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 |
|
|
257 |
|
|
258 |
|
} |
259 |
|
|
260 |
< |
dumpOut->writeFinal(); |
260 |
> |
dumpOut->writeFinal(currTime); |
261 |
|
|
262 |
|
delete dumpOut; |
263 |
|
delete statOut; |
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]; |
411 |
|
|
412 |
|
int i,j,k; |
413 |
|
int done; |
414 |
< |
double pxab, pyab, pzab; |
415 |
< |
double rxab, ryab, rzab; |
414 |
> |
double pab[3]; |
415 |
> |
double rab[3]; |
416 |
|
int a, b, ax, ay, az, bx, by, bz; |
417 |
|
double rma, rmb; |
418 |
|
double dx, dy, dz; |
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]; |
453 |
> |
pab[0] = pos[ax] - pos[bx]; |
454 |
> |
pab[1] = pos[ay] - pos[by]; |
455 |
> |
pab[2] = pos[az] - pos[bz]; |
456 |
|
|
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) |
467 |
< |
* (int)( fabs(pzab / info->box_z) + 0.5); |
468 |
< |
|
469 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
457 |
> |
//periodic boundary condition |
458 |
> |
|
459 |
> |
info->wrapVector( pab ); |
460 |
> |
|
461 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
462 |
> |
|
463 |
|
rabsq = constrainedDsqr[i]; |
464 |
< |
diffsq = pabsq - rabsq; |
464 |
> |
diffsq = rabsq - pabsq; |
465 |
|
|
466 |
|
// the original rattle code from alan tidesley |
467 |
|
if (fabs(diffsq) > (tol*rabsq*2)) { |
468 |
< |
rxab = oldPos[ax] - oldPos[bx]; |
469 |
< |
ryab = oldPos[ay] - oldPos[by]; |
470 |
< |
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); |
468 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
469 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
470 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
471 |
|
|
472 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
472 |
> |
info->wrapVector( rab ); |
473 |
> |
|
474 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
475 |
> |
|
476 |
|
rpabsq = rpab * rpab; |
477 |
|
|
478 |
|
|
479 |
|
if (rpabsq < (rabsq * -diffsq)){ |
480 |
|
|
492 |
– |
cerr << "rpabsq = " << rpabsq << ", rabsq = " << rabsq |
493 |
– |
<< ", -diffsq = " << -diffsq << "\n"; |
494 |
– |
|
481 |
|
#ifdef IS_MPI |
482 |
|
a = atoms[a]->getGlobalIndex(); |
483 |
|
b = atoms[b]->getGlobalIndex(); |
491 |
|
|
492 |
|
rma = 1.0 / atoms[a]->getMass(); |
493 |
|
rmb = 1.0 / atoms[b]->getMass(); |
494 |
< |
|
494 |
> |
|
495 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
510 |
– |
dx = rxab * gab; |
511 |
– |
dy = ryab * gab; |
512 |
– |
dz = rzab * gab; |
496 |
|
|
497 |
+ |
dx = rab[0] * gab; |
498 |
+ |
dy = rab[1] * gab; |
499 |
+ |
dz = rab[2] * gab; |
500 |
+ |
|
501 |
|
pos[ax] += rma * dx; |
502 |
|
pos[ay] += rma * dy; |
503 |
|
pos[az] += rma * dz; |
532 |
|
} |
533 |
|
|
534 |
|
iteration++; |
548 |
– |
cerr << "iterainA = " << iteration << "\n"; |
535 |
|
} |
536 |
|
|
537 |
|
if( !done ){ |
550 |
|
int i,j,k; |
551 |
|
int done; |
552 |
|
double vxab, vyab, vzab; |
553 |
< |
double rxab, ryab, rzab; |
553 |
> |
double rab[3]; |
554 |
|
int a, b, ax, ay, az, bx, by, bz; |
555 |
|
double rma, rmb; |
556 |
|
double dx, dy, dz; |
568 |
|
iteration = 0; |
569 |
|
while( !done && (iteration < maxIteration ) ){ |
570 |
|
|
571 |
+ |
done = 1; |
572 |
+ |
|
573 |
|
for(i=0; i<nConstrained; i++){ |
574 |
|
|
575 |
|
a = constrainedA[i]; |
576 |
|
b = constrainedB[i]; |
577 |
|
|
578 |
< |
ax = 3*a +0; |
579 |
< |
ay = 3*a +1; |
580 |
< |
az = 3*a +2; |
578 |
> |
ax = (a*3) + 0; |
579 |
> |
ay = (a*3) + 1; |
580 |
> |
az = (a*3) + 2; |
581 |
|
|
582 |
< |
bx = 3*b +0; |
583 |
< |
by = 3*b +1; |
584 |
< |
bz = 3*b +2; |
582 |
> |
bx = (b*3) + 0; |
583 |
> |
by = (b*3) + 1; |
584 |
> |
bz = (b*3) + 2; |
585 |
|
|
586 |
|
if( moved[a] || moved[b] ){ |
587 |
|
|
589 |
|
vyab = vel[ay] - vel[by]; |
590 |
|
vzab = vel[az] - vel[bz]; |
591 |
|
|
592 |
< |
rxab = pos[ax] - pos[bx]; |
593 |
< |
ryab = pos[ay] - pos[by]; |
594 |
< |
rzab = pos[az] - pos[bz]; |
592 |
> |
rab[0] = pos[ax] - pos[bx]; |
593 |
> |
rab[1] = pos[ay] - pos[by]; |
594 |
> |
rab[2] = pos[az] - pos[bz]; |
595 |
|
|
596 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
597 |
< |
* (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); |
614 |
< |
|
596 |
> |
info->wrapVector( rab ); |
597 |
> |
|
598 |
|
rma = 1.0 / atoms[a]->getMass(); |
599 |
|
rmb = 1.0 / atoms[b]->getMass(); |
600 |
|
|
601 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
601 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
602 |
|
|
603 |
|
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
604 |
|
|
605 |
|
if (fabs(gab) > tol) { |
606 |
|
|
607 |
< |
dx = rxab * gab; |
608 |
< |
dy = ryab * gab; |
609 |
< |
dz = rzab * gab; |
607 |
> |
dx = rab[0] * gab; |
608 |
> |
dy = rab[1] * gab; |
609 |
> |
dz = rab[2] * gab; |
610 |
|
|
611 |
|
vel[ax] += rma * dx; |
612 |
|
vel[ay] += rma * dy; |