1 |
#include <iostream> |
2 |
#include <cstdlib> |
3 |
#include <cmath> |
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 |
int i, j; // loop counters |
150 |
|
151 |
double runTime = info->run_time; |
152 |
double sampleTime = info->sampleTime; |
153 |
double statusTime = info->statusTime; |
154 |
double thermalTime = info->thermalTime; |
155 |
double resetTime = info->resetTime; |
156 |
|
157 |
|
158 |
double currSample; |
159 |
double currThermal; |
160 |
double currStatus; |
161 |
double currReset; |
162 |
|
163 |
int calcPot, calcStress; |
164 |
int isError; |
165 |
|
166 |
tStats = new Thermo(info); |
167 |
statOut = new StatWriter(info); |
168 |
dumpOut = new DumpWriter(info); |
169 |
|
170 |
atoms = info->atoms; |
171 |
DirectionalAtom* dAtom; |
172 |
|
173 |
dt = info->dt; |
174 |
dt2 = 0.5 * dt; |
175 |
|
176 |
readyCheck(); |
177 |
|
178 |
// initialize the forces before the first step |
179 |
|
180 |
calcForce(1, 1); |
181 |
|
182 |
if (nConstrained){ |
183 |
preMove(); |
184 |
constrainA(); |
185 |
calcForce(1, 1); |
186 |
constrainB(); |
187 |
} |
188 |
|
189 |
if (info->setTemp){ |
190 |
thermalize(); |
191 |
} |
192 |
|
193 |
calcPot = 0; |
194 |
calcStress = 0; |
195 |
currSample = sampleTime + info->getTime(); |
196 |
currThermal = thermalTime+ info->getTime(); |
197 |
currStatus = statusTime + info->getTime(); |
198 |
currReset = resetTime + info->getTime(); |
199 |
|
200 |
dumpOut->writeDump(info->getTime()); |
201 |
statOut->writeStat(info->getTime()); |
202 |
|
203 |
|
204 |
|
205 |
#ifdef IS_MPI |
206 |
strcpy(checkPointMsg, "The integrator is ready to go."); |
207 |
MPIcheckPoint(); |
208 |
#endif // is_mpi |
209 |
|
210 |
while (info->getTime() < runTime){ |
211 |
if ((info->getTime() + dt) >= currStatus){ |
212 |
calcPot = 1; |
213 |
calcStress = 1; |
214 |
} |
215 |
|
216 |
integrateStep(calcPot, calcStress); |
217 |
|
218 |
info->incrTime(dt); |
219 |
|
220 |
if (info->setTemp){ |
221 |
if (info->getTime() >= currThermal){ |
222 |
thermalize(); |
223 |
currThermal += thermalTime; |
224 |
} |
225 |
} |
226 |
|
227 |
if (info->getTime() >= currSample){ |
228 |
dumpOut->writeDump(info->getTime()); |
229 |
currSample += sampleTime; |
230 |
} |
231 |
|
232 |
if (info->getTime() >= currStatus){ |
233 |
statOut->writeStat(info->getTime()); |
234 |
calcPot = 0; |
235 |
calcStress = 0; |
236 |
currStatus += statusTime; |
237 |
} |
238 |
|
239 |
if (info->resetIntegrator){ |
240 |
if (info->getTime() >= currReset){ |
241 |
this->resetIntegrator(); |
242 |
currReset += resetTime; |
243 |
} |
244 |
} |
245 |
|
246 |
#ifdef IS_MPI |
247 |
strcpy(checkPointMsg, "successfully took a time step."); |
248 |
MPIcheckPoint(); |
249 |
#endif // is_mpi |
250 |
} |
251 |
|
252 |
dumpOut->writeFinal(info->getTime()); |
253 |
|
254 |
delete dumpOut; |
255 |
delete statOut; |
256 |
} |
257 |
|
258 |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
259 |
int calcStress){ |
260 |
// Position full step, and velocity half step |
261 |
preMove(); |
262 |
|
263 |
moveA(); |
264 |
|
265 |
|
266 |
|
267 |
|
268 |
#ifdef IS_MPI |
269 |
strcpy(checkPointMsg, "Succesful moveA\n"); |
270 |
MPIcheckPoint(); |
271 |
#endif // is_mpi |
272 |
|
273 |
|
274 |
// calc forces |
275 |
|
276 |
calcForce(calcPot, calcStress); |
277 |
|
278 |
#ifdef IS_MPI |
279 |
strcpy(checkPointMsg, "Succesful doForces\n"); |
280 |
MPIcheckPoint(); |
281 |
#endif // is_mpi |
282 |
|
283 |
|
284 |
// finish the velocity half step |
285 |
|
286 |
moveB(); |
287 |
|
288 |
|
289 |
|
290 |
#ifdef IS_MPI |
291 |
strcpy(checkPointMsg, "Succesful moveB\n"); |
292 |
MPIcheckPoint(); |
293 |
#endif // is_mpi |
294 |
} |
295 |
|
296 |
|
297 |
template<typename T> void Integrator<T>::moveA(void){ |
298 |
int i, j; |
299 |
DirectionalAtom* dAtom; |
300 |
double Tb[3], ji[3]; |
301 |
double vel[3], pos[3], frc[3]; |
302 |
double mass; |
303 |
|
304 |
for (i = 0; i < nAtoms; i++){ |
305 |
atoms[i]->getVel(vel); |
306 |
atoms[i]->getPos(pos); |
307 |
atoms[i]->getFrc(frc); |
308 |
|
309 |
mass = atoms[i]->getMass(); |
310 |
|
311 |
for (j = 0; j < 3; j++){ |
312 |
// velocity half step |
313 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
314 |
// position whole step |
315 |
pos[j] += dt * vel[j]; |
316 |
} |
317 |
|
318 |
atoms[i]->setVel(vel); |
319 |
atoms[i]->setPos(pos); |
320 |
|
321 |
if (atoms[i]->isDirectional()){ |
322 |
dAtom = (DirectionalAtom *) atoms[i]; |
323 |
|
324 |
// get and convert the torque to body frame |
325 |
|
326 |
dAtom->getTrq(Tb); |
327 |
dAtom->lab2Body(Tb); |
328 |
|
329 |
// get the angular momentum, and propagate a half step |
330 |
|
331 |
dAtom->getJ(ji); |
332 |
|
333 |
for (j = 0; j < 3; j++) |
334 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
335 |
|
336 |
this->rotationPropagation( dAtom, ji ); |
337 |
|
338 |
dAtom->setJ(ji); |
339 |
} |
340 |
} |
341 |
|
342 |
if (nConstrained){ |
343 |
constrainA(); |
344 |
} |
345 |
} |
346 |
|
347 |
|
348 |
template<typename T> void Integrator<T>::moveB(void){ |
349 |
int i, j; |
350 |
DirectionalAtom* dAtom; |
351 |
double Tb[3], ji[3]; |
352 |
double vel[3], frc[3]; |
353 |
double mass; |
354 |
|
355 |
for (i = 0; i < nAtoms; i++){ |
356 |
atoms[i]->getVel(vel); |
357 |
atoms[i]->getFrc(frc); |
358 |
|
359 |
mass = atoms[i]->getMass(); |
360 |
|
361 |
// velocity half step |
362 |
for (j = 0; j < 3; j++) |
363 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
364 |
|
365 |
atoms[i]->setVel(vel); |
366 |
|
367 |
if (atoms[i]->isDirectional()){ |
368 |
dAtom = (DirectionalAtom *) atoms[i]; |
369 |
|
370 |
// get and convert the torque to body frame |
371 |
|
372 |
dAtom->getTrq(Tb); |
373 |
dAtom->lab2Body(Tb); |
374 |
|
375 |
// get the angular momentum, and propagate a half step |
376 |
|
377 |
dAtom->getJ(ji); |
378 |
|
379 |
for (j = 0; j < 3; j++) |
380 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
381 |
|
382 |
|
383 |
dAtom->setJ(ji); |
384 |
} |
385 |
} |
386 |
|
387 |
if (nConstrained){ |
388 |
constrainB(); |
389 |
} |
390 |
} |
391 |
|
392 |
template<typename T> void Integrator<T>::preMove(void){ |
393 |
int i, j; |
394 |
double pos[3]; |
395 |
|
396 |
if (nConstrained){ |
397 |
for (i = 0; i < nAtoms; i++){ |
398 |
atoms[i]->getPos(pos); |
399 |
|
400 |
for (j = 0; j < 3; j++){ |
401 |
oldPos[3 * i + j] = pos[j]; |
402 |
} |
403 |
} |
404 |
} |
405 |
} |
406 |
|
407 |
template<typename T> void Integrator<T>::constrainA(){ |
408 |
int i, j, k; |
409 |
int done; |
410 |
double posA[3], posB[3]; |
411 |
double velA[3], velB[3]; |
412 |
double pab[3]; |
413 |
double rab[3]; |
414 |
int a, b, ax, ay, az, bx, by, bz; |
415 |
double rma, rmb; |
416 |
double dx, dy, dz; |
417 |
double rpab; |
418 |
double rabsq, pabsq, rpabsq; |
419 |
double diffsq; |
420 |
double gab; |
421 |
int iteration; |
422 |
|
423 |
for (i = 0; i < nAtoms; i++){ |
424 |
moving[i] = 0; |
425 |
moved[i] = 1; |
426 |
} |
427 |
|
428 |
iteration = 0; |
429 |
done = 0; |
430 |
while (!done && (iteration < maxIteration)){ |
431 |
done = 1; |
432 |
for (i = 0; i < nConstrained; i++){ |
433 |
a = constrainedA[i]; |
434 |
b = constrainedB[i]; |
435 |
|
436 |
ax = (a * 3) + 0; |
437 |
ay = (a * 3) + 1; |
438 |
az = (a * 3) + 2; |
439 |
|
440 |
bx = (b * 3) + 0; |
441 |
by = (b * 3) + 1; |
442 |
bz = (b * 3) + 2; |
443 |
|
444 |
if (moved[a] || moved[b]){ |
445 |
atoms[a]->getPos(posA); |
446 |
atoms[b]->getPos(posB); |
447 |
|
448 |
for (j = 0; j < 3; j++) |
449 |
pab[j] = posA[j] - posB[j]; |
450 |
|
451 |
//periodic boundary condition |
452 |
|
453 |
info->wrapVector(pab); |
454 |
|
455 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
456 |
|
457 |
rabsq = constrainedDsqr[i]; |
458 |
diffsq = rabsq - pabsq; |
459 |
|
460 |
// the original rattle code from alan tidesley |
461 |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
462 |
rab[0] = oldPos[ax] - oldPos[bx]; |
463 |
rab[1] = oldPos[ay] - oldPos[by]; |
464 |
rab[2] = oldPos[az] - oldPos[bz]; |
465 |
|
466 |
info->wrapVector(rab); |
467 |
|
468 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
469 |
|
470 |
rpabsq = rpab * rpab; |
471 |
|
472 |
|
473 |
if (rpabsq < (rabsq * -diffsq)){ |
474 |
#ifdef IS_MPI |
475 |
a = atoms[a]->getGlobalIndex(); |
476 |
b = atoms[b]->getGlobalIndex(); |
477 |
#endif //is_mpi |
478 |
sprintf(painCave.errMsg, |
479 |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
480 |
b); |
481 |
painCave.isFatal = 1; |
482 |
simError(); |
483 |
} |
484 |
|
485 |
rma = 1.0 / atoms[a]->getMass(); |
486 |
rmb = 1.0 / atoms[b]->getMass(); |
487 |
|
488 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
489 |
|
490 |
dx = rab[0] * gab; |
491 |
dy = rab[1] * gab; |
492 |
dz = rab[2] * gab; |
493 |
|
494 |
posA[0] += rma * dx; |
495 |
posA[1] += rma * dy; |
496 |
posA[2] += rma * dz; |
497 |
|
498 |
atoms[a]->setPos(posA); |
499 |
|
500 |
posB[0] -= rmb * dx; |
501 |
posB[1] -= rmb * dy; |
502 |
posB[2] -= rmb * dz; |
503 |
|
504 |
atoms[b]->setPos(posB); |
505 |
|
506 |
dx = dx / dt; |
507 |
dy = dy / dt; |
508 |
dz = dz / dt; |
509 |
|
510 |
atoms[a]->getVel(velA); |
511 |
|
512 |
velA[0] += rma * dx; |
513 |
velA[1] += rma * dy; |
514 |
velA[2] += rma * dz; |
515 |
|
516 |
atoms[a]->setVel(velA); |
517 |
|
518 |
atoms[b]->getVel(velB); |
519 |
|
520 |
velB[0] -= rmb * dx; |
521 |
velB[1] -= rmb * dy; |
522 |
velB[2] -= rmb * dz; |
523 |
|
524 |
atoms[b]->setVel(velB); |
525 |
|
526 |
moving[a] = 1; |
527 |
moving[b] = 1; |
528 |
done = 0; |
529 |
} |
530 |
} |
531 |
} |
532 |
|
533 |
for (i = 0; i < nAtoms; i++){ |
534 |
moved[i] = moving[i]; |
535 |
moving[i] = 0; |
536 |
} |
537 |
|
538 |
iteration++; |
539 |
} |
540 |
|
541 |
if (!done){ |
542 |
sprintf(painCave.errMsg, |
543 |
"Constraint failure in constrainA, too many iterations: %d\n", |
544 |
iteration); |
545 |
painCave.isFatal = 1; |
546 |
simError(); |
547 |
} |
548 |
|
549 |
} |
550 |
|
551 |
template<typename T> void Integrator<T>::constrainB(void){ |
552 |
int i, j, k; |
553 |
int done; |
554 |
double posA[3], posB[3]; |
555 |
double velA[3], velB[3]; |
556 |
double vxab, vyab, vzab; |
557 |
double rab[3]; |
558 |
int a, b, ax, ay, az, bx, by, bz; |
559 |
double rma, rmb; |
560 |
double dx, dy, dz; |
561 |
double rabsq, pabsq, rvab; |
562 |
double diffsq; |
563 |
double gab; |
564 |
int iteration; |
565 |
|
566 |
for (i = 0; i < nAtoms; i++){ |
567 |
moving[i] = 0; |
568 |
moved[i] = 1; |
569 |
} |
570 |
|
571 |
done = 0; |
572 |
iteration = 0; |
573 |
while (!done && (iteration < maxIteration)){ |
574 |
done = 1; |
575 |
|
576 |
for (i = 0; i < nConstrained; i++){ |
577 |
a = constrainedA[i]; |
578 |
b = constrainedB[i]; |
579 |
|
580 |
ax = (a * 3) + 0; |
581 |
ay = (a * 3) + 1; |
582 |
az = (a * 3) + 2; |
583 |
|
584 |
bx = (b * 3) + 0; |
585 |
by = (b * 3) + 1; |
586 |
bz = (b * 3) + 2; |
587 |
|
588 |
if (moved[a] || moved[b]){ |
589 |
atoms[a]->getVel(velA); |
590 |
atoms[b]->getVel(velB); |
591 |
|
592 |
vxab = velA[0] - velB[0]; |
593 |
vyab = velA[1] - velB[1]; |
594 |
vzab = velA[2] - velB[2]; |
595 |
|
596 |
atoms[a]->getPos(posA); |
597 |
atoms[b]->getPos(posB); |
598 |
|
599 |
for (j = 0; j < 3; j++) |
600 |
rab[j] = posA[j] - posB[j]; |
601 |
|
602 |
info->wrapVector(rab); |
603 |
|
604 |
rma = 1.0 / atoms[a]->getMass(); |
605 |
rmb = 1.0 / atoms[b]->getMass(); |
606 |
|
607 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
608 |
|
609 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
610 |
|
611 |
if (fabs(gab) > tol){ |
612 |
dx = rab[0] * gab; |
613 |
dy = rab[1] * gab; |
614 |
dz = rab[2] * gab; |
615 |
|
616 |
velA[0] += rma * dx; |
617 |
velA[1] += rma * dy; |
618 |
velA[2] += rma * dz; |
619 |
|
620 |
atoms[a]->setVel(velA); |
621 |
|
622 |
velB[0] -= rmb * dx; |
623 |
velB[1] -= rmb * dy; |
624 |
velB[2] -= rmb * dz; |
625 |
|
626 |
atoms[b]->setVel(velB); |
627 |
|
628 |
moving[a] = 1; |
629 |
moving[b] = 1; |
630 |
done = 0; |
631 |
} |
632 |
} |
633 |
} |
634 |
|
635 |
for (i = 0; i < nAtoms; i++){ |
636 |
moved[i] = moving[i]; |
637 |
moving[i] = 0; |
638 |
} |
639 |
|
640 |
iteration++; |
641 |
} |
642 |
|
643 |
if (!done){ |
644 |
sprintf(painCave.errMsg, |
645 |
"Constraint failure in constrainB, too many iterations: %d\n", |
646 |
iteration); |
647 |
painCave.isFatal = 1; |
648 |
simError(); |
649 |
} |
650 |
} |
651 |
|
652 |
template<typename T> void Integrator<T>::rotationPropagation |
653 |
( DirectionalAtom* dAtom, double ji[3] ){ |
654 |
|
655 |
double angle; |
656 |
double A[3][3], I[3][3]; |
657 |
|
658 |
// use the angular velocities to propagate the rotation matrix a |
659 |
// full time step |
660 |
|
661 |
dAtom->getA(A); |
662 |
dAtom->getI(I); |
663 |
|
664 |
// rotate about the x-axis |
665 |
angle = dt2 * ji[0] / I[0][0]; |
666 |
this->rotate( 1, 2, angle, ji, A ); |
667 |
|
668 |
// rotate about the y-axis |
669 |
angle = dt2 * ji[1] / I[1][1]; |
670 |
this->rotate( 2, 0, angle, ji, A ); |
671 |
|
672 |
// rotate about the z-axis |
673 |
angle = dt * ji[2] / I[2][2]; |
674 |
this->rotate( 0, 1, angle, ji, A); |
675 |
|
676 |
// rotate about the y-axis |
677 |
angle = dt2 * ji[1] / I[1][1]; |
678 |
this->rotate( 2, 0, angle, ji, A ); |
679 |
|
680 |
// rotate about the x-axis |
681 |
angle = dt2 * ji[0] / I[0][0]; |
682 |
this->rotate( 1, 2, angle, ji, A ); |
683 |
|
684 |
dAtom->setA( A ); |
685 |
} |
686 |
|
687 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
688 |
double angle, double ji[3], |
689 |
double A[3][3]){ |
690 |
int i, j, k; |
691 |
double sinAngle; |
692 |
double cosAngle; |
693 |
double angleSqr; |
694 |
double angleSqrOver4; |
695 |
double top, bottom; |
696 |
double rot[3][3]; |
697 |
double tempA[3][3]; |
698 |
double tempJ[3]; |
699 |
|
700 |
// initialize the tempA |
701 |
|
702 |
for (i = 0; i < 3; i++){ |
703 |
for (j = 0; j < 3; j++){ |
704 |
tempA[j][i] = A[i][j]; |
705 |
} |
706 |
} |
707 |
|
708 |
// initialize the tempJ |
709 |
|
710 |
for (i = 0; i < 3; i++) |
711 |
tempJ[i] = ji[i]; |
712 |
|
713 |
// initalize rot as a unit matrix |
714 |
|
715 |
rot[0][0] = 1.0; |
716 |
rot[0][1] = 0.0; |
717 |
rot[0][2] = 0.0; |
718 |
|
719 |
rot[1][0] = 0.0; |
720 |
rot[1][1] = 1.0; |
721 |
rot[1][2] = 0.0; |
722 |
|
723 |
rot[2][0] = 0.0; |
724 |
rot[2][1] = 0.0; |
725 |
rot[2][2] = 1.0; |
726 |
|
727 |
// use a small angle aproximation for sin and cosine |
728 |
|
729 |
angleSqr = angle * angle; |
730 |
angleSqrOver4 = angleSqr / 4.0; |
731 |
top = 1.0 - angleSqrOver4; |
732 |
bottom = 1.0 + angleSqrOver4; |
733 |
|
734 |
cosAngle = top / bottom; |
735 |
sinAngle = angle / bottom; |
736 |
|
737 |
rot[axes1][axes1] = cosAngle; |
738 |
rot[axes2][axes2] = cosAngle; |
739 |
|
740 |
rot[axes1][axes2] = sinAngle; |
741 |
rot[axes2][axes1] = -sinAngle; |
742 |
|
743 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
744 |
|
745 |
for (i = 0; i < 3; i++){ |
746 |
ji[i] = 0.0; |
747 |
for (k = 0; k < 3; k++){ |
748 |
ji[i] += rot[i][k] * tempJ[k]; |
749 |
} |
750 |
} |
751 |
|
752 |
// rotate the Rotation matrix acording to: |
753 |
// A[][] = A[][] * transpose(rot[][]) |
754 |
|
755 |
|
756 |
// NOte for as yet unknown reason, we are performing the |
757 |
// calculation as: |
758 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
759 |
|
760 |
for (i = 0; i < 3; i++){ |
761 |
for (j = 0; j < 3; j++){ |
762 |
A[j][i] = 0.0; |
763 |
for (k = 0; k < 3; k++){ |
764 |
A[j][i] += tempA[i][k] * rot[j][k]; |
765 |
} |
766 |
} |
767 |
} |
768 |
} |
769 |
|
770 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
771 |
myFF->doForces(calcPot, calcStress); |
772 |
} |
773 |
|
774 |
template<typename T> void Integrator<T>::thermalize(){ |
775 |
tStats->velocitize(); |
776 |
} |
777 |
|
778 |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
779 |
return tStats->getTotalE(); |
780 |
} |