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