| 257 |
|
|
| 258 |
|
} |
| 259 |
|
|
| 260 |
< |
dumpOut->writeFinal(); |
| 260 |
> |
dumpOut->writeFinal(currTime); |
| 261 |
|
|
| 262 |
|
delete dumpOut; |
| 263 |
|
delete statOut; |
| 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; |
| 450 |
|
|
| 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) |
| 463 |
– |
* (int)( fabs(pzab / info->box_z) + 0.5); |
| 458 |
|
|
| 459 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
| 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 = 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]; |
| 468 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
| 469 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
| 470 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
| 471 |
|
|
| 472 |
< |
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) |
| 479 |
< |
* (int)( fabs(ryab / info->box_y) + 0.5); |
| 480 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
| 481 |
< |
* (int)( fabs(rzab / info->box_z) + 0.5); |
| 472 |
> |
info->wrapVector( rab ); |
| 473 |
|
|
| 474 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
| 474 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 475 |
|
|
| 476 |
|
rpabsq = rpab * rpab; |
| 477 |
|
|
| 494 |
|
|
| 495 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
| 496 |
|
|
| 497 |
< |
dx = rxab * gab; |
| 498 |
< |
dy = ryab * gab; |
| 499 |
< |
dz = rzab * gab; |
| 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; |
| 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; |
| 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 |
< |
|
| 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); |
| 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; |
