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