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 |
Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){ |
15 |
|
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 ) delete info->the_integrator; |
26 |
info->the_integrator = this; |
27 |
|
28 |
nAtoms = info->n_atoms; |
29 |
|
30 |
// check for constraints |
31 |
|
32 |
constrainedA = NULL; |
33 |
constrainedB = NULL; |
34 |
constrainedDsqr = NULL; |
35 |
moving = NULL; |
36 |
moved = NULL; |
37 |
oldPos = NULL; |
38 |
|
39 |
nConstrained = 0; |
40 |
|
41 |
checkConstraints(); |
42 |
} |
43 |
|
44 |
Integrator::~Integrator() { |
45 |
|
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 |
|
57 |
void Integrator::checkConstraints( void ){ |
58 |
|
59 |
|
60 |
isConstrained = 0; |
61 |
|
62 |
Constraint *temp_con; |
63 |
Constraint *dummy_plug; |
64 |
temp_con = new Constraint[info->n_SRI]; |
65 |
nConstrained = 0; |
66 |
int constrained = 0; |
67 |
|
68 |
SRI** theArray; |
69 |
for(int i = 0; i < nMols; i++){ |
70 |
|
71 |
theArray = (SRI**) molecules[i].getMyBonds(); |
72 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
73 |
|
74 |
constrained = theArray[j]->is_constrained(); |
75 |
|
76 |
if(constrained){ |
77 |
|
78 |
dummy_plug = theArray[j]->get_constraint(); |
79 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
80 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
81 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
82 |
|
83 |
nConstrained++; |
84 |
constrained = 0; |
85 |
} |
86 |
} |
87 |
|
88 |
theArray = (SRI**) molecules[i].getMyBends(); |
89 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
90 |
|
91 |
constrained = theArray[j]->is_constrained(); |
92 |
|
93 |
if(constrained){ |
94 |
|
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].getMyTorsions(); |
106 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
107 |
|
108 |
constrained = theArray[j]->is_constrained(); |
109 |
|
110 |
if(constrained){ |
111 |
|
112 |
dummy_plug = theArray[j]->get_constraint(); |
113 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
114 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
115 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
116 |
|
117 |
nConstrained++; |
118 |
constrained = 0; |
119 |
} |
120 |
} |
121 |
} |
122 |
|
123 |
if(nConstrained > 0){ |
124 |
|
125 |
isConstrained = 1; |
126 |
|
127 |
if(constrainedA != NULL ) delete[] constrainedA; |
128 |
if(constrainedB != NULL ) delete[] constrainedB; |
129 |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
130 |
|
131 |
constrainedA = new int[nConstrained]; |
132 |
constrainedB = new int[nConstrained]; |
133 |
constrainedDsqr = new double[nConstrained]; |
134 |
|
135 |
for( int i = 0; i < nConstrained; i++){ |
136 |
|
137 |
constrainedA[i] = temp_con[i].get_a(); |
138 |
constrainedB[i] = temp_con[i].get_b(); |
139 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
140 |
|
141 |
} |
142 |
|
143 |
|
144 |
// save oldAtoms to check for lode balanceing later on. |
145 |
|
146 |
oldAtoms = nAtoms; |
147 |
|
148 |
moving = new int[nAtoms]; |
149 |
moved = new int[nAtoms]; |
150 |
|
151 |
oldPos = new double[nAtoms*3]; |
152 |
} |
153 |
|
154 |
delete[] temp_con; |
155 |
} |
156 |
|
157 |
|
158 |
void Integrator::integrate( void ){ |
159 |
|
160 |
int i, j; // loop counters |
161 |
|
162 |
double runTime = info->run_time; |
163 |
double sampleTime = info->sampleTime; |
164 |
double statusTime = info->statusTime; |
165 |
double thermalTime = info->thermalTime; |
166 |
|
167 |
double currSample; |
168 |
double currThermal; |
169 |
double currStatus; |
170 |
double currTime; |
171 |
|
172 |
int calcPot, calcStress; |
173 |
int isError; |
174 |
|
175 |
|
176 |
|
177 |
tStats = new Thermo( info ); |
178 |
statOut = new StatWriter( info ); |
179 |
dumpOut = new DumpWriter( info ); |
180 |
|
181 |
atoms = info->atoms; |
182 |
DirectionalAtom* dAtom; |
183 |
|
184 |
dt = info->dt; |
185 |
dt2 = 0.5 * dt; |
186 |
|
187 |
// initialize the forces before the first step |
188 |
|
189 |
myFF->doForces(1,1); |
190 |
|
191 |
if( info->setTemp ){ |
192 |
|
193 |
tStats->velocitize(); |
194 |
} |
195 |
|
196 |
dumpOut->writeDump( 0.0 ); |
197 |
statOut->writeStat( 0.0 ); |
198 |
|
199 |
calcPot = 0; |
200 |
calcStress = 0; |
201 |
currSample = sampleTime; |
202 |
currThermal = thermalTime; |
203 |
currStatus = statusTime; |
204 |
currTime = 0.0;; |
205 |
|
206 |
|
207 |
readyCheck(); |
208 |
|
209 |
#ifdef IS_MPI |
210 |
strcpy( checkPointMsg, |
211 |
"The integrator is ready to go." ); |
212 |
MPIcheckPoint(); |
213 |
#endif // is_mpi |
214 |
|
215 |
|
216 |
pos = Atom::getPosArray(); |
217 |
vel = Atom::getVelArray(); |
218 |
frc = Atom::getFrcArray(); |
219 |
trq = Atom::getTrqArray(); |
220 |
Amat = Atom::getAmatArray(); |
221 |
|
222 |
while( currTime < runTime ){ |
223 |
|
224 |
if( (currTime+dt) >= currStatus ){ |
225 |
calcPot = 1; |
226 |
calcStress = 1; |
227 |
} |
228 |
|
229 |
integrateStep( calcPot, calcStress ); |
230 |
|
231 |
currTime += dt; |
232 |
|
233 |
if( info->setTemp ){ |
234 |
if( currTime >= currThermal ){ |
235 |
tStats->velocitize(); |
236 |
currThermal += thermalTime; |
237 |
} |
238 |
} |
239 |
|
240 |
if( currTime >= currSample ){ |
241 |
dumpOut->writeDump( currTime ); |
242 |
currSample += sampleTime; |
243 |
} |
244 |
|
245 |
if( currTime >= currStatus ){ |
246 |
statOut->writeStat( currTime ); |
247 |
calcPot = 0; |
248 |
calcStress = 0; |
249 |
currStatus += statusTime; |
250 |
} |
251 |
|
252 |
#ifdef IS_MPI |
253 |
strcpy( checkPointMsg, |
254 |
"successfully took a time step." ); |
255 |
MPIcheckPoint(); |
256 |
#endif // is_mpi |
257 |
|
258 |
} |
259 |
|
260 |
dumpOut->writeFinal(currTime); |
261 |
|
262 |
delete dumpOut; |
263 |
delete statOut; |
264 |
} |
265 |
|
266 |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
267 |
|
268 |
|
269 |
|
270 |
// Position full step, and velocity half step |
271 |
|
272 |
preMove(); |
273 |
moveA(); |
274 |
if( nConstrained ) constrainA(); |
275 |
|
276 |
// calc forces |
277 |
|
278 |
myFF->doForces(calcPot,calcStress); |
279 |
|
280 |
// finish the velocity half step |
281 |
|
282 |
moveB(); |
283 |
if( nConstrained ) constrainB(); |
284 |
|
285 |
} |
286 |
|
287 |
|
288 |
void Integrator::moveA( void ){ |
289 |
|
290 |
int i,j,k; |
291 |
int atomIndex, aMatIndex; |
292 |
DirectionalAtom* dAtom; |
293 |
double Tb[3]; |
294 |
double ji[3]; |
295 |
double angle; |
296 |
|
297 |
|
298 |
|
299 |
for( i=0; i<nAtoms; i++ ){ |
300 |
atomIndex = i * 3; |
301 |
aMatIndex = i * 9; |
302 |
|
303 |
// velocity half step |
304 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
305 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
306 |
|
307 |
// position whole step |
308 |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
309 |
|
310 |
if( atoms[i]->isDirectional() ){ |
311 |
|
312 |
dAtom = (DirectionalAtom *)atoms[i]; |
313 |
|
314 |
// get and convert the torque to body frame |
315 |
|
316 |
Tb[0] = dAtom->getTx(); |
317 |
Tb[1] = dAtom->getTy(); |
318 |
Tb[2] = dAtom->getTz(); |
319 |
|
320 |
dAtom->lab2Body( Tb ); |
321 |
|
322 |
// get the angular momentum, and propagate a half step |
323 |
|
324 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
325 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
326 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
327 |
|
328 |
// use the angular velocities to propagate the rotation matrix a |
329 |
// full time step |
330 |
|
331 |
// rotate about the x-axis |
332 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
333 |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
334 |
|
335 |
// rotate about the y-axis |
336 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
337 |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
338 |
|
339 |
// rotate about the z-axis |
340 |
angle = dt * ji[2] / dAtom->getIzz(); |
341 |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
342 |
|
343 |
// rotate about the y-axis |
344 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
345 |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
346 |
|
347 |
// rotate about the x-axis |
348 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
349 |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
350 |
|
351 |
dAtom->setJx( ji[0] ); |
352 |
dAtom->setJy( ji[1] ); |
353 |
dAtom->setJz( ji[2] ); |
354 |
} |
355 |
|
356 |
} |
357 |
} |
358 |
|
359 |
|
360 |
void Integrator::moveB( void ){ |
361 |
int i,j,k; |
362 |
int atomIndex; |
363 |
DirectionalAtom* dAtom; |
364 |
double Tb[3]; |
365 |
double ji[3]; |
366 |
|
367 |
for( i=0; i<nAtoms; i++ ){ |
368 |
atomIndex = i * 3; |
369 |
|
370 |
// velocity half step |
371 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
372 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
373 |
|
374 |
if( atoms[i]->isDirectional() ){ |
375 |
|
376 |
dAtom = (DirectionalAtom *)atoms[i]; |
377 |
|
378 |
// get and convert the torque to body frame |
379 |
|
380 |
Tb[0] = dAtom->getTx(); |
381 |
Tb[1] = dAtom->getTy(); |
382 |
Tb[2] = dAtom->getTz(); |
383 |
|
384 |
dAtom->lab2Body( Tb ); |
385 |
|
386 |
// get the angular momentum, and complete the angular momentum |
387 |
// half step |
388 |
|
389 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
390 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
391 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
392 |
|
393 |
dAtom->setJx( ji[0] ); |
394 |
dAtom->setJy( ji[1] ); |
395 |
dAtom->setJz( ji[2] ); |
396 |
} |
397 |
} |
398 |
|
399 |
} |
400 |
|
401 |
void Integrator::preMove( void ){ |
402 |
int i; |
403 |
|
404 |
if( nConstrained ){ |
405 |
|
406 |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
407 |
} |
408 |
} |
409 |
|
410 |
void Integrator::constrainA(){ |
411 |
|
412 |
int i,j,k; |
413 |
int done; |
414 |
double pab[3]; |
415 |
double rab[3]; |
416 |
int a, b, ax, ay, az, bx, by, bz; |
417 |
double rma, rmb; |
418 |
double dx, dy, dz; |
419 |
double rpab; |
420 |
double rabsq, pabsq, rpabsq; |
421 |
double diffsq; |
422 |
double gab; |
423 |
int iteration; |
424 |
|
425 |
|
426 |
|
427 |
for( i=0; i<nAtoms; i++){ |
428 |
|
429 |
moving[i] = 0; |
430 |
moved[i] = 1; |
431 |
} |
432 |
|
433 |
iteration = 0; |
434 |
done = 0; |
435 |
while( !done && (iteration < maxIteration )){ |
436 |
|
437 |
done = 1; |
438 |
for(i=0; i<nConstrained; i++){ |
439 |
|
440 |
a = constrainedA[i]; |
441 |
b = constrainedB[i]; |
442 |
|
443 |
ax = (a*3) + 0; |
444 |
ay = (a*3) + 1; |
445 |
az = (a*3) + 2; |
446 |
|
447 |
bx = (b*3) + 0; |
448 |
by = (b*3) + 1; |
449 |
bz = (b*3) + 2; |
450 |
|
451 |
if( moved[a] || moved[b] ){ |
452 |
|
453 |
pab[0] = pos[ax] - pos[bx]; |
454 |
pab[1] = pos[ay] - pos[by]; |
455 |
pab[2] = pos[az] - pos[bz]; |
456 |
|
457 |
//periodic boundary condition |
458 |
|
459 |
info->wrapVector( pab ); |
460 |
|
461 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
462 |
|
463 |
rabsq = constrainedDsqr[i]; |
464 |
diffsq = rabsq - pabsq; |
465 |
|
466 |
// the original rattle code from alan tidesley |
467 |
if (fabs(diffsq) > (tol*rabsq*2)) { |
468 |
rab[0] = oldPos[ax] - oldPos[bx]; |
469 |
rab[1] = oldPos[ay] - oldPos[by]; |
470 |
rab[2] = oldPos[az] - oldPos[bz]; |
471 |
|
472 |
info->wrapVector( rab ); |
473 |
|
474 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
475 |
|
476 |
rpabsq = rpab * rpab; |
477 |
|
478 |
|
479 |
if (rpabsq < (rabsq * -diffsq)){ |
480 |
|
481 |
#ifdef IS_MPI |
482 |
a = atoms[a]->getGlobalIndex(); |
483 |
b = atoms[b]->getGlobalIndex(); |
484 |
#endif //is_mpi |
485 |
sprintf( painCave.errMsg, |
486 |
"Constraint failure in constrainA at atom %d and %d.\n", |
487 |
a, b ); |
488 |
painCave.isFatal = 1; |
489 |
simError(); |
490 |
} |
491 |
|
492 |
rma = 1.0 / atoms[a]->getMass(); |
493 |
rmb = 1.0 / atoms[b]->getMass(); |
494 |
|
495 |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
496 |
|
497 |
dx = rab[0] * gab; |
498 |
dy = rab[1] * gab; |
499 |
dz = rab[2] * gab; |
500 |
|
501 |
pos[ax] += rma * dx; |
502 |
pos[ay] += rma * dy; |
503 |
pos[az] += rma * dz; |
504 |
|
505 |
pos[bx] -= rmb * dx; |
506 |
pos[by] -= rmb * dy; |
507 |
pos[bz] -= rmb * dz; |
508 |
|
509 |
dx = dx / dt; |
510 |
dy = dy / dt; |
511 |
dz = dz / dt; |
512 |
|
513 |
vel[ax] += rma * dx; |
514 |
vel[ay] += rma * dy; |
515 |
vel[az] += rma * dz; |
516 |
|
517 |
vel[bx] -= rmb * dx; |
518 |
vel[by] -= rmb * dy; |
519 |
vel[bz] -= rmb * dz; |
520 |
|
521 |
moving[a] = 1; |
522 |
moving[b] = 1; |
523 |
done = 0; |
524 |
} |
525 |
} |
526 |
} |
527 |
|
528 |
for(i=0; i<nAtoms; i++){ |
529 |
|
530 |
moved[i] = moving[i]; |
531 |
moving[i] = 0; |
532 |
} |
533 |
|
534 |
iteration++; |
535 |
} |
536 |
|
537 |
if( !done ){ |
538 |
|
539 |
sprintf( painCave.errMsg, |
540 |
"Constraint failure in constrainA, too many iterations: %d\n", |
541 |
iteration ); |
542 |
painCave.isFatal = 1; |
543 |
simError(); |
544 |
} |
545 |
|
546 |
} |
547 |
|
548 |
void Integrator::constrainB( void ){ |
549 |
|
550 |
int i,j,k; |
551 |
int done; |
552 |
double vxab, vyab, vzab; |
553 |
double rab[3]; |
554 |
int a, b, ax, ay, az, bx, by, bz; |
555 |
double rma, rmb; |
556 |
double dx, dy, dz; |
557 |
double rabsq, pabsq, rvab; |
558 |
double diffsq; |
559 |
double gab; |
560 |
int iteration; |
561 |
|
562 |
for(i=0; i<nAtoms; i++){ |
563 |
moving[i] = 0; |
564 |
moved[i] = 1; |
565 |
} |
566 |
|
567 |
done = 0; |
568 |
iteration = 0; |
569 |
while( !done && (iteration < maxIteration ) ){ |
570 |
|
571 |
done = 1; |
572 |
|
573 |
for(i=0; i<nConstrained; i++){ |
574 |
|
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 |
|
588 |
vxab = vel[ax] - vel[bx]; |
589 |
vyab = vel[ay] - vel[by]; |
590 |
vzab = vel[az] - vel[bz]; |
591 |
|
592 |
rab[0] = pos[ax] - pos[bx]; |
593 |
rab[1] = pos[ay] - pos[by]; |
594 |
rab[2] = pos[az] - pos[bz]; |
595 |
|
596 |
info->wrapVector( rab ); |
597 |
|
598 |
rma = 1.0 / atoms[a]->getMass(); |
599 |
rmb = 1.0 / atoms[b]->getMass(); |
600 |
|
601 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
602 |
|
603 |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
604 |
|
605 |
if (fabs(gab) > tol) { |
606 |
|
607 |
dx = rab[0] * gab; |
608 |
dy = rab[1] * gab; |
609 |
dz = rab[2] * gab; |
610 |
|
611 |
vel[ax] += rma * dx; |
612 |
vel[ay] += rma * dy; |
613 |
vel[az] += rma * dz; |
614 |
|
615 |
vel[bx] -= rmb * dx; |
616 |
vel[by] -= rmb * dy; |
617 |
vel[bz] -= rmb * dz; |
618 |
|
619 |
moving[a] = 1; |
620 |
moving[b] = 1; |
621 |
done = 0; |
622 |
} |
623 |
} |
624 |
} |
625 |
|
626 |
for(i=0; i<nAtoms; i++){ |
627 |
moved[i] = moving[i]; |
628 |
moving[i] = 0; |
629 |
} |
630 |
|
631 |
iteration++; |
632 |
} |
633 |
|
634 |
if( !done ){ |
635 |
|
636 |
|
637 |
sprintf( painCave.errMsg, |
638 |
"Constraint failure in constrainB, too many iterations: %d\n", |
639 |
iteration ); |
640 |
painCave.isFatal = 1; |
641 |
simError(); |
642 |
} |
643 |
|
644 |
} |
645 |
|
646 |
|
647 |
|
648 |
|
649 |
|
650 |
|
651 |
|
652 |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
653 |
double A[9] ){ |
654 |
|
655 |
int i,j,k; |
656 |
double sinAngle; |
657 |
double cosAngle; |
658 |
double angleSqr; |
659 |
double angleSqrOver4; |
660 |
double top, bottom; |
661 |
double rot[3][3]; |
662 |
double tempA[3][3]; |
663 |
double tempJ[3]; |
664 |
|
665 |
// initialize the tempA |
666 |
|
667 |
for(i=0; i<3; i++){ |
668 |
for(j=0; j<3; j++){ |
669 |
tempA[j][i] = A[3*i + j]; |
670 |
} |
671 |
} |
672 |
|
673 |
// initialize the tempJ |
674 |
|
675 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
676 |
|
677 |
// initalize rot as a unit matrix |
678 |
|
679 |
rot[0][0] = 1.0; |
680 |
rot[0][1] = 0.0; |
681 |
rot[0][2] = 0.0; |
682 |
|
683 |
rot[1][0] = 0.0; |
684 |
rot[1][1] = 1.0; |
685 |
rot[1][2] = 0.0; |
686 |
|
687 |
rot[2][0] = 0.0; |
688 |
rot[2][1] = 0.0; |
689 |
rot[2][2] = 1.0; |
690 |
|
691 |
// use a small angle aproximation for sin and cosine |
692 |
|
693 |
angleSqr = angle * angle; |
694 |
angleSqrOver4 = angleSqr / 4.0; |
695 |
top = 1.0 - angleSqrOver4; |
696 |
bottom = 1.0 + angleSqrOver4; |
697 |
|
698 |
cosAngle = top / bottom; |
699 |
sinAngle = angle / bottom; |
700 |
|
701 |
rot[axes1][axes1] = cosAngle; |
702 |
rot[axes2][axes2] = cosAngle; |
703 |
|
704 |
rot[axes1][axes2] = sinAngle; |
705 |
rot[axes2][axes1] = -sinAngle; |
706 |
|
707 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
708 |
|
709 |
for(i=0; i<3; i++){ |
710 |
ji[i] = 0.0; |
711 |
for(k=0; k<3; k++){ |
712 |
ji[i] += rot[i][k] * tempJ[k]; |
713 |
} |
714 |
} |
715 |
|
716 |
// rotate the Rotation matrix acording to: |
717 |
// A[][] = A[][] * transpose(rot[][]) |
718 |
|
719 |
|
720 |
// NOte for as yet unknown reason, we are performing the |
721 |
// calculation as: |
722 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
723 |
|
724 |
for(i=0; i<3; i++){ |
725 |
for(j=0; j<3; j++){ |
726 |
A[3*j + i] = 0.0; |
727 |
for(k=0; k<3; k++){ |
728 |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
729 |
} |
730 |
} |
731 |
} |
732 |
} |