1 |
#include <iostream> |
2 |
#include <stdlib.h> |
3 |
#include <math.h> |
4 |
#include "Rattle.hpp" |
5 |
#include "Roll.hpp" |
6 |
#ifdef IS_MPI |
7 |
#include "mpiSimulation.hpp" |
8 |
#include <unistd.h> |
9 |
#endif //is_mpi |
10 |
|
11 |
#ifdef PROFILE |
12 |
#include "mdProfile.hpp" |
13 |
#endif // profile |
14 |
|
15 |
#include "Integrator.hpp" |
16 |
#include "simError.h" |
17 |
|
18 |
|
19 |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
20 |
ForceFields* the_ff){ |
21 |
info = theInfo; |
22 |
myFF = the_ff; |
23 |
isFirst = 1; |
24 |
|
25 |
molecules = info->molecules; |
26 |
nMols = info->n_mol; |
27 |
|
28 |
// give a little love back to the SimInfo object |
29 |
|
30 |
if (info->the_integrator != NULL){ |
31 |
delete info->the_integrator; |
32 |
} |
33 |
|
34 |
nAtoms = info->n_atoms; |
35 |
integrableObjects = info->integrableObjects; |
36 |
|
37 |
consFramework = new RollFramework(info); |
38 |
|
39 |
if(consFramework == NULL){ |
40 |
sprintf(painCave.errMsg, |
41 |
"Integrator::Intergrator() Error: Memory allocation error for RattleFramework" ); |
42 |
painCave.isFatal = 1; |
43 |
simError(); |
44 |
} |
45 |
|
46 |
/* |
47 |
// check for constraints |
48 |
|
49 |
constrainedA = NULL; |
50 |
constrainedB = NULL; |
51 |
constrainedDsqr = NULL; |
52 |
moving = NULL; |
53 |
moved = NULL; |
54 |
oldPos = NULL; |
55 |
|
56 |
nConstrained = 0; |
57 |
|
58 |
checkConstraints(); |
59 |
*/ |
60 |
} |
61 |
|
62 |
template<typename T> Integrator<T>::~Integrator(){ |
63 |
if (consFramework != NULL) |
64 |
delete consFramework; |
65 |
/* |
66 |
if (nConstrained){ |
67 |
delete[] constrainedA; |
68 |
delete[] constrainedB; |
69 |
delete[] constrainedDsqr; |
70 |
delete[] moving; |
71 |
delete[] moved; |
72 |
delete[] oldPos; |
73 |
} |
74 |
*/ |
75 |
} |
76 |
|
77 |
/* |
78 |
template<typename T> void Integrator<T>::checkConstraints(void){ |
79 |
isConstrained = 0; |
80 |
|
81 |
Constraint* temp_con; |
82 |
Constraint* dummy_plug; |
83 |
temp_con = new Constraint[info->n_SRI]; |
84 |
nConstrained = 0; |
85 |
int constrained = 0; |
86 |
|
87 |
SRI** theArray; |
88 |
for (int i = 0; i < nMols; i++){ |
89 |
|
90 |
theArray = (SRI * *) molecules[i].getMyBonds(); |
91 |
for (int j = 0; j < molecules[i].getNBonds(); j++){ |
92 |
constrained = theArray[j]->is_constrained(); |
93 |
|
94 |
if (constrained){ |
95 |
dummy_plug = theArray[j]->get_constraint(); |
96 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
97 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
98 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
99 |
|
100 |
nConstrained++; |
101 |
constrained = 0; |
102 |
} |
103 |
} |
104 |
|
105 |
theArray = (SRI * *) molecules[i].getMyBends(); |
106 |
for (int j = 0; j < molecules[i].getNBends(); j++){ |
107 |
constrained = theArray[j]->is_constrained(); |
108 |
|
109 |
if (constrained){ |
110 |
dummy_plug = theArray[j]->get_constraint(); |
111 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
112 |
temp_con[nConstrained].set_b(Dummy_plug->get_b()); |
113 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
114 |
|
115 |
nConstrained++; |
116 |
constrained = 0; |
117 |
} |
118 |
} |
119 |
|
120 |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
121 |
for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
122 |
constrained = theArray[j]->is_constrained(); |
123 |
|
124 |
if (constrained){ |
125 |
dummy_plug = theArray[j]->get_constraint(); |
126 |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
127 |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
128 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
129 |
|
130 |
nConstrained++; |
131 |
constrained = 0; |
132 |
} |
133 |
} |
134 |
} |
135 |
|
136 |
|
137 |
if (nConstrained > 0){ |
138 |
isConstrained = 1; |
139 |
|
140 |
if (constrainedA != NULL) |
141 |
delete[] constrainedA; |
142 |
if (constrainedB != NULL) |
143 |
delete[] constrainedB; |
144 |
if (constrainedDsqr != NULL) |
145 |
delete[] constrainedDsqr; |
146 |
|
147 |
constrainedA = new int[nConstrained]; |
148 |
constrainedB = new int[nConstrained]; |
149 |
constrainedDsqr = new double[nConstrained]; |
150 |
|
151 |
for (int i = 0; i < nConstrained; i++){ |
152 |
constrainedA[i] = temp_con[i].get_a(); |
153 |
constrainedB[i] = temp_con[i].get_b(); |
154 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
155 |
} |
156 |
|
157 |
|
158 |
// save oldAtoms to check for lode balancing later on. |
159 |
|
160 |
oldAtoms = nAtoms; |
161 |
|
162 |
moving = new int[nAtoms]; |
163 |
moved = new int[nAtoms]; |
164 |
|
165 |
oldPos = new double[nAtoms * 3]; |
166 |
} |
167 |
|
168 |
delete[] temp_con; |
169 |
} |
170 |
*/ |
171 |
|
172 |
template<typename T> void Integrator<T>::integrate(void){ |
173 |
|
174 |
double runTime = info->run_time; |
175 |
double sampleTime = info->sampleTime; |
176 |
double statusTime = info->statusTime; |
177 |
double thermalTime = info->thermalTime; |
178 |
double resetTime = info->resetTime; |
179 |
|
180 |
double difference; |
181 |
double currSample; |
182 |
double currThermal; |
183 |
double currStatus; |
184 |
double currReset; |
185 |
|
186 |
int calcPot, calcStress; |
187 |
|
188 |
tStats = new Thermo(info); |
189 |
statOut = new StatWriter(info); |
190 |
dumpOut = new DumpWriter(info); |
191 |
|
192 |
atoms = info->atoms; |
193 |
|
194 |
dt = info->dt; |
195 |
dt2 = 0.5 * dt; |
196 |
|
197 |
readyCheck(); |
198 |
|
199 |
// remove center of mass drift velocity (in case we passed in a configuration |
200 |
// that was drifting |
201 |
tStats->removeCOMdrift(); |
202 |
//tStats->removeAngularMomentum(); |
203 |
|
204 |
// initialize the retraints if necessary |
205 |
if (info->useSolidThermInt && !info->useLiquidThermInt) { |
206 |
myFF->initRestraints(); |
207 |
} |
208 |
|
209 |
// initialize the forces before the first step |
210 |
|
211 |
calcForce(1, 1); |
212 |
|
213 |
//execute constraint algorithm to make sure at the very beginning the system is constrained |
214 |
//consFramework->doPreConstraint(); |
215 |
//consFramework->doConstrainA(); |
216 |
//calcForce(1, 1); |
217 |
//consFramework->doConstrainB(); |
218 |
|
219 |
if (info->setTemp){ |
220 |
thermalize(); |
221 |
} |
222 |
|
223 |
calcPot = 0; |
224 |
calcStress = 0; |
225 |
currSample = sampleTime + info->getTime(); |
226 |
currThermal = thermalTime+ info->getTime(); |
227 |
currStatus = statusTime + info->getTime(); |
228 |
currReset = resetTime + info->getTime(); |
229 |
|
230 |
dumpOut->writeDump(info->getTime()); |
231 |
statOut->writeStat(info->getTime()); |
232 |
|
233 |
|
234 |
#ifdef IS_MPI |
235 |
strcpy(checkPointMsg, "The integrator is ready to go."); |
236 |
MPIcheckPoint(); |
237 |
#endif // is_mpi |
238 |
|
239 |
while (info->getTime() < runTime && !stopIntegrator()){ |
240 |
difference = info->getTime() + dt - currStatus; |
241 |
if (difference > 0 || fabs(difference) < 1e-4 ){ |
242 |
calcPot = 1; |
243 |
calcStress = 1; |
244 |
} |
245 |
|
246 |
#ifdef PROFILE |
247 |
startProfile( pro1 ); |
248 |
#endif |
249 |
|
250 |
integrateStep(calcPot, calcStress); |
251 |
|
252 |
#ifdef PROFILE |
253 |
endProfile( pro1 ); |
254 |
|
255 |
startProfile( pro2 ); |
256 |
#endif // profile |
257 |
|
258 |
info->incrTime(dt); |
259 |
|
260 |
if (info->setTemp){ |
261 |
if (info->getTime() >= currThermal){ |
262 |
thermalize(); |
263 |
currThermal += thermalTime; |
264 |
} |
265 |
} |
266 |
|
267 |
if (info->getTime() >= currSample){ |
268 |
dumpOut->writeDump(info->getTime()); |
269 |
currSample += sampleTime; |
270 |
} |
271 |
|
272 |
if (info->getTime() >= currStatus){ |
273 |
statOut->writeStat(info->getTime()); |
274 |
calcPot = 0; |
275 |
calcStress = 0; |
276 |
currStatus += statusTime; |
277 |
} |
278 |
|
279 |
if (info->resetIntegrator){ |
280 |
if (info->getTime() >= currReset){ |
281 |
this->resetIntegrator(); |
282 |
currReset += resetTime; |
283 |
} |
284 |
} |
285 |
|
286 |
#ifdef PROFILE |
287 |
endProfile( pro2 ); |
288 |
#endif //profile |
289 |
|
290 |
#ifdef IS_MPI |
291 |
strcpy(checkPointMsg, "successfully took a time step."); |
292 |
MPIcheckPoint(); |
293 |
#endif // is_mpi |
294 |
} |
295 |
|
296 |
// dump out a file containing the omega values for the final configuration |
297 |
if (info->useSolidThermInt && !info->useLiquidThermInt) |
298 |
myFF->dumpzAngle(); |
299 |
|
300 |
|
301 |
delete dumpOut; |
302 |
delete statOut; |
303 |
} |
304 |
|
305 |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
306 |
int calcStress){ |
307 |
// Position full step, and velocity half step |
308 |
|
309 |
#ifdef PROFILE |
310 |
startProfile(pro3); |
311 |
#endif //profile |
312 |
|
313 |
//save old state (position, velocity etc) |
314 |
consFramework->doPreConstraint(); |
315 |
|
316 |
#ifdef PROFILE |
317 |
endProfile(pro3); |
318 |
|
319 |
startProfile(pro4); |
320 |
#endif // profile |
321 |
|
322 |
moveA(); |
323 |
|
324 |
#ifdef PROFILE |
325 |
endProfile(pro4); |
326 |
|
327 |
startProfile(pro5); |
328 |
#endif//profile |
329 |
|
330 |
|
331 |
#ifdef IS_MPI |
332 |
strcpy(checkPointMsg, "Succesful moveA\n"); |
333 |
MPIcheckPoint(); |
334 |
#endif // is_mpi |
335 |
|
336 |
// calc forces |
337 |
calcForce(calcPot, calcStress); |
338 |
|
339 |
#ifdef IS_MPI |
340 |
strcpy(checkPointMsg, "Succesful doForces\n"); |
341 |
MPIcheckPoint(); |
342 |
#endif // is_mpi |
343 |
|
344 |
#ifdef PROFILE |
345 |
endProfile( pro5 ); |
346 |
|
347 |
startProfile( pro6 ); |
348 |
#endif //profile |
349 |
|
350 |
consFramework->doPreConstraint(); |
351 |
|
352 |
// finish the velocity half step |
353 |
|
354 |
moveB(); |
355 |
|
356 |
#ifdef PROFILE |
357 |
endProfile(pro6); |
358 |
#endif // profile |
359 |
|
360 |
#ifdef IS_MPI |
361 |
strcpy(checkPointMsg, "Succesful moveB\n"); |
362 |
MPIcheckPoint(); |
363 |
#endif // is_mpi |
364 |
} |
365 |
|
366 |
|
367 |
template<typename T> void Integrator<T>::moveA(void){ |
368 |
size_t i, j; |
369 |
DirectionalAtom* dAtom; |
370 |
double Tb[3], ji[3]; |
371 |
double vel[3], pos[3], frc[3]; |
372 |
double mass; |
373 |
double omega; |
374 |
|
375 |
for (i = 0; i < integrableObjects.size() ; i++){ |
376 |
integrableObjects[i]->getVel(vel); |
377 |
integrableObjects[i]->getPos(pos); |
378 |
integrableObjects[i]->getFrc(frc); |
379 |
|
380 |
mass = integrableObjects[i]->getMass(); |
381 |
|
382 |
for (j = 0; j < 3; j++){ |
383 |
// velocity half step |
384 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
385 |
// position whole step |
386 |
pos[j] += dt * vel[j]; |
387 |
} |
388 |
|
389 |
integrableObjects[i]->setVel(vel); |
390 |
integrableObjects[i]->setPos(pos); |
391 |
|
392 |
if (integrableObjects[i]->isDirectional()){ |
393 |
|
394 |
// get and convert the torque to body frame |
395 |
|
396 |
integrableObjects[i]->getTrq(Tb); |
397 |
integrableObjects[i]->lab2Body(Tb); |
398 |
|
399 |
// get the angular momentum, and propagate a half step |
400 |
|
401 |
integrableObjects[i]->getJ(ji); |
402 |
|
403 |
for (j = 0; j < 3; j++) |
404 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
405 |
|
406 |
this->rotationPropagation( integrableObjects[i], ji ); |
407 |
|
408 |
integrableObjects[i]->setJ(ji); |
409 |
|
410 |
} |
411 |
} |
412 |
|
413 |
consFramework->doConstrainA(); |
414 |
} |
415 |
|
416 |
|
417 |
template<typename T> void Integrator<T>::moveB(void){ |
418 |
int i, j; |
419 |
double Tb[3], ji[3]; |
420 |
double vel[3], frc[3]; |
421 |
double mass; |
422 |
|
423 |
for (i = 0; i < integrableObjects.size(); i++){ |
424 |
integrableObjects[i]->getVel(vel); |
425 |
integrableObjects[i]->getFrc(frc); |
426 |
|
427 |
mass = integrableObjects[i]->getMass(); |
428 |
|
429 |
// velocity half step |
430 |
for (j = 0; j < 3; j++) |
431 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
432 |
|
433 |
integrableObjects[i]->setVel(vel); |
434 |
|
435 |
if (integrableObjects[i]->isDirectional()){ |
436 |
|
437 |
// get and convert the torque to body frame |
438 |
|
439 |
integrableObjects[i]->getTrq(Tb); |
440 |
integrableObjects[i]->lab2Body(Tb); |
441 |
|
442 |
// get the angular momentum, and propagate a half step |
443 |
|
444 |
integrableObjects[i]->getJ(ji); |
445 |
|
446 |
for (j = 0; j < 3; j++) |
447 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
448 |
|
449 |
|
450 |
integrableObjects[i]->setJ(ji); |
451 |
} |
452 |
|
453 |
} |
454 |
|
455 |
consFramework->doConstrainB(); |
456 |
} |
457 |
|
458 |
/* |
459 |
template<typename T> void Integrator<T>::preMove(void){ |
460 |
int i, j; |
461 |
double pos[3]; |
462 |
|
463 |
if (nConstrained){ |
464 |
for (i = 0; i < nAtoms; i++){ |
465 |
atoms[i]->getPos(pos); |
466 |
|
467 |
for (j = 0; j < 3; j++){ |
468 |
oldPos[3 * i + j] = pos[j]; |
469 |
} |
470 |
} |
471 |
} |
472 |
} |
473 |
|
474 |
template<typename T> void Integrator<T>::constrainA(){ |
475 |
int i, j; |
476 |
int done; |
477 |
double posA[3], posB[3]; |
478 |
double velA[3], velB[3]; |
479 |
double pab[3]; |
480 |
double rab[3]; |
481 |
int a, b, ax, ay, az, bx, by, bz; |
482 |
double rma, rmb; |
483 |
double dx, dy, dz; |
484 |
double rpab; |
485 |
double rabsq, pabsq, rpabsq; |
486 |
double diffsq; |
487 |
double gab; |
488 |
int iteration; |
489 |
|
490 |
for (i = 0; i < nAtoms; i++){ |
491 |
moving[i] = 0; |
492 |
moved[i] = 1; |
493 |
} |
494 |
|
495 |
iteration = 0; |
496 |
done = 0; |
497 |
while (!done && (iteration < maxIteration)){ |
498 |
done = 1; |
499 |
for (i = 0; i < nConstrained; i++){ |
500 |
a = constrainedA[i]; |
501 |
b = constrainedB[i]; |
502 |
|
503 |
ax = (a * 3) + 0; |
504 |
ay = (a * 3) + 1; |
505 |
az = (a * 3) + 2; |
506 |
|
507 |
bx = (b * 3) + 0; |
508 |
by = (b * 3) + 1; |
509 |
bz = (b * 3) + 2; |
510 |
|
511 |
if (moved[a] || moved[b]){ |
512 |
atoms[a]->getPos(posA); |
513 |
atoms[b]->getPos(posB); |
514 |
|
515 |
for (j = 0; j < 3; j++) |
516 |
pab[j] = posA[j] - posB[j]; |
517 |
|
518 |
//periodic boundary condition |
519 |
|
520 |
info->wrapVector(pab); |
521 |
|
522 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
523 |
|
524 |
rabsq = constrainedDsqr[i]; |
525 |
diffsq = rabsq - pabsq; |
526 |
|
527 |
// the original rattle code from alan tidesley |
528 |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
529 |
rab[0] = oldPos[ax] - oldPos[bx]; |
530 |
rab[1] = oldPos[ay] - oldPos[by]; |
531 |
rab[2] = oldPos[az] - oldPos[bz]; |
532 |
|
533 |
info->wrapVector(rab); |
534 |
|
535 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
536 |
|
537 |
rpabsq = rpab * rpab; |
538 |
|
539 |
|
540 |
if (rpabsq < (rabsq * -diffsq)){ |
541 |
#ifdef IS_MPI |
542 |
a = atoms[a]->getGlobalIndex(); |
543 |
b = atoms[b]->getGlobalIndex(); |
544 |
#endif //is_mpi |
545 |
sprintf(painCave.errMsg, |
546 |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
547 |
b); |
548 |
painCave.isFatal = 1; |
549 |
simError(); |
550 |
} |
551 |
|
552 |
rma = 1.0 / atoms[a]->getMass(); |
553 |
rmb = 1.0 / atoms[b]->getMass(); |
554 |
|
555 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
556 |
|
557 |
dx = rab[0] * gab; |
558 |
dy = rab[1] * gab; |
559 |
dz = rab[2] * gab; |
560 |
|
561 |
posA[0] += rma * dx; |
562 |
posA[1] += rma * dy; |
563 |
posA[2] += rma * dz; |
564 |
|
565 |
atoms[a]->setPos(posA); |
566 |
|
567 |
posB[0] -= rmb * dx; |
568 |
posB[1] -= rmb * dy; |
569 |
posB[2] -= rmb * dz; |
570 |
|
571 |
atoms[b]->setPos(posB); |
572 |
|
573 |
dx = dx / dt; |
574 |
dy = dy / dt; |
575 |
dz = dz / dt; |
576 |
|
577 |
atoms[a]->getVel(velA); |
578 |
|
579 |
velA[0] += rma * dx; |
580 |
velA[1] += rma * dy; |
581 |
velA[2] += rma * dz; |
582 |
|
583 |
atoms[a]->setVel(velA); |
584 |
|
585 |
atoms[b]->getVel(velB); |
586 |
|
587 |
velB[0] -= rmb * dx; |
588 |
velB[1] -= rmb * dy; |
589 |
velB[2] -= rmb * dz; |
590 |
|
591 |
atoms[b]->setVel(velB); |
592 |
|
593 |
moving[a] = 1; |
594 |
moving[b] = 1; |
595 |
done = 0; |
596 |
} |
597 |
} |
598 |
} |
599 |
|
600 |
for (i = 0; i < nAtoms; i++){ |
601 |
moved[i] = moving[i]; |
602 |
moving[i] = 0; |
603 |
} |
604 |
|
605 |
iteration++; |
606 |
} |
607 |
|
608 |
if (!done){ |
609 |
sprintf(painCave.errMsg, |
610 |
"Constraint failure in constrainA, too many iterations: %d\n", |
611 |
iteration); |
612 |
painCave.isFatal = 1; |
613 |
simError(); |
614 |
} |
615 |
|
616 |
} |
617 |
|
618 |
template<typename T> void Integrator<T>::constrainB(void){ |
619 |
int i, j; |
620 |
int done; |
621 |
double posA[3], posB[3]; |
622 |
double velA[3], velB[3]; |
623 |
double vxab, vyab, vzab; |
624 |
double rab[3]; |
625 |
int a, b, ax, ay, az, bx, by, bz; |
626 |
double rma, rmb; |
627 |
double dx, dy, dz; |
628 |
double rvab; |
629 |
double gab; |
630 |
int iteration; |
631 |
|
632 |
for (i = 0; i < nAtoms; i++){ |
633 |
moving[i] = 0; |
634 |
moved[i] = 1; |
635 |
} |
636 |
|
637 |
done = 0; |
638 |
iteration = 0; |
639 |
while (!done && (iteration < maxIteration)){ |
640 |
done = 1; |
641 |
|
642 |
for (i = 0; i < nConstrained; i++){ |
643 |
a = constrainedA[i]; |
644 |
b = constrainedB[i]; |
645 |
|
646 |
ax = (a * 3) + 0; |
647 |
ay = (a * 3) + 1; |
648 |
az = (a * 3) + 2; |
649 |
|
650 |
bx = (b * 3) + 0; |
651 |
by = (b * 3) + 1; |
652 |
bz = (b * 3) + 2; |
653 |
|
654 |
if (moved[a] || moved[b]){ |
655 |
atoms[a]->getVel(velA); |
656 |
atoms[b]->getVel(velB); |
657 |
|
658 |
vxab = velA[0] - velB[0]; |
659 |
vyab = velA[1] - velB[1]; |
660 |
vzab = velA[2] - velB[2]; |
661 |
|
662 |
atoms[a]->getPos(posA); |
663 |
atoms[b]->getPos(posB); |
664 |
|
665 |
for (j = 0; j < 3; j++) |
666 |
rab[j] = posA[j] - posB[j]; |
667 |
|
668 |
info->wrapVector(rab); |
669 |
|
670 |
rma = 1.0 / atoms[a]->getMass(); |
671 |
rmb = 1.0 / atoms[b]->getMass(); |
672 |
|
673 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
674 |
|
675 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
676 |
|
677 |
if (fabs(gab) > tol){ |
678 |
dx = rab[0] * gab; |
679 |
dy = rab[1] * gab; |
680 |
dz = rab[2] * gab; |
681 |
|
682 |
velA[0] += rma * dx; |
683 |
velA[1] += rma * dy; |
684 |
velA[2] += rma * dz; |
685 |
|
686 |
atoms[a]->setVel(velA); |
687 |
|
688 |
velB[0] -= rmb * dx; |
689 |
velB[1] -= rmb * dy; |
690 |
velB[2] -= rmb * dz; |
691 |
|
692 |
atoms[b]->setVel(velB); |
693 |
|
694 |
moving[a] = 1; |
695 |
moving[b] = 1; |
696 |
done = 0; |
697 |
} |
698 |
} |
699 |
} |
700 |
|
701 |
for (i = 0; i < nAtoms; i++){ |
702 |
moved[i] = moving[i]; |
703 |
moving[i] = 0; |
704 |
} |
705 |
|
706 |
iteration++; |
707 |
} |
708 |
|
709 |
if (!done){ |
710 |
sprintf(painCave.errMsg, |
711 |
"Constraint failure in constrainB, too many iterations: %d\n", |
712 |
iteration); |
713 |
painCave.isFatal = 1; |
714 |
simError(); |
715 |
} |
716 |
} |
717 |
*/ |
718 |
template<typename T> void Integrator<T>::rotationPropagation |
719 |
( StuntDouble* sd, double ji[3] ){ |
720 |
|
721 |
double angle; |
722 |
double A[3][3], I[3][3]; |
723 |
int i, j, k; |
724 |
|
725 |
// use the angular velocities to propagate the rotation matrix a |
726 |
// full time step |
727 |
|
728 |
sd->getA(A); |
729 |
sd->getI(I); |
730 |
|
731 |
if (sd->isLinear()) { |
732 |
i = sd->linearAxis(); |
733 |
j = (i+1)%3; |
734 |
k = (i+2)%3; |
735 |
|
736 |
angle = dt2 * ji[j] / I[j][j]; |
737 |
this->rotate( k, i, angle, ji, A ); |
738 |
|
739 |
angle = dt * ji[k] / I[k][k]; |
740 |
this->rotate( i, j, angle, ji, A); |
741 |
|
742 |
angle = dt2 * ji[j] / I[j][j]; |
743 |
this->rotate( k, i, angle, ji, A ); |
744 |
|
745 |
} else { |
746 |
// rotate about the x-axis |
747 |
angle = dt2 * ji[0] / I[0][0]; |
748 |
this->rotate( 1, 2, angle, ji, A ); |
749 |
|
750 |
// rotate about the y-axis |
751 |
angle = dt2 * ji[1] / I[1][1]; |
752 |
this->rotate( 2, 0, angle, ji, A ); |
753 |
|
754 |
// rotate about the z-axis |
755 |
angle = dt * ji[2] / I[2][2]; |
756 |
sd->addZangle(angle); |
757 |
this->rotate( 0, 1, angle, ji, A); |
758 |
|
759 |
// rotate about the y-axis |
760 |
angle = dt2 * ji[1] / I[1][1]; |
761 |
this->rotate( 2, 0, angle, ji, A ); |
762 |
|
763 |
// rotate about the x-axis |
764 |
angle = dt2 * ji[0] / I[0][0]; |
765 |
this->rotate( 1, 2, angle, ji, A ); |
766 |
|
767 |
} |
768 |
sd->setA( A ); |
769 |
} |
770 |
|
771 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
772 |
double angle, double ji[3], |
773 |
double A[3][3]){ |
774 |
int i, j, k; |
775 |
double sinAngle; |
776 |
double cosAngle; |
777 |
double angleSqr; |
778 |
double angleSqrOver4; |
779 |
double top, bottom; |
780 |
double rot[3][3]; |
781 |
double tempA[3][3]; |
782 |
double tempJ[3]; |
783 |
|
784 |
// initialize the tempA |
785 |
|
786 |
for (i = 0; i < 3; i++){ |
787 |
for (j = 0; j < 3; j++){ |
788 |
tempA[j][i] = A[i][j]; |
789 |
} |
790 |
} |
791 |
|
792 |
// initialize the tempJ |
793 |
|
794 |
for (i = 0; i < 3; i++) |
795 |
tempJ[i] = ji[i]; |
796 |
|
797 |
// initalize rot as a unit matrix |
798 |
|
799 |
rot[0][0] = 1.0; |
800 |
rot[0][1] = 0.0; |
801 |
rot[0][2] = 0.0; |
802 |
|
803 |
rot[1][0] = 0.0; |
804 |
rot[1][1] = 1.0; |
805 |
rot[1][2] = 0.0; |
806 |
|
807 |
rot[2][0] = 0.0; |
808 |
rot[2][1] = 0.0; |
809 |
rot[2][2] = 1.0; |
810 |
|
811 |
// use a small angle aproximation for sin and cosine |
812 |
|
813 |
angleSqr = angle * angle; |
814 |
angleSqrOver4 = angleSqr / 4.0; |
815 |
top = 1.0 - angleSqrOver4; |
816 |
bottom = 1.0 + angleSqrOver4; |
817 |
|
818 |
cosAngle = top / bottom; |
819 |
sinAngle = angle / bottom; |
820 |
|
821 |
rot[axes1][axes1] = cosAngle; |
822 |
rot[axes2][axes2] = cosAngle; |
823 |
|
824 |
rot[axes1][axes2] = sinAngle; |
825 |
rot[axes2][axes1] = -sinAngle; |
826 |
|
827 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
828 |
|
829 |
for (i = 0; i < 3; i++){ |
830 |
ji[i] = 0.0; |
831 |
for (k = 0; k < 3; k++){ |
832 |
ji[i] += rot[i][k] * tempJ[k]; |
833 |
} |
834 |
} |
835 |
|
836 |
// rotate the Rotation matrix acording to: |
837 |
// A[][] = A[][] * transpose(rot[][]) |
838 |
|
839 |
|
840 |
// NOte for as yet unknown reason, we are performing the |
841 |
// calculation as: |
842 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
843 |
|
844 |
for (i = 0; i < 3; i++){ |
845 |
for (j = 0; j < 3; j++){ |
846 |
A[j][i] = 0.0; |
847 |
for (k = 0; k < 3; k++){ |
848 |
A[j][i] += tempA[i][k] * rot[j][k]; |
849 |
} |
850 |
} |
851 |
} |
852 |
} |
853 |
|
854 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
855 |
myFF->doForces(calcPot, calcStress); |
856 |
} |
857 |
|
858 |
template<typename T> void Integrator<T>::thermalize(){ |
859 |
tStats->velocitize(); |
860 |
} |
861 |
|
862 |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
863 |
return tStats->getTotalE(); |
864 |
} |
865 |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
866 |
//By default, return a null string |
867 |
//The reason we use string instead of char* is that if we use char*, we will |
868 |
//return a pointer point to local variable which might cause problem |
869 |
return string(); |
870 |
} |
871 |
|
872 |
|
873 |
template<typename T> void Integrator<T>::printQuaternion(StuntDouble* sd){ |
874 |
Mat4x4d S; |
875 |
double I[3][3]; |
876 |
Vector4d j4; |
877 |
Vector3d j; |
878 |
Vector3d tempJ; |
879 |
Vector4d qdot; |
880 |
Vector4d omega4; |
881 |
Mat4x4d I4; |
882 |
Quaternion q; |
883 |
double I0; |
884 |
Vector4d p_qua; |
885 |
|
886 |
if (sd->isDirectional()){ |
887 |
sd->getQ(q.vec); |
888 |
sd->getI(I); |
889 |
sd->getJ(j.vec); |
890 |
|
891 |
//omega4[0] = 0.0; |
892 |
//omega4[1] = j[0]/I[0][0]; |
893 |
//omega4[2] = j[1]/I[1][1]; |
894 |
//omega4[3] = j[2]/I[2][2]; |
895 |
|
896 |
//S = getS(q); |
897 |
//qdot = 0.5 * S * omega4; |
898 |
|
899 |
//I0 = (qdot[1] * q[1] * I[0][0] + qdot[2] * q[2] * I[1][1] + qdot[3] * q[3] * I[2][2])/(qdot[1] * q[1]+ qdot[2] * q[2] + qdot[3] * q[3]); |
900 |
|
901 |
//I4.element[0][0] = I0; |
902 |
//I4.element[1][1] = I[0][0]; |
903 |
//I4.element[2][2] = I[1][1]; |
904 |
//I4.element[3][3] = I[2][2]; |
905 |
|
906 |
S = getS(q); |
907 |
j4[0] = 0.0; |
908 |
j4[1] = j[0]; |
909 |
j4[2] = j[1]; |
910 |
j4[3] = j[2]; |
911 |
|
912 |
p_qua = 2 * S * j4; |
913 |
|
914 |
j4 = 0.5 * S.transpose() * p_qua; |
915 |
//cout << "q0^2 + q1^2 + q2^2 + q3^2 = " << q[0]*q[0] + q[1]*q[1] + q[2]*q[2] + q[3]*q[3] << endl; |
916 |
//cout << "q0*q0dot + q1*q1dot + q2 *q2dot + q3*q3dot = " <<q[0]*qdot[0] + q[1]*qdot[1] + q[2]*qdot[2] + q[3]*qdot[3] << endl; |
917 |
//cout << "q1*q1dot* Ixx + q2*q2dot* Iyy + q3 *q3dot* Izz = " << qdot[1] * q[1] * I[0][0] + qdot[2] * q[2] * I[1][1] + qdot[3] * q[3] * I[2][2] << endl; |
918 |
//cout << "q1*q1dot + q2 *q2dot + q3*q3dot = " << qdot[1] * q[1]+ qdot[2] * q[2] + qdot[3] * q[3] << endl; |
919 |
//cout << "I0 = " << I0 << endl; |
920 |
cout << "p_qua[0] = " << p_qua[0] << endl; |
921 |
} |
922 |
} |
923 |
|
924 |
template<typename T> Mat4x4d Integrator<T>::getS(const Quaternion& q){ |
925 |
Mat4x4d result; |
926 |
|
927 |
result.element[0][0] = q.x; |
928 |
result.element[0][1] = -q.y; |
929 |
result.element[0][2] = -q.z; |
930 |
result.element[0][3] = -q.w; |
931 |
|
932 |
result.element[1][0] = q.y; |
933 |
result.element[1][1] = q.x; |
934 |
result.element[1][2] = -q.w; |
935 |
result.element[1][3] = q.z; |
936 |
|
937 |
result.element[2][0] = q.z; |
938 |
result.element[2][1] = q.w; |
939 |
result.element[2][2] = q.x; |
940 |
result.element[2][3] = -q.y; |
941 |
|
942 |
result.element[3][0] = q.w; |
943 |
result.element[3][1] = -q.z; |
944 |
result.element[3][2] = q.y; |
945 |
result.element[3][3] = q.x; |
946 |
|
947 |
return result; |
948 |
} |
949 |
|