700 |
iteration++; |
701 |
} |
702 |
|
703 |
if (!done){ |
704 |
sprintf(painCave.errMsg, |
705 |
"Constraint failure in constrainB, too many iterations: %d\n", |
706 |
iteration); |
707 |
painCave.isFatal = 1; |
708 |
simError(); |
709 |
} |
710 |
} |
711 |
*/ |
712 |
template<typename T> void Integrator<T>::rotationPropagation |
713 |
( StuntDouble* sd, double ji[3] ){ |
714 |
|
715 |
double angle; |
716 |
double A[3][3], I[3][3]; |
717 |
int i, j, k; |
718 |
|
719 |
// use the angular velocities to propagate the rotation matrix a |
720 |
// full time step |
721 |
|
722 |
sd->getA(A); |
723 |
sd->getI(I); |
724 |
|
725 |
if (sd->isLinear()) { |
726 |
i = sd->linearAxis(); |
727 |
j = (i+1)%3; |
728 |
k = (i+2)%3; |
729 |
|
730 |
angle = dt2 * ji[j] / I[j][j]; |
731 |
this->rotate( k, i, angle, ji, A ); |
732 |
|
733 |
angle = dt * ji[k] / I[k][k]; |
734 |
this->rotate( i, j, angle, ji, A); |
735 |
|
736 |
angle = dt2 * ji[j] / I[j][j]; |
737 |
this->rotate( k, i, angle, ji, A ); |
738 |
|
739 |
} else { |
740 |
// rotate about the x-axis |
741 |
angle = dt2 * ji[0] / I[0][0]; |
742 |
this->rotate( 1, 2, 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 z-axis |
749 |
angle = dt * ji[2] / I[2][2]; |
750 |
sd->addZangle(angle); |
751 |
this->rotate( 0, 1, angle, ji, A); |
752 |
|
753 |
// rotate about the y-axis |
754 |
angle = dt2 * ji[1] / I[1][1]; |
755 |
this->rotate( 2, 0, angle, ji, A ); |
756 |
|
757 |
// rotate about the x-axis |
758 |
angle = dt2 * ji[0] / I[0][0]; |
759 |
this->rotate( 1, 2, angle, ji, A ); |
760 |
|
761 |
} |
762 |
sd->setA( A ); |
763 |
} |
764 |
|
765 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
766 |
double angle, double ji[3], |
767 |
double A[3][3]){ |
768 |
int i, j, k; |
769 |
double sinAngle; |
770 |
double cosAngle; |
771 |
double angleSqr; |
772 |
double angleSqrOver4; |
773 |
double top, bottom; |
774 |
double rot[3][3]; |
775 |
double tempA[3][3]; |
776 |
double tempJ[3]; |
777 |
|
778 |
// initialize the tempA |
779 |
|
780 |
for (i = 0; i < 3; i++){ |
781 |
for (j = 0; j < 3; j++){ |
782 |
tempA[j][i] = A[i][j]; |
783 |
} |
784 |
} |
785 |
|
786 |
// initialize the tempJ |
787 |
|
788 |
for (i = 0; i < 3; i++) |
789 |
tempJ[i] = ji[i]; |
790 |
|
791 |
// initalize rot as a unit matrix |
792 |
|
793 |
rot[0][0] = 1.0; |
794 |
rot[0][1] = 0.0; |
795 |
rot[0][2] = 0.0; |
796 |
|
797 |
rot[1][0] = 0.0; |
798 |
rot[1][1] = 1.0; |
799 |
rot[1][2] = 0.0; |
800 |
|
801 |
rot[2][0] = 0.0; |
802 |
rot[2][1] = 0.0; |
803 |
rot[2][2] = 1.0; |
804 |
|
805 |
// use a small angle aproximation for sin and cosine |
806 |
|
807 |
angleSqr = angle * angle; |
808 |
angleSqrOver4 = angleSqr / 4.0; |
809 |
top = 1.0 - angleSqrOver4; |
810 |
bottom = 1.0 + angleSqrOver4; |
811 |
|
812 |
cosAngle = top / bottom; |
813 |
sinAngle = angle / bottom; |
814 |
|
815 |
rot[axes1][axes1] = cosAngle; |
816 |
rot[axes2][axes2] = cosAngle; |
817 |
|
818 |
rot[axes1][axes2] = sinAngle; |
819 |
rot[axes2][axes1] = -sinAngle; |
820 |
|
821 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
822 |
|
823 |
for (i = 0; i < 3; i++){ |
824 |
ji[i] = 0.0; |
825 |
for (k = 0; k < 3; k++){ |
826 |
ji[i] += rot[i][k] * tempJ[k]; |
827 |
} |
828 |
} |
829 |
|
830 |
// rotate the Rotation matrix acording to: |
831 |
// A[][] = A[][] * transpose(rot[][]) |
832 |
|
833 |
|
834 |
// NOte for as yet unknown reason, we are performing the |
835 |
// calculation as: |
836 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
837 |
|
838 |
for (i = 0; i < 3; i++){ |
839 |
for (j = 0; j < 3; j++){ |
840 |
A[j][i] = 0.0; |
841 |
for (k = 0; k < 3; k++){ |
842 |
A[j][i] += tempA[i][k] * rot[j][k]; |
843 |
} |
844 |
} |
845 |
} |
846 |
} |
847 |
|
848 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
849 |
myFF->doForces(calcPot, calcStress); |
850 |
} |
851 |
|
852 |
template<typename T> void Integrator<T>::thermalize(){ |
853 |
tStats->velocitize(); |
854 |
} |
855 |
|
856 |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
857 |
return tStats->getTotalE(); |
858 |
} |
859 |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
860 |
//By default, return a null string |
861 |
//The reason we use string instead of char* is that if we use char*, we will |
862 |
//return a pointer point to local variable which might cause problem |
863 |
return string(); |
864 |
} |