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