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 |
trq = Atom::getTrqArray(); |
228 |
Amat = Atom::getAmatArray(); |
229 |
|
230 |
while( currTime < runTime ){ |
231 |
|
232 |
if( (currTime+dt) >= currStatus ){ |
233 |
calcPot = 1; |
234 |
calcStress = 1; |
235 |
} |
236 |
|
237 |
std::cerr << "calcPot = " << calcPot << "; calcStress = " |
238 |
<< calcStress << "\n"; |
239 |
|
240 |
integrateStep( calcPot, calcStress ); |
241 |
|
242 |
currTime += dt; |
243 |
|
244 |
if( info->setTemp ){ |
245 |
if( currTime >= currThermal ){ |
246 |
tStats->velocitize(); |
247 |
currThermal += thermalTime; |
248 |
} |
249 |
} |
250 |
|
251 |
if( currTime >= currSample ){ |
252 |
dumpOut->writeDump( currTime ); |
253 |
currSample += sampleTime; |
254 |
} |
255 |
|
256 |
if( currTime >= currStatus ){ |
257 |
statOut->writeStat( currTime ); |
258 |
calcPot = 0; |
259 |
calcStress = 0; |
260 |
currStatus += statusTime; |
261 |
} |
262 |
|
263 |
#ifdef IS_MPI |
264 |
strcpy( checkPointMsg, |
265 |
"successfully took a time step." ); |
266 |
MPIcheckPoint(); |
267 |
#endif // is_mpi |
268 |
|
269 |
} |
270 |
|
271 |
dumpOut->writeFinal(currTime); |
272 |
|
273 |
delete dumpOut; |
274 |
delete statOut; |
275 |
} |
276 |
|
277 |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
278 |
|
279 |
|
280 |
|
281 |
// Position full step, and velocity half step |
282 |
|
283 |
preMove(); |
284 |
moveA(); |
285 |
if( nConstrained ) constrainA(); |
286 |
|
287 |
// calc forces |
288 |
|
289 |
myFF->doForces(calcPot,calcStress); |
290 |
|
291 |
// finish the velocity half step |
292 |
|
293 |
moveB(); |
294 |
if( nConstrained ) constrainB(); |
295 |
|
296 |
} |
297 |
|
298 |
|
299 |
void Integrator::moveA( void ){ |
300 |
|
301 |
int i,j,k; |
302 |
int atomIndex, aMatIndex; |
303 |
DirectionalAtom* dAtom; |
304 |
double Tb[3]; |
305 |
double ji[3]; |
306 |
double angle; |
307 |
double A[3][3]; |
308 |
|
309 |
|
310 |
for( i=0; i<nAtoms; i++ ){ |
311 |
atomIndex = i * 3; |
312 |
aMatIndex = i * 9; |
313 |
|
314 |
// velocity half step |
315 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
316 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
317 |
|
318 |
std::cerr<< "MoveA vel[" << i << "] = " |
319 |
<< vel[atomIndex] << "\t" |
320 |
<< vel[atomIndex+1]<< "\t" |
321 |
<< vel[atomIndex+2]<< "\n"; |
322 |
|
323 |
// position whole step |
324 |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
325 |
|
326 |
|
327 |
std::cerr<< "MoveA pos[" << i << "] = " |
328 |
<< pos[atomIndex] << "\t" |
329 |
<< pos[atomIndex+1]<< "\t" |
330 |
<< pos[atomIndex+2]<< "\n"; |
331 |
|
332 |
if( atoms[i]->isDirectional() ){ |
333 |
|
334 |
dAtom = (DirectionalAtom *)atoms[i]; |
335 |
|
336 |
// get and convert the torque to body frame |
337 |
|
338 |
Tb[0] = dAtom->getTx(); |
339 |
Tb[1] = dAtom->getTy(); |
340 |
Tb[2] = dAtom->getTz(); |
341 |
|
342 |
dAtom->lab2Body( Tb ); |
343 |
|
344 |
// get the angular momentum, and propagate a half step |
345 |
|
346 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
347 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
348 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
349 |
|
350 |
// use the angular velocities to propagate the rotation matrix a |
351 |
// full time step |
352 |
|
353 |
// get the atom's rotation matrix |
354 |
|
355 |
A[0][0] = dAtom->getAxx(); |
356 |
A[0][1] = dAtom->getAxy(); |
357 |
A[0][2] = dAtom->getAxz(); |
358 |
|
359 |
A[1][0] = dAtom->getAyx(); |
360 |
A[1][1] = dAtom->getAyy(); |
361 |
A[1][2] = dAtom->getAyz(); |
362 |
|
363 |
A[2][0] = dAtom->getAzx(); |
364 |
A[2][1] = dAtom->getAzy(); |
365 |
A[2][2] = dAtom->getAzz(); |
366 |
|
367 |
// rotate about the x-axis |
368 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
369 |
this->rotate( 1, 2, angle, ji, A ); |
370 |
|
371 |
// rotate about the y-axis |
372 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
373 |
this->rotate( 2, 0, angle, ji, A ); |
374 |
|
375 |
// rotate about the z-axis |
376 |
angle = dt * ji[2] / dAtom->getIzz(); |
377 |
this->rotate( 0, 1, angle, ji, A ); |
378 |
|
379 |
// rotate about the y-axis |
380 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
381 |
this->rotate( 2, 0, angle, ji, A ); |
382 |
|
383 |
// rotate about the x-axis |
384 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
385 |
this->rotate( 1, 2, angle, ji, A ); |
386 |
|
387 |
dAtom->setJx( ji[0] ); |
388 |
dAtom->setJy( ji[1] ); |
389 |
dAtom->setJz( ji[2] ); |
390 |
} |
391 |
|
392 |
} |
393 |
} |
394 |
|
395 |
|
396 |
void Integrator::moveB( void ){ |
397 |
int i,j,k; |
398 |
int atomIndex; |
399 |
DirectionalAtom* dAtom; |
400 |
double Tb[3]; |
401 |
double ji[3]; |
402 |
|
403 |
for( i=0; i<nAtoms; i++ ){ |
404 |
atomIndex = i * 3; |
405 |
|
406 |
// velocity half step |
407 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
408 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
409 |
|
410 |
std::cerr<< "MoveB vel[" << i << "] = " |
411 |
<< vel[atomIndex] << "\t" |
412 |
<< vel[atomIndex+1]<< "\t" |
413 |
<< vel[atomIndex+2]<< "\n"; |
414 |
|
415 |
|
416 |
if( atoms[i]->isDirectional() ){ |
417 |
|
418 |
dAtom = (DirectionalAtom *)atoms[i]; |
419 |
|
420 |
// get and convert the torque to body frame |
421 |
|
422 |
Tb[0] = dAtom->getTx(); |
423 |
Tb[1] = dAtom->getTy(); |
424 |
Tb[2] = dAtom->getTz(); |
425 |
|
426 |
dAtom->lab2Body( Tb ); |
427 |
|
428 |
// get the angular momentum, and complete the angular momentum |
429 |
// half step |
430 |
|
431 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
432 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
433 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
434 |
|
435 |
dAtom->setJx( ji[0] ); |
436 |
dAtom->setJy( ji[1] ); |
437 |
dAtom->setJz( ji[2] ); |
438 |
} |
439 |
} |
440 |
|
441 |
} |
442 |
|
443 |
void Integrator::preMove( void ){ |
444 |
int i; |
445 |
|
446 |
if( nConstrained ){ |
447 |
|
448 |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
449 |
} |
450 |
} |
451 |
|
452 |
void Integrator::constrainA(){ |
453 |
|
454 |
int i,j,k; |
455 |
int done; |
456 |
double pab[3]; |
457 |
double rab[3]; |
458 |
int a, b, ax, ay, az, bx, by, bz; |
459 |
double rma, rmb; |
460 |
double dx, dy, dz; |
461 |
double rpab; |
462 |
double rabsq, pabsq, rpabsq; |
463 |
double diffsq; |
464 |
double gab; |
465 |
int iteration; |
466 |
|
467 |
for( i=0; i<nAtoms; i++){ |
468 |
|
469 |
moving[i] = 0; |
470 |
moved[i] = 1; |
471 |
} |
472 |
|
473 |
iteration = 0; |
474 |
done = 0; |
475 |
while( !done && (iteration < maxIteration )){ |
476 |
|
477 |
done = 1; |
478 |
for(i=0; i<nConstrained; i++){ |
479 |
|
480 |
a = constrainedA[i]; |
481 |
b = constrainedB[i]; |
482 |
|
483 |
ax = (a*3) + 0; |
484 |
ay = (a*3) + 1; |
485 |
az = (a*3) + 2; |
486 |
|
487 |
bx = (b*3) + 0; |
488 |
by = (b*3) + 1; |
489 |
bz = (b*3) + 2; |
490 |
|
491 |
if( moved[a] || moved[b] ){ |
492 |
|
493 |
pab[0] = pos[ax] - pos[bx]; |
494 |
pab[1] = pos[ay] - pos[by]; |
495 |
pab[2] = pos[az] - pos[bz]; |
496 |
|
497 |
//periodic boundary condition |
498 |
|
499 |
info->wrapVector( pab ); |
500 |
|
501 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
502 |
|
503 |
rabsq = constrainedDsqr[i]; |
504 |
diffsq = rabsq - pabsq; |
505 |
|
506 |
// the original rattle code from alan tidesley |
507 |
if (fabs(diffsq) > (tol*rabsq*2)) { |
508 |
rab[0] = oldPos[ax] - oldPos[bx]; |
509 |
rab[1] = oldPos[ay] - oldPos[by]; |
510 |
rab[2] = oldPos[az] - oldPos[bz]; |
511 |
|
512 |
info->wrapVector( rab ); |
513 |
|
514 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
515 |
|
516 |
rpabsq = rpab * rpab; |
517 |
|
518 |
|
519 |
if (rpabsq < (rabsq * -diffsq)){ |
520 |
|
521 |
#ifdef IS_MPI |
522 |
a = atoms[a]->getGlobalIndex(); |
523 |
b = atoms[b]->getGlobalIndex(); |
524 |
#endif //is_mpi |
525 |
sprintf( painCave.errMsg, |
526 |
"Constraint failure in constrainA at atom %d and %d.\n", |
527 |
a, b ); |
528 |
painCave.isFatal = 1; |
529 |
simError(); |
530 |
} |
531 |
|
532 |
rma = 1.0 / atoms[a]->getMass(); |
533 |
rmb = 1.0 / atoms[b]->getMass(); |
534 |
|
535 |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
536 |
|
537 |
dx = rab[0] * gab; |
538 |
dy = rab[1] * gab; |
539 |
dz = rab[2] * gab; |
540 |
|
541 |
pos[ax] += rma * dx; |
542 |
pos[ay] += rma * dy; |
543 |
pos[az] += rma * dz; |
544 |
|
545 |
pos[bx] -= rmb * dx; |
546 |
pos[by] -= rmb * dy; |
547 |
pos[bz] -= rmb * dz; |
548 |
|
549 |
dx = dx / dt; |
550 |
dy = dy / dt; |
551 |
dz = dz / dt; |
552 |
|
553 |
vel[ax] += rma * dx; |
554 |
vel[ay] += rma * dy; |
555 |
vel[az] += rma * dz; |
556 |
|
557 |
vel[bx] -= rmb * dx; |
558 |
vel[by] -= rmb * dy; |
559 |
vel[bz] -= rmb * dz; |
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 vxab, vyab, vzab; |
593 |
double rab[3]; |
594 |
int a, b, ax, ay, az, bx, by, bz; |
595 |
double rma, rmb; |
596 |
double dx, dy, dz; |
597 |
double rabsq, pabsq, rvab; |
598 |
double diffsq; |
599 |
double gab; |
600 |
int iteration; |
601 |
|
602 |
for(i=0; i<nAtoms; i++){ |
603 |
moving[i] = 0; |
604 |
moved[i] = 1; |
605 |
} |
606 |
|
607 |
done = 0; |
608 |
iteration = 0; |
609 |
while( !done && (iteration < maxIteration ) ){ |
610 |
|
611 |
done = 1; |
612 |
|
613 |
for(i=0; i<nConstrained; i++){ |
614 |
|
615 |
a = constrainedA[i]; |
616 |
b = constrainedB[i]; |
617 |
|
618 |
ax = (a*3) + 0; |
619 |
ay = (a*3) + 1; |
620 |
az = (a*3) + 2; |
621 |
|
622 |
bx = (b*3) + 0; |
623 |
by = (b*3) + 1; |
624 |
bz = (b*3) + 2; |
625 |
|
626 |
if( moved[a] || moved[b] ){ |
627 |
|
628 |
vxab = vel[ax] - vel[bx]; |
629 |
vyab = vel[ay] - vel[by]; |
630 |
vzab = vel[az] - vel[bz]; |
631 |
|
632 |
rab[0] = pos[ax] - pos[bx]; |
633 |
rab[1] = pos[ay] - pos[by]; |
634 |
rab[2] = pos[az] - pos[bz]; |
635 |
|
636 |
info->wrapVector( rab ); |
637 |
|
638 |
rma = 1.0 / atoms[a]->getMass(); |
639 |
rmb = 1.0 / atoms[b]->getMass(); |
640 |
|
641 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
642 |
|
643 |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
644 |
|
645 |
if (fabs(gab) > tol) { |
646 |
|
647 |
dx = rab[0] * gab; |
648 |
dy = rab[1] * gab; |
649 |
dz = rab[2] * gab; |
650 |
|
651 |
vel[ax] += rma * dx; |
652 |
vel[ay] += rma * dy; |
653 |
vel[az] += rma * dz; |
654 |
|
655 |
vel[bx] -= rmb * dx; |
656 |
vel[by] -= rmb * dy; |
657 |
vel[bz] -= rmb * dz; |
658 |
|
659 |
moving[a] = 1; |
660 |
moving[b] = 1; |
661 |
done = 0; |
662 |
} |
663 |
} |
664 |
} |
665 |
|
666 |
for(i=0; i<nAtoms; i++){ |
667 |
moved[i] = moving[i]; |
668 |
moving[i] = 0; |
669 |
} |
670 |
|
671 |
iteration++; |
672 |
} |
673 |
|
674 |
if( !done ){ |
675 |
|
676 |
|
677 |
sprintf( painCave.errMsg, |
678 |
"Constraint failure in constrainB, too many iterations: %d\n", |
679 |
iteration ); |
680 |
painCave.isFatal = 1; |
681 |
simError(); |
682 |
} |
683 |
|
684 |
} |
685 |
|
686 |
|
687 |
|
688 |
|
689 |
|
690 |
|
691 |
|
692 |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
693 |
double A[3][3] ){ |
694 |
|
695 |
int i,j,k; |
696 |
double sinAngle; |
697 |
double cosAngle; |
698 |
double angleSqr; |
699 |
double angleSqrOver4; |
700 |
double top, bottom; |
701 |
double rot[3][3]; |
702 |
double tempA[3][3]; |
703 |
double tempJ[3]; |
704 |
|
705 |
// initialize the tempA |
706 |
|
707 |
for(i=0; i<3; i++){ |
708 |
for(j=0; j<3; j++){ |
709 |
tempA[j][i] = A[i][j]; |
710 |
} |
711 |
} |
712 |
|
713 |
// initialize the tempJ |
714 |
|
715 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
716 |
|
717 |
// initalize rot as a unit matrix |
718 |
|
719 |
rot[0][0] = 1.0; |
720 |
rot[0][1] = 0.0; |
721 |
rot[0][2] = 0.0; |
722 |
|
723 |
rot[1][0] = 0.0; |
724 |
rot[1][1] = 1.0; |
725 |
rot[1][2] = 0.0; |
726 |
|
727 |
rot[2][0] = 0.0; |
728 |
rot[2][1] = 0.0; |
729 |
rot[2][2] = 1.0; |
730 |
|
731 |
// use a small angle aproximation for sin and cosine |
732 |
|
733 |
angleSqr = angle * angle; |
734 |
angleSqrOver4 = angleSqr / 4.0; |
735 |
top = 1.0 - angleSqrOver4; |
736 |
bottom = 1.0 + angleSqrOver4; |
737 |
|
738 |
cosAngle = top / bottom; |
739 |
sinAngle = angle / bottom; |
740 |
|
741 |
rot[axes1][axes1] = cosAngle; |
742 |
rot[axes2][axes2] = cosAngle; |
743 |
|
744 |
rot[axes1][axes2] = sinAngle; |
745 |
rot[axes2][axes1] = -sinAngle; |
746 |
|
747 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
748 |
|
749 |
for(i=0; i<3; i++){ |
750 |
ji[i] = 0.0; |
751 |
for(k=0; k<3; k++){ |
752 |
ji[i] += rot[i][k] * tempJ[k]; |
753 |
} |
754 |
} |
755 |
|
756 |
// rotate the Rotation matrix acording to: |
757 |
// A[][] = A[][] * transpose(rot[][]) |
758 |
|
759 |
|
760 |
// NOte for as yet unknown reason, we are performing the |
761 |
// calculation as: |
762 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
763 |
|
764 |
for(i=0; i<3; i++){ |
765 |
for(j=0; j<3; j++){ |
766 |
A[j][i] = 0.0; |
767 |
for(k=0; k<3; k++){ |
768 |
A[j][i] += tempA[i][k] * rot[j][k]; |
769 |
} |
770 |
} |
771 |
} |
772 |
} |