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