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