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 |
|
|
294 |
|
double ji[3]; |
295 |
|
double angle; |
296 |
|
|
297 |
+ |
|
298 |
+ |
|
299 |
|
for( i=0; i<nAtoms; i++ ){ |
300 |
|
atomIndex = i * 3; |
301 |
|
aMatIndex = i * 9; |
302 |
< |
|
302 |
> |
|
303 |
|
// velocity half step |
304 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
305 |
|
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
306 |
|
|
307 |
|
// position whole step |
308 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
309 |
< |
pos[j] += dt * vel[j]; |
310 |
< |
|
311 |
< |
|
308 |
> |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
309 |
> |
|
310 |
|
if( atoms[i]->isDirectional() ){ |
311 |
|
|
312 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
429 |
|
moving[i] = 0; |
430 |
|
moved[i] = 1; |
431 |
|
} |
432 |
< |
|
435 |
< |
|
432 |
> |
|
433 |
|
iteration = 0; |
434 |
|
done = 0; |
435 |
|
while( !done && (iteration < maxIteration )){ |
448 |
|
by = (b*3) + 1; |
449 |
|
bz = (b*3) + 2; |
450 |
|
|
454 |
– |
|
451 |
|
if( moved[a] || moved[b] ){ |
452 |
|
|
453 |
|
pxab = pos[ax] - pos[bx]; |
454 |
|
pyab = pos[ay] - pos[by]; |
455 |
|
pzab = pos[az] - pos[bz]; |
456 |
|
|
457 |
< |
//periodic boundary condition |
457 |
> |
//periodic boundary condition |
458 |
|
pxab = pxab - info->box_x * copysign(1, pxab) |
459 |
|
* (int)( fabs(pxab / info->box_x) + 0.5); |
460 |
|
pyab = pyab - info->box_y * copysign(1, pyab) |
461 |
|
* (int)( fabs(pyab / info->box_y) + 0.5); |
462 |
|
pzab = pzab - info->box_z * copysign(1, pzab) |
463 |
|
* (int)( fabs(pzab / info->box_z) + 0.5); |
464 |
< |
|
465 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
464 |
> |
|
465 |
> |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
466 |
> |
|
467 |
|
rabsq = constrainedDsqr[i]; |
468 |
< |
diffsq = pabsq - rabsq; |
468 |
> |
diffsq = rabsq - pabsq; |
469 |
|
|
470 |
|
// the original rattle code from alan tidesley |
471 |
|
if (fabs(diffsq) > (tol*rabsq*2)) { |
472 |
|
rxab = oldPos[ax] - oldPos[bx]; |
473 |
|
ryab = oldPos[ay] - oldPos[by]; |
474 |
|
rzab = oldPos[az] - oldPos[bz]; |
475 |
< |
|
475 |
> |
|
476 |
|
rxab = rxab - info->box_x * copysign(1, rxab) |
477 |
|
* (int)( fabs(rxab / info->box_x) + 0.5); |
478 |
|
ryab = ryab - info->box_y * copysign(1, ryab) |
481 |
|
* (int)( fabs(rzab / info->box_z) + 0.5); |
482 |
|
|
483 |
|
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
484 |
+ |
|
485 |
|
rpabsq = rpab * rpab; |
486 |
|
|
487 |
|
|
488 |
|
if (rpabsq < (rabsq * -diffsq)){ |
489 |
|
|
492 |
– |
cerr << "rpabsq = " << rpabsq << ", rabsq = " << rabsq |
493 |
– |
<< ", -diffsq = " << -diffsq << "\n"; |
494 |
– |
|
490 |
|
#ifdef IS_MPI |
491 |
|
a = atoms[a]->getGlobalIndex(); |
492 |
|
b = atoms[b]->getGlobalIndex(); |
500 |
|
|
501 |
|
rma = 1.0 / atoms[a]->getMass(); |
502 |
|
rmb = 1.0 / atoms[b]->getMass(); |
503 |
< |
|
503 |
> |
|
504 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
505 |
+ |
|
506 |
|
dx = rxab * gab; |
507 |
|
dy = ryab * gab; |
508 |
|
dz = rzab * gab; |
541 |
|
} |
542 |
|
|
543 |
|
iteration++; |
548 |
– |
cerr << "iterainA = " << iteration << "\n"; |
544 |
|
} |
545 |
|
|
546 |
|
if( !done ){ |
577 |
|
iteration = 0; |
578 |
|
while( !done && (iteration < maxIteration ) ){ |
579 |
|
|
580 |
+ |
done = 1; |
581 |
+ |
|
582 |
|
for(i=0; i<nConstrained; i++){ |
583 |
|
|
584 |
|
a = constrainedA[i]; |
585 |
|
b = constrainedB[i]; |
586 |
|
|
587 |
< |
ax = 3*a +0; |
588 |
< |
ay = 3*a +1; |
589 |
< |
az = 3*a +2; |
587 |
> |
ax = (a*3) + 0; |
588 |
> |
ay = (a*3) + 1; |
589 |
> |
az = (a*3) + 2; |
590 |
|
|
591 |
< |
bx = 3*b +0; |
592 |
< |
by = 3*b +1; |
593 |
< |
bz = 3*b +2; |
591 |
> |
bx = (b*3) + 0; |
592 |
> |
by = (b*3) + 1; |
593 |
> |
bz = (b*3) + 2; |
594 |
|
|
595 |
|
if( moved[a] || moved[b] ){ |
596 |
|
|
602 |
|
ryab = pos[ay] - pos[by]; |
603 |
|
rzab = pos[az] - pos[bz]; |
604 |
|
|
605 |
+ |
|
606 |
|
rxab = rxab - info->box_x * copysign(1, rxab) |
607 |
|
* (int)( fabs(rxab / info->box_x) + 0.5); |
608 |
|
ryab = ryab - info->box_y * copysign(1, ryab) |
609 |
|
* (int)( fabs(ryab / info->box_y) + 0.5); |
610 |
|
rzab = rzab - info->box_z * copysign(1, rzab) |
611 |
|
* (int)( fabs(rzab / info->box_z) + 0.5); |
612 |
< |
|
612 |
> |
|
613 |
|
rma = 1.0 / atoms[a]->getMass(); |
614 |
|
rmb = 1.0 / atoms[b]->getMass(); |
615 |
|
|