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 |
std::cerr << "integ nAtoms = " << nAtoms << "\n"; |
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 |
Integrator::~Integrator() { |
47 |
|
48 |
if( nConstrained ){ |
49 |
delete[] constrainedA; |
50 |
delete[] constrainedB; |
51 |
delete[] constrainedDsqr; |
52 |
delete[] moving; |
53 |
delete[] moved; |
54 |
delete[] oldPos; |
55 |
} |
56 |
|
57 |
} |
58 |
|
59 |
void Integrator::checkConstraints( void ){ |
60 |
|
61 |
|
62 |
isConstrained = 0; |
63 |
|
64 |
Constraint *temp_con; |
65 |
Constraint *dummy_plug; |
66 |
temp_con = new Constraint[info->n_SRI]; |
67 |
nConstrained = 0; |
68 |
int constrained = 0; |
69 |
|
70 |
SRI** theArray; |
71 |
for(int i = 0; i < nMols; i++){ |
72 |
|
73 |
theArray = (SRI**) molecules[i].getMyBonds(); |
74 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
75 |
|
76 |
constrained = theArray[j]->is_constrained(); |
77 |
|
78 |
std::cerr << "Is the folowing bond constrained \n"; |
79 |
theArray[j]->printMe(); |
80 |
|
81 |
if(constrained){ |
82 |
|
83 |
std::cerr << "Yes\n"; |
84 |
|
85 |
dummy_plug = theArray[j]->get_constraint(); |
86 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
87 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
88 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
89 |
|
90 |
nConstrained++; |
91 |
constrained = 0; |
92 |
} |
93 |
else std::cerr << "No.\n"; |
94 |
} |
95 |
|
96 |
theArray = (SRI**) molecules[i].getMyBends(); |
97 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
98 |
|
99 |
constrained = theArray[j]->is_constrained(); |
100 |
|
101 |
if(constrained){ |
102 |
|
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 |
theArray = (SRI**) molecules[i].getMyTorsions(); |
114 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
115 |
|
116 |
constrained = theArray[j]->is_constrained(); |
117 |
|
118 |
if(constrained){ |
119 |
|
120 |
dummy_plug = theArray[j]->get_constraint(); |
121 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
122 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
123 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
124 |
|
125 |
nConstrained++; |
126 |
constrained = 0; |
127 |
} |
128 |
} |
129 |
} |
130 |
|
131 |
if(nConstrained > 0){ |
132 |
|
133 |
isConstrained = 1; |
134 |
|
135 |
if(constrainedA != NULL ) delete[] constrainedA; |
136 |
if(constrainedB != NULL ) delete[] constrainedB; |
137 |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
138 |
|
139 |
constrainedA = new int[nConstrained]; |
140 |
constrainedB = new int[nConstrained]; |
141 |
constrainedDsqr = new double[nConstrained]; |
142 |
|
143 |
for( int i = 0; i < nConstrained; i++){ |
144 |
|
145 |
constrainedA[i] = temp_con[i].get_a(); |
146 |
constrainedB[i] = temp_con[i].get_b(); |
147 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
148 |
|
149 |
} |
150 |
|
151 |
|
152 |
// save oldAtoms to check for lode balanceing later on. |
153 |
|
154 |
oldAtoms = nAtoms; |
155 |
|
156 |
moving = new int[nAtoms]; |
157 |
moved = new int[nAtoms]; |
158 |
|
159 |
oldPos = new double[nAtoms*3]; |
160 |
} |
161 |
|
162 |
delete[] temp_con; |
163 |
} |
164 |
|
165 |
|
166 |
void Integrator::integrate( void ){ |
167 |
|
168 |
int i, j; // loop counters |
169 |
|
170 |
double runTime = info->run_time; |
171 |
double sampleTime = info->sampleTime; |
172 |
double statusTime = info->statusTime; |
173 |
double thermalTime = info->thermalTime; |
174 |
|
175 |
double currSample; |
176 |
double currThermal; |
177 |
double currStatus; |
178 |
double currTime; |
179 |
|
180 |
int calcPot, calcStress; |
181 |
int isError; |
182 |
|
183 |
|
184 |
|
185 |
tStats = new Thermo( info ); |
186 |
statOut = new StatWriter( info ); |
187 |
dumpOut = new DumpWriter( info ); |
188 |
|
189 |
atoms = info->atoms; |
190 |
DirectionalAtom* dAtom; |
191 |
|
192 |
dt = info->dt; |
193 |
dt2 = 0.5 * dt; |
194 |
|
195 |
// initialize the forces before the first step |
196 |
|
197 |
myFF->doForces(1,1); |
198 |
|
199 |
if( info->setTemp ){ |
200 |
|
201 |
tStats->velocitize(); |
202 |
} |
203 |
|
204 |
dumpOut->writeDump( 0.0 ); |
205 |
statOut->writeStat( 0.0 ); |
206 |
|
207 |
calcPot = 0; |
208 |
calcStress = 0; |
209 |
currSample = sampleTime; |
210 |
currThermal = thermalTime; |
211 |
currStatus = statusTime; |
212 |
currTime = 0.0;; |
213 |
|
214 |
|
215 |
readyCheck(); |
216 |
|
217 |
#ifdef IS_MPI |
218 |
strcpy( checkPointMsg, |
219 |
"The integrator is ready to go." ); |
220 |
MPIcheckPoint(); |
221 |
#endif // is_mpi |
222 |
|
223 |
|
224 |
pos = Atom::getPosArray(); |
225 |
vel = Atom::getVelArray(); |
226 |
frc = Atom::getFrcArray(); |
227 |
|
228 |
while( currTime < runTime ){ |
229 |
|
230 |
if( (currTime+dt) >= currStatus ){ |
231 |
calcPot = 1; |
232 |
calcStress = 1; |
233 |
} |
234 |
|
235 |
std::cerr << currTime << "\n"; |
236 |
|
237 |
integrateStep( calcPot, calcStress ); |
238 |
|
239 |
currTime += dt; |
240 |
|
241 |
if( info->setTemp ){ |
242 |
if( currTime >= currThermal ){ |
243 |
tStats->velocitize(); |
244 |
currThermal += thermalTime; |
245 |
} |
246 |
} |
247 |
|
248 |
if( currTime >= currSample ){ |
249 |
dumpOut->writeDump( currTime ); |
250 |
currSample += sampleTime; |
251 |
} |
252 |
|
253 |
if( currTime >= currStatus ){ |
254 |
statOut->writeStat( currTime ); |
255 |
calcPot = 0; |
256 |
calcStress = 0; |
257 |
currStatus += statusTime; |
258 |
} |
259 |
|
260 |
#ifdef IS_MPI |
261 |
strcpy( checkPointMsg, |
262 |
"successfully took a time step." ); |
263 |
MPIcheckPoint(); |
264 |
#endif // is_mpi |
265 |
|
266 |
} |
267 |
|
268 |
dumpOut->writeFinal(currTime); |
269 |
|
270 |
delete dumpOut; |
271 |
delete statOut; |
272 |
} |
273 |
|
274 |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
275 |
|
276 |
|
277 |
|
278 |
// Position full step, and velocity half step |
279 |
|
280 |
preMove(); |
281 |
moveA(); |
282 |
//if( nConstrained ) constrainA(); |
283 |
|
284 |
// calc forces |
285 |
|
286 |
myFF->doForces(calcPot,calcStress); |
287 |
|
288 |
// finish the velocity half step |
289 |
|
290 |
moveB(); |
291 |
if( nConstrained ) constrainB(); |
292 |
|
293 |
} |
294 |
|
295 |
|
296 |
void Integrator::moveA( void ){ |
297 |
|
298 |
int i,j,k; |
299 |
int atomIndex, aMatIndex; |
300 |
DirectionalAtom* dAtom; |
301 |
double Tb[3]; |
302 |
double ji[3]; |
303 |
double angle; |
304 |
double A[3][3], At[3][3]; |
305 |
|
306 |
|
307 |
for( i=0; i<nAtoms; i++ ){ |
308 |
atomIndex = i * 3; |
309 |
aMatIndex = i * 9; |
310 |
|
311 |
// velocity half step |
312 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
313 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
314 |
|
315 |
|
316 |
// position whole step |
317 |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
318 |
|
319 |
|
320 |
if( atoms[i]->isDirectional() ){ |
321 |
|
322 |
dAtom = (DirectionalAtom *)atoms[i]; |
323 |
|
324 |
// get and convert the torque to body frame |
325 |
|
326 |
Tb[0] = dAtom->getTx(); |
327 |
Tb[1] = dAtom->getTy(); |
328 |
Tb[2] = dAtom->getTz(); |
329 |
|
330 |
dAtom->lab2Body( Tb ); |
331 |
|
332 |
// get the angular momentum, and propagate a half step |
333 |
|
334 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
335 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
336 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
337 |
|
338 |
// use the angular velocities to propagate the rotation matrix a |
339 |
// full time step |
340 |
|
341 |
// rotate about the x-axis |
342 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
343 |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
344 |
|
345 |
// rotate about the y-axis |
346 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
347 |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
348 |
|
349 |
// rotate about the z-axis |
350 |
angle = dt * ji[2] / dAtom->getIzz(); |
351 |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
352 |
|
353 |
// rotate about the y-axis |
354 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
355 |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
356 |
|
357 |
// rotate about the x-axis |
358 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
359 |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
360 |
|
361 |
dAtom->setJx( ji[0] ); |
362 |
dAtom->setJy( ji[1] ); |
363 |
dAtom->setJz( ji[2] ); |
364 |
|
365 |
std::cerr << "Amat[" << i << "]\n"; |
366 |
info->printMat9( &Amat[aMatIndex] ); |
367 |
|
368 |
std::cerr << "ji[" << i << "]\t" |
369 |
<< ji[0] << "\t" |
370 |
<< ji[1] << "\t" |
371 |
<< ji[2] << "\n"; |
372 |
|
373 |
} |
374 |
|
375 |
} |
376 |
} |
377 |
|
378 |
|
379 |
void Integrator::moveB( void ){ |
380 |
int i,j,k; |
381 |
int atomIndex, aMatIndex; |
382 |
DirectionalAtom* dAtom; |
383 |
double Tb[3]; |
384 |
double ji[3]; |
385 |
|
386 |
for( i=0; i<nAtoms; i++ ){ |
387 |
atomIndex = i * 3; |
388 |
aMatIndex = i * 9; |
389 |
|
390 |
// velocity half step |
391 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
392 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
393 |
|
394 |
|
395 |
if( atoms[i]->isDirectional() ){ |
396 |
|
397 |
dAtom = (DirectionalAtom *)atoms[i]; |
398 |
|
399 |
// get and convert the torque to body frame |
400 |
|
401 |
Tb[0] = dAtom->getTx(); |
402 |
Tb[1] = dAtom->getTy(); |
403 |
Tb[2] = dAtom->getTz(); |
404 |
|
405 |
std::cerr << "TrqB[" << i << "]\t" |
406 |
<< Tb[0] << "\t" |
407 |
<< Tb[1] << "\t" |
408 |
<< Tb[2] << "\n"; |
409 |
|
410 |
dAtom->lab2Body( Tb ); |
411 |
|
412 |
// get the angular momentum, and complete the angular momentum |
413 |
// half step |
414 |
|
415 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
416 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
417 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
418 |
|
419 |
dAtom->setJx( ji[0] ); |
420 |
dAtom->setJy( ji[1] ); |
421 |
dAtom->setJz( ji[2] ); |
422 |
|
423 |
|
424 |
std::cerr << "Amat[" << i << "]\n"; |
425 |
info->printMat9( &Amat[aMatIndex] ); |
426 |
|
427 |
std::cerr << "ji[" << i << "]\t" |
428 |
<< ji[0] << "\t" |
429 |
<< ji[1] << "\t" |
430 |
<< ji[2] << "\n"; |
431 |
} |
432 |
} |
433 |
|
434 |
} |
435 |
|
436 |
void Integrator::preMove( void ){ |
437 |
int i; |
438 |
|
439 |
if( nConstrained ){ |
440 |
|
441 |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
442 |
} |
443 |
} |
444 |
|
445 |
void Integrator::constrainA(){ |
446 |
|
447 |
int i,j,k; |
448 |
int done; |
449 |
double pab[3]; |
450 |
double rab[3]; |
451 |
int a, b, ax, ay, az, bx, by, bz; |
452 |
double rma, rmb; |
453 |
double dx, dy, dz; |
454 |
double rpab; |
455 |
double rabsq, pabsq, rpabsq; |
456 |
double diffsq; |
457 |
double gab; |
458 |
int iteration; |
459 |
|
460 |
for( i=0; i<nAtoms; i++){ |
461 |
|
462 |
moving[i] = 0; |
463 |
moved[i] = 1; |
464 |
} |
465 |
|
466 |
iteration = 0; |
467 |
done = 0; |
468 |
while( !done && (iteration < maxIteration )){ |
469 |
|
470 |
done = 1; |
471 |
for(i=0; i<nConstrained; i++){ |
472 |
|
473 |
a = constrainedA[i]; |
474 |
b = constrainedB[i]; |
475 |
|
476 |
ax = (a*3) + 0; |
477 |
ay = (a*3) + 1; |
478 |
az = (a*3) + 2; |
479 |
|
480 |
bx = (b*3) + 0; |
481 |
by = (b*3) + 1; |
482 |
bz = (b*3) + 2; |
483 |
|
484 |
if( moved[a] || moved[b] ){ |
485 |
|
486 |
pab[0] = pos[ax] - pos[bx]; |
487 |
pab[1] = pos[ay] - pos[by]; |
488 |
pab[2] = pos[az] - pos[bz]; |
489 |
|
490 |
//periodic boundary condition |
491 |
|
492 |
info->wrapVector( pab ); |
493 |
|
494 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
495 |
|
496 |
rabsq = constrainedDsqr[i]; |
497 |
diffsq = rabsq - pabsq; |
498 |
|
499 |
// the original rattle code from alan tidesley |
500 |
if (fabs(diffsq) > (tol*rabsq*2)) { |
501 |
rab[0] = oldPos[ax] - oldPos[bx]; |
502 |
rab[1] = oldPos[ay] - oldPos[by]; |
503 |
rab[2] = oldPos[az] - oldPos[bz]; |
504 |
|
505 |
info->wrapVector( rab ); |
506 |
|
507 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
508 |
|
509 |
rpabsq = rpab * rpab; |
510 |
|
511 |
|
512 |
if (rpabsq < (rabsq * -diffsq)){ |
513 |
|
514 |
#ifdef IS_MPI |
515 |
a = atoms[a]->getGlobalIndex(); |
516 |
b = atoms[b]->getGlobalIndex(); |
517 |
#endif //is_mpi |
518 |
sprintf( painCave.errMsg, |
519 |
"Constraint failure in constrainA at atom %d and %d.\n", |
520 |
a, b ); |
521 |
painCave.isFatal = 1; |
522 |
simError(); |
523 |
} |
524 |
|
525 |
rma = 1.0 / atoms[a]->getMass(); |
526 |
rmb = 1.0 / atoms[b]->getMass(); |
527 |
|
528 |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
529 |
|
530 |
dx = rab[0] * gab; |
531 |
dy = rab[1] * gab; |
532 |
dz = rab[2] * gab; |
533 |
|
534 |
pos[ax] += rma * dx; |
535 |
pos[ay] += rma * dy; |
536 |
pos[az] += rma * dz; |
537 |
|
538 |
pos[bx] -= rmb * dx; |
539 |
pos[by] -= rmb * dy; |
540 |
pos[bz] -= rmb * dz; |
541 |
|
542 |
dx = dx / dt; |
543 |
dy = dy / dt; |
544 |
dz = dz / dt; |
545 |
|
546 |
vel[ax] += rma * dx; |
547 |
vel[ay] += rma * dy; |
548 |
vel[az] += rma * dz; |
549 |
|
550 |
vel[bx] -= rmb * dx; |
551 |
vel[by] -= rmb * dy; |
552 |
vel[bz] -= rmb * dz; |
553 |
|
554 |
moving[a] = 1; |
555 |
moving[b] = 1; |
556 |
done = 0; |
557 |
} |
558 |
} |
559 |
} |
560 |
|
561 |
for(i=0; i<nAtoms; i++){ |
562 |
|
563 |
moved[i] = moving[i]; |
564 |
moving[i] = 0; |
565 |
} |
566 |
|
567 |
iteration++; |
568 |
} |
569 |
|
570 |
if( !done ){ |
571 |
|
572 |
sprintf( painCave.errMsg, |
573 |
"Constraint failure in constrainA, too many iterations: %d\n", |
574 |
iteration ); |
575 |
painCave.isFatal = 1; |
576 |
simError(); |
577 |
} |
578 |
|
579 |
} |
580 |
|
581 |
void Integrator::constrainB( void ){ |
582 |
|
583 |
int i,j,k; |
584 |
int done; |
585 |
double vxab, vyab, vzab; |
586 |
double rab[3]; |
587 |
int a, b, ax, ay, az, bx, by, bz; |
588 |
double rma, rmb; |
589 |
double dx, dy, dz; |
590 |
double rabsq, pabsq, rvab; |
591 |
double diffsq; |
592 |
double gab; |
593 |
int iteration; |
594 |
|
595 |
for(i=0; i<nAtoms; i++){ |
596 |
moving[i] = 0; |
597 |
moved[i] = 1; |
598 |
} |
599 |
|
600 |
done = 0; |
601 |
iteration = 0; |
602 |
while( !done && (iteration < maxIteration ) ){ |
603 |
|
604 |
done = 1; |
605 |
|
606 |
for(i=0; i<nConstrained; i++){ |
607 |
|
608 |
a = constrainedA[i]; |
609 |
b = constrainedB[i]; |
610 |
|
611 |
ax = (a*3) + 0; |
612 |
ay = (a*3) + 1; |
613 |
az = (a*3) + 2; |
614 |
|
615 |
bx = (b*3) + 0; |
616 |
by = (b*3) + 1; |
617 |
bz = (b*3) + 2; |
618 |
|
619 |
if( moved[a] || moved[b] ){ |
620 |
|
621 |
vxab = vel[ax] - vel[bx]; |
622 |
vyab = vel[ay] - vel[by]; |
623 |
vzab = vel[az] - vel[bz]; |
624 |
|
625 |
rab[0] = pos[ax] - pos[bx]; |
626 |
rab[1] = pos[ay] - pos[by]; |
627 |
rab[2] = pos[az] - pos[bz]; |
628 |
|
629 |
info->wrapVector( rab ); |
630 |
|
631 |
rma = 1.0 / atoms[a]->getMass(); |
632 |
rmb = 1.0 / atoms[b]->getMass(); |
633 |
|
634 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
635 |
|
636 |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
637 |
|
638 |
if (fabs(gab) > tol) { |
639 |
|
640 |
dx = rab[0] * gab; |
641 |
dy = rab[1] * gab; |
642 |
dz = rab[2] * gab; |
643 |
|
644 |
vel[ax] += rma * dx; |
645 |
vel[ay] += rma * dy; |
646 |
vel[az] += rma * dz; |
647 |
|
648 |
vel[bx] -= rmb * dx; |
649 |
vel[by] -= rmb * dy; |
650 |
vel[bz] -= rmb * dz; |
651 |
|
652 |
moving[a] = 1; |
653 |
moving[b] = 1; |
654 |
done = 0; |
655 |
} |
656 |
} |
657 |
} |
658 |
|
659 |
for(i=0; i<nAtoms; i++){ |
660 |
moved[i] = moving[i]; |
661 |
moving[i] = 0; |
662 |
} |
663 |
|
664 |
iteration++; |
665 |
} |
666 |
|
667 |
if( !done ){ |
668 |
|
669 |
|
670 |
sprintf( painCave.errMsg, |
671 |
"Constraint failure in constrainB, too many iterations: %d\n", |
672 |
iteration ); |
673 |
painCave.isFatal = 1; |
674 |
simError(); |
675 |
} |
676 |
|
677 |
} |
678 |
|
679 |
|
680 |
|
681 |
|
682 |
|
683 |
|
684 |
|
685 |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
686 |
double A[9] ){ |
687 |
|
688 |
int i,j,k; |
689 |
double sinAngle; |
690 |
double cosAngle; |
691 |
double angleSqr; |
692 |
double angleSqrOver4; |
693 |
double top, bottom; |
694 |
double rot[3][3]; |
695 |
double tempA[3][3]; |
696 |
double tempJ[3]; |
697 |
|
698 |
|
699 |
// initialize the tempA |
700 |
|
701 |
for(i=0; i<3; i++){ |
702 |
for(j=0; j<3; j++){ |
703 |
tempA[j][i] = A[3*i+j]; |
704 |
} |
705 |
} |
706 |
|
707 |
// initialize the tempJ |
708 |
|
709 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
710 |
|
711 |
// initalize rot as a unit matrix |
712 |
|
713 |
rot[0][0] = 1.0; |
714 |
rot[0][1] = 0.0; |
715 |
rot[0][2] = 0.0; |
716 |
|
717 |
rot[1][0] = 0.0; |
718 |
rot[1][1] = 1.0; |
719 |
rot[1][2] = 0.0; |
720 |
|
721 |
rot[2][0] = 0.0; |
722 |
rot[2][1] = 0.0; |
723 |
rot[2][2] = 1.0; |
724 |
|
725 |
// use a small angle aproximation for sin and cosine |
726 |
|
727 |
angleSqr = angle * angle; |
728 |
angleSqrOver4 = angleSqr / 4.0; |
729 |
top = 1.0 - angleSqrOver4; |
730 |
bottom = 1.0 + angleSqrOver4; |
731 |
|
732 |
cosAngle = top / bottom; |
733 |
sinAngle = angle / bottom; |
734 |
|
735 |
rot[axes1][axes1] = cosAngle; |
736 |
rot[axes2][axes2] = cosAngle; |
737 |
|
738 |
rot[axes1][axes2] = sinAngle; |
739 |
rot[axes2][axes1] = -sinAngle; |
740 |
|
741 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
742 |
|
743 |
for(i=0; i<3; i++){ |
744 |
ji[i] = 0.0; |
745 |
for(k=0; k<3; k++){ |
746 |
ji[i] += rot[i][k] * tempJ[k]; |
747 |
} |
748 |
} |
749 |
|
750 |
// rotate the Rotation matrix acording to: |
751 |
// A[][] = A[][] * transpose(rot[][]) |
752 |
|
753 |
|
754 |
// NOte for as yet unknown reason, we are performing the |
755 |
// calculation as: |
756 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
757 |
|
758 |
for(i=0; i<3; i++){ |
759 |
for(j=0; j<3; j++){ |
760 |
A[3*j+i] = 0.0; |
761 |
for(k=0; k<3; k++){ |
762 |
A[3*j+i] += tempA[i][k] * rot[j][k]; |
763 |
} |
764 |
} |
765 |
} |
766 |
} |