72 |
|
for(int j=0; j<molecules[i].getNBonds(); j++){ |
73 |
|
|
74 |
|
constrained = theArray[j]->is_constrained(); |
75 |
< |
|
75 |
> |
|
76 |
|
if(constrained){ |
77 |
< |
|
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() ); |
82 |
|
|
83 |
|
nConstrained++; |
84 |
|
constrained = 0; |
85 |
< |
} |
85 |
> |
} |
86 |
|
} |
87 |
|
|
88 |
|
theArray = (SRI**) molecules[i].getMyBends(); |
138 |
|
constrainedB[i] = temp_con[i].get_b(); |
139 |
|
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
140 |
|
|
141 |
– |
cerr << "constraint " << constrainedA[i] << " <-> " << constrainedB[i] |
142 |
– |
<< " => " << constrainedDsqr[i] << "\n"; |
141 |
|
} |
142 |
|
|
143 |
|
|
172 |
|
int calcPot, calcStress; |
173 |
|
int isError; |
174 |
|
|
177 |
– |
|
178 |
– |
|
175 |
|
tStats = new Thermo( info ); |
176 |
|
statOut = new StatWriter( info ); |
177 |
|
dumpOut = new DumpWriter( info ); |
209 |
|
"The integrator is ready to go." ); |
210 |
|
MPIcheckPoint(); |
211 |
|
#endif // is_mpi |
216 |
– |
|
217 |
– |
|
218 |
– |
pos = Atom::getPosArray(); |
219 |
– |
vel = Atom::getVelArray(); |
220 |
– |
frc = Atom::getFrcArray(); |
221 |
– |
trq = Atom::getTrqArray(); |
222 |
– |
Amat = Atom::getAmatArray(); |
212 |
|
|
213 |
|
while( currTime < runTime ){ |
214 |
|
|
248 |
|
|
249 |
|
} |
250 |
|
|
251 |
< |
dumpOut->writeFinal(); |
251 |
> |
dumpOut->writeFinal(currTime); |
252 |
|
|
253 |
|
delete dumpOut; |
254 |
|
delete statOut; |
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 |
< |
|
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,k; |
293 |
< |
int atomIndex, aMatIndex; |
300 |
> |
int i, j; |
301 |
|
DirectionalAtom* dAtom; |
302 |
< |
double Tb[3]; |
303 |
< |
double ji[3]; |
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++ ){ |
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; |
309 |
|
|
310 |
< |
// position whole step |
311 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
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 |
< |
|
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 |
< |
Tb[0] = dAtom->getTx(); |
319 |
< |
Tb[1] = dAtom->getTy(); |
320 |
< |
Tb[2] = dAtom->getTz(); |
321 |
< |
|
332 |
> |
dAtom->getTrq( Tb ); |
333 |
|
dAtom->lab2Body( Tb ); |
334 |
< |
|
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 |
|
|
326 |
– |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
327 |
– |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
328 |
– |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
329 |
– |
|
342 |
|
// use the angular velocities to propagate the rotation matrix a |
343 |
|
// full time step |
344 |
< |
|
344 |
> |
|
345 |
> |
dAtom->getA(A); |
346 |
> |
dAtom->getI(I); |
347 |
> |
|
348 |
|
// rotate about the x-axis |
349 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
350 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
351 |
< |
|
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] / dAtom->getIyy(); |
354 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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] / dAtom->getIzz(); |
358 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
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] / dAtom->getIyy(); |
362 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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] / dAtom->getIxx(); |
366 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
365 |
> |
angle = dt2 * ji[0] / I[0][0]; |
366 |
> |
this->rotate( 1, 2, angle, ji, A ); |
367 |
|
|
368 |
< |
dAtom->setJx( ji[0] ); |
369 |
< |
dAtom->setJy( ji[1] ); |
370 |
< |
dAtom->setJz( ji[2] ); |
371 |
< |
} |
372 |
< |
|
368 |
> |
|
369 |
> |
dAtom->setJ( ji ); |
370 |
> |
dAtom->setA( A ); |
371 |
> |
|
372 |
> |
} |
373 |
|
} |
374 |
|
} |
375 |
|
|
376 |
|
|
377 |
|
void Integrator::moveB( void ){ |
378 |
< |
int i,j,k; |
364 |
< |
int atomIndex; |
378 |
> |
int i, j; |
379 |
|
DirectionalAtom* dAtom; |
380 |
< |
double Tb[3]; |
381 |
< |
double ji[3]; |
380 |
> |
double Tb[3], ji[3]; |
381 |
> |
double vel[3], frc[3]; |
382 |
> |
double mass; |
383 |
|
|
384 |
|
for( i=0; i<nAtoms; i++ ){ |
385 |
< |
atomIndex = i * 3; |
385 |
> |
|
386 |
> |
atoms[i]->getVel( vel ); |
387 |
> |
atoms[i]->getFrc( frc ); |
388 |
|
|
389 |
< |
// velocity half step |
373 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
374 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
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 |
< |
|
398 |
> |
|
399 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
400 |
< |
|
401 |
< |
// get and convert the torque to body frame |
402 |
< |
|
403 |
< |
Tb[0] = dAtom->getTx(); |
383 |
< |
Tb[1] = dAtom->getTy(); |
384 |
< |
Tb[2] = dAtom->getTz(); |
385 |
< |
|
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 |
< |
// get the angular momentum, and complete the angular momentum |
414 |
< |
// half step |
390 |
< |
|
391 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
392 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
393 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
394 |
< |
|
395 |
< |
dAtom->setJx( ji[0] ); |
396 |
< |
dAtom->setJy( ji[1] ); |
397 |
< |
dAtom->setJz( ji[2] ); |
413 |
> |
|
414 |
> |
dAtom->setJ( ji ); |
415 |
|
} |
416 |
|
} |
400 |
– |
|
417 |
|
} |
418 |
|
|
419 |
|
void Integrator::preMove( void ){ |
420 |
< |
int i; |
420 |
> |
int i, j; |
421 |
> |
double pos[3]; |
422 |
|
|
423 |
|
if( nConstrained ){ |
424 |
|
|
425 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
426 |
< |
} |
427 |
< |
} |
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 pxab, pyab, pzab; |
442 |
< |
double rxab, ryab, rzab; |
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; |
451 |
|
double gab; |
452 |
|
int iteration; |
453 |
|
|
454 |
< |
|
428 |
< |
|
429 |
< |
for( i=0; i<nAtoms; i++){ |
430 |
< |
|
454 |
> |
for( i=0; i<nAtoms; i++){ |
455 |
|
moving[i] = 0; |
456 |
|
moved[i] = 1; |
457 |
|
} |
458 |
< |
|
435 |
< |
|
458 |
> |
|
459 |
|
iteration = 0; |
460 |
|
done = 0; |
461 |
|
while( !done && (iteration < maxIteration )){ |
474 |
|
by = (b*3) + 1; |
475 |
|
bz = (b*3) + 2; |
476 |
|
|
454 |
– |
|
477 |
|
if( moved[a] || moved[b] ){ |
478 |
< |
|
479 |
< |
pxab = pos[ax] - pos[bx]; |
480 |
< |
pyab = pos[ay] - pos[by]; |
481 |
< |
pzab = pos[az] - pos[bz]; |
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 |
< |
//periodic boundary condition |
488 |
< |
pxab = pxab - info->box_x * copysign(1, pxab) |
489 |
< |
* (int)( fabs(pxab / info->box_x) + 0.5); |
490 |
< |
pyab = pyab - info->box_y * copysign(1, pyab) |
465 |
< |
* (int)( fabs(pyab / info->box_y) + 0.5); |
466 |
< |
pzab = pzab - info->box_z * copysign(1, pzab) |
467 |
< |
* (int)( fabs(pzab / info->box_z) + 0.5); |
468 |
< |
|
469 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
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 = pabsq - rabsq; |
492 |
> |
diffsq = rabsq - pabsq; |
493 |
|
|
494 |
|
// the original rattle code from alan tidesley |
495 |
|
if (fabs(diffsq) > (tol*rabsq*2)) { |
496 |
< |
rxab = oldPos[ax] - oldPos[bx]; |
497 |
< |
ryab = oldPos[ay] - oldPos[by]; |
498 |
< |
rzab = oldPos[az] - oldPos[bz]; |
478 |
< |
|
479 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
480 |
< |
* (int)( fabs(rxab / info->box_x) + 0.5); |
481 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
482 |
< |
* (int)( fabs(ryab / info->box_y) + 0.5); |
483 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
484 |
< |
* (int)( fabs(rzab / info->box_z) + 0.5); |
496 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
497 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
498 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
499 |
|
|
500 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
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 |
|
|
492 |
– |
cerr << "rpabsq = " << rpabsq << ", rabsq = " << rabsq |
493 |
– |
<< ", -diffsq = " << -diffsq << "\n"; |
494 |
– |
|
509 |
|
#ifdef IS_MPI |
510 |
|
a = atoms[a]->getGlobalIndex(); |
511 |
|
b = atoms[b]->getGlobalIndex(); |
519 |
|
|
520 |
|
rma = 1.0 / atoms[a]->getMass(); |
521 |
|
rmb = 1.0 / atoms[b]->getMass(); |
522 |
< |
|
522 |
> |
|
523 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
510 |
– |
dx = rxab * gab; |
511 |
– |
dy = ryab * gab; |
512 |
– |
dz = rzab * gab; |
524 |
|
|
525 |
< |
pos[ax] += rma * dx; |
526 |
< |
pos[ay] += rma * dy; |
527 |
< |
pos[az] += rma * dz; |
525 |
> |
dx = rab[0] * gab; |
526 |
> |
dy = rab[1] * gab; |
527 |
> |
dz = rab[2] * gab; |
528 |
|
|
529 |
< |
pos[bx] -= rmb * dx; |
530 |
< |
pos[by] -= rmb * dy; |
531 |
< |
pos[bz] -= rmb * dz; |
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 |
< |
vel[ax] += rma * dx; |
527 |
< |
vel[ay] += rma * dy; |
528 |
< |
vel[az] += rma * dz; |
545 |
> |
atoms[a]->getVel( velA ); |
546 |
|
|
547 |
< |
vel[bx] -= rmb * dx; |
548 |
< |
vel[by] -= rmb * dy; |
549 |
< |
vel[bz] -= rmb * dz; |
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; |
572 |
|
} |
573 |
|
|
574 |
|
iteration++; |
548 |
– |
cerr << "iterainA = " << iteration << "\n"; |
575 |
|
} |
576 |
|
|
577 |
|
if( !done ){ |
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 rxab, ryab, rzab; |
595 |
> |
double rab[3]; |
596 |
|
int a, b, ax, ay, az, bx, by, bz; |
597 |
|
double rma, rmb; |
598 |
|
double dx, dy, dz; |
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 = 3*a +0; |
621 |
< |
ay = 3*a +1; |
622 |
< |
az = 3*a +2; |
620 |
> |
ax = (a*3) + 0; |
621 |
> |
ay = (a*3) + 1; |
622 |
> |
az = (a*3) + 2; |
623 |
|
|
624 |
< |
bx = 3*b +0; |
625 |
< |
by = 3*b +1; |
626 |
< |
bz = 3*b +2; |
624 |
> |
bx = (b*3) + 0; |
625 |
> |
by = (b*3) + 1; |
626 |
> |
bz = (b*3) + 2; |
627 |
|
|
628 |
|
if( moved[a] || moved[b] ){ |
599 |
– |
|
600 |
– |
vxab = vel[ax] - vel[bx]; |
601 |
– |
vyab = vel[ay] - vel[by]; |
602 |
– |
vzab = vel[az] - vel[bz]; |
629 |
|
|
630 |
< |
rxab = pos[ax] - pos[bx]; |
631 |
< |
ryab = pos[ay] - pos[by]; |
632 |
< |
rzab = pos[az] - pos[bz]; |
633 |
< |
|
634 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
635 |
< |
* (int)( fabs(rxab / info->box_x) + 0.5); |
610 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
611 |
< |
* (int)( fabs(ryab / info->box_y) + 0.5); |
612 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
613 |
< |
* (int)( fabs(rzab / info->box_z) + 0.5); |
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 = rxab * vxab + ryab * vyab + rzab * vzab; |
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 = rxab * gab; |
655 |
< |
dy = ryab * gab; |
656 |
< |
dz = rzab * gab; |
657 |
< |
|
658 |
< |
vel[ax] += rma * dx; |
659 |
< |
vel[ay] += rma * dy; |
660 |
< |
vel[az] += rma * dz; |
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 |
< |
vel[bx] -= rmb * dx; |
663 |
< |
vel[by] -= rmb * dy; |
664 |
< |
vel[bz] -= rmb * dz; |
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; |
681 |
|
|
682 |
|
iteration++; |
683 |
|
} |
684 |
< |
|
684 |
> |
|
685 |
|
if( !done ){ |
686 |
|
|
687 |
|
|
694 |
|
|
695 |
|
} |
696 |
|
|
663 |
– |
|
664 |
– |
|
665 |
– |
|
666 |
– |
|
667 |
– |
|
668 |
– |
|
697 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
698 |
< |
double A[9] ){ |
698 |
> |
double A[3][3] ){ |
699 |
|
|
700 |
|
int i,j,k; |
701 |
|
double sinAngle; |
711 |
|
|
712 |
|
for(i=0; i<3; i++){ |
713 |
|
for(j=0; j<3; j++){ |
714 |
< |
tempA[j][i] = A[3*i + j]; |
714 |
> |
tempA[j][i] = A[i][j]; |
715 |
|
} |
716 |
|
} |
717 |
|
|
768 |
|
|
769 |
|
for(i=0; i<3; i++){ |
770 |
|
for(j=0; j<3; j++){ |
771 |
< |
A[3*j + i] = 0.0; |
771 |
> |
A[j][i] = 0.0; |
772 |
|
for(k=0; k<3; k++){ |
773 |
< |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
773 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
774 |
|
} |
775 |
|
} |
776 |
|
} |