137 |
|
constrainedA[i] = temp_con[i].get_a(); |
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"; |
143 |
|
} |
144 |
|
|
145 |
|
|
405 |
|
|
406 |
|
if( nConstrained ){ |
407 |
|
|
405 |
– |
// if( oldAtoms != nAtoms ){ |
406 |
– |
|
407 |
– |
// // save oldAtoms to check for lode balanceing later on. |
408 |
– |
|
409 |
– |
// oldAtoms = nAtoms; |
410 |
– |
|
411 |
– |
// delete[] moving; |
412 |
– |
// delete[] moved; |
413 |
– |
// delete[] oldPos; |
414 |
– |
|
415 |
– |
// moving = new int[nAtoms]; |
416 |
– |
// moved = new int[nAtoms]; |
417 |
– |
|
418 |
– |
// oldPos = new double[nAtoms*3]; |
419 |
– |
// } |
420 |
– |
|
408 |
|
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
409 |
|
} |
410 |
|
} |
415 |
|
int done; |
416 |
|
double pxab, pyab, pzab; |
417 |
|
double rxab, ryab, rzab; |
418 |
< |
int a, b; |
418 |
> |
int a, b, ax, ay, az, bx, by, bz; |
419 |
|
double rma, rmb; |
420 |
|
double dx, dy, dz; |
421 |
|
double rpab; |
442 |
|
|
443 |
|
a = constrainedA[i]; |
444 |
|
b = constrainedB[i]; |
445 |
< |
|
445 |
> |
|
446 |
> |
ax = (a*3) + 0; |
447 |
> |
ay = (a*3) + 1; |
448 |
> |
az = (a*3) + 2; |
449 |
> |
|
450 |
> |
bx = (b*3) + 0; |
451 |
> |
by = (b*3) + 1; |
452 |
> |
bz = (b*3) + 2; |
453 |
> |
|
454 |
> |
|
455 |
|
if( moved[a] || moved[b] ){ |
456 |
|
|
457 |
< |
pxab = pos[3*a+0] - pos[3*b+0]; |
458 |
< |
pyab = pos[3*a+1] - pos[3*b+1]; |
459 |
< |
pzab = pos[3*a+2] - pos[3*b+2]; |
457 |
> |
pxab = pos[ax] - pos[bx]; |
458 |
> |
pyab = pos[ay] - pos[by]; |
459 |
> |
pzab = pos[az] - pos[bz]; |
460 |
|
|
461 |
|
//periodic boundary condition |
462 |
|
pxab = pxab - info->box_x * copysign(1, pxab) |
463 |
< |
* int( fabs(pxab) / info->box_x + 0.5); |
463 |
> |
* (int)( fabs(pxab / info->box_x) + 0.5); |
464 |
|
pyab = pyab - info->box_y * copysign(1, pyab) |
465 |
< |
* int( fabs(pyab) / info->box_y + 0.5); |
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); |
467 |
> |
* (int)( fabs(pzab / info->box_z) + 0.5); |
468 |
|
|
469 |
|
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
470 |
|
rabsq = constrainedDsqr[i]; |
471 |
|
diffsq = pabsq - rabsq; |
472 |
|
|
473 |
|
// the original rattle code from alan tidesley |
474 |
< |
if (fabs(diffsq) > tol*rabsq*2) { |
475 |
< |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
476 |
< |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
477 |
< |
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
474 |
> |
if (fabs(diffsq) > (tol*rabsq*2)) { |
475 |
> |
rxab = oldPos[ax] - oldPos[bx]; |
476 |
> |
ryab = oldPos[ay] - oldPos[by]; |
477 |
> |
rzab = oldPos[az] - oldPos[bz]; |
478 |
|
|
479 |
|
rxab = rxab - info->box_x * copysign(1, rxab) |
480 |
< |
* int( fabs(rxab) / info->box_x + 0.5); |
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); |
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); |
484 |
> |
* (int)( fabs(rzab / info->box_z) + 0.5); |
485 |
|
|
486 |
|
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
487 |
|
rpabsq = rpab * rpab; |
488 |
|
|
489 |
|
|
490 |
|
if (rpabsq < (rabsq * -diffsq)){ |
491 |
+ |
|
492 |
+ |
cerr << "rpabsq = " << rpabsq << ", rabsq = " << rabsq |
493 |
+ |
<< ", -diffsq = " << -diffsq << "\n"; |
494 |
+ |
|
495 |
|
#ifdef IS_MPI |
496 |
|
a = atoms[a]->getGlobalIndex(); |
497 |
|
b = atoms[b]->getGlobalIndex(); |
498 |
|
#endif //is_mpi |
499 |
|
sprintf( painCave.errMsg, |
500 |
< |
"Constraint failure in constrainA at atom %d and %d\n.", |
500 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", |
501 |
|
a, b ); |
502 |
|
painCave.isFatal = 1; |
503 |
|
simError(); |
511 |
|
dy = ryab * gab; |
512 |
|
dz = rzab * gab; |
513 |
|
|
514 |
< |
pos[3*a+0] += rma * dx; |
515 |
< |
pos[3*a+1] += rma * dy; |
516 |
< |
pos[3*a+2] += rma * dz; |
514 |
> |
pos[ax] += rma * dx; |
515 |
> |
pos[ay] += rma * dy; |
516 |
> |
pos[az] += rma * dz; |
517 |
|
|
518 |
< |
pos[3*b+0] -= rmb * dx; |
519 |
< |
pos[3*b+1] -= rmb * dy; |
520 |
< |
pos[3*b+2] -= rmb * dz; |
518 |
> |
pos[bx] -= rmb * dx; |
519 |
> |
pos[by] -= rmb * dy; |
520 |
> |
pos[bz] -= rmb * dz; |
521 |
|
|
522 |
|
dx = dx / dt; |
523 |
|
dy = dy / dt; |
524 |
|
dz = dz / dt; |
525 |
|
|
526 |
< |
vel[3*a+0] += rma * dx; |
527 |
< |
vel[3*a+1] += rma * dy; |
528 |
< |
vel[3*a+2] += rma * dz; |
526 |
> |
vel[ax] += rma * dx; |
527 |
> |
vel[ay] += rma * dy; |
528 |
> |
vel[az] += rma * dz; |
529 |
|
|
530 |
< |
vel[3*b+0] -= rmb * dx; |
531 |
< |
vel[3*b+1] -= rmb * dy; |
532 |
< |
vel[3*b+2] -= rmb * dz; |
530 |
> |
vel[bx] -= rmb * dx; |
531 |
> |
vel[by] -= rmb * dy; |
532 |
> |
vel[bz] -= rmb * dz; |
533 |
|
|
534 |
|
moving[a] = 1; |
535 |
|
moving[b] = 1; |
545 |
|
} |
546 |
|
|
547 |
|
iteration++; |
548 |
+ |
cerr << "iterainA = " << iteration << "\n"; |
549 |
|
} |
550 |
|
|
551 |
|
if( !done ){ |
565 |
|
int done; |
566 |
|
double vxab, vyab, vzab; |
567 |
|
double rxab, ryab, rzab; |
568 |
< |
int a, b; |
568 |
> |
int a, b, ax, ay, az, bx, by, bz; |
569 |
|
double rma, rmb; |
570 |
|
double dx, dy, dz; |
571 |
|
double rabsq, pabsq, rvab; |
587 |
|
a = constrainedA[i]; |
588 |
|
b = constrainedB[i]; |
589 |
|
|
590 |
+ |
ax = 3*a +0; |
591 |
+ |
ay = 3*a +1; |
592 |
+ |
az = 3*a +2; |
593 |
+ |
|
594 |
+ |
bx = 3*b +0; |
595 |
+ |
by = 3*b +1; |
596 |
+ |
bz = 3*b +2; |
597 |
+ |
|
598 |
|
if( moved[a] || moved[b] ){ |
599 |
|
|
600 |
< |
vxab = vel[3*a+0] - vel[3*b+0]; |
601 |
< |
vyab = vel[3*a+1] - vel[3*b+1]; |
602 |
< |
vzab = vel[3*a+2] - vel[3*b+2]; |
600 |
> |
vxab = vel[ax] - vel[bx]; |
601 |
> |
vyab = vel[ay] - vel[by]; |
602 |
> |
vzab = vel[az] - vel[bz]; |
603 |
|
|
604 |
< |
rxab = pos[3*a+0] - pos[3*b+0]; |
605 |
< |
ryab = pos[3*a+1] - pos[3*b+1]; |
606 |
< |
rzab = pos[3*a+2] - pos[3*b+2]; |
604 |
> |
rxab = pos[ax] - pos[bx]; |
605 |
> |
ryab = pos[ay] - pos[by]; |
606 |
> |
rzab = pos[az] - pos[bz]; |
607 |
|
|
608 |
|
rxab = rxab - info->box_x * copysign(1, rxab) |
609 |
< |
* int( fabs(rxab) / info->box_x + 0.5); |
609 |
> |
* (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); |
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); |
613 |
> |
* (int)( fabs(rzab / info->box_z) + 0.5); |
614 |
|
|
615 |
|
rma = 1.0 / atoms[a]->getMass(); |
616 |
|
rmb = 1.0 / atoms[b]->getMass(); |
625 |
|
dy = ryab * gab; |
626 |
|
dz = rzab * gab; |
627 |
|
|
628 |
< |
vel[3*a+0] += rma * dx; |
629 |
< |
vel[3*a+1] += rma * dy; |
630 |
< |
vel[3*a+2] += rma * dz; |
628 |
> |
vel[ax] += rma * dx; |
629 |
> |
vel[ay] += rma * dy; |
630 |
> |
vel[az] += rma * dz; |
631 |
|
|
632 |
< |
vel[3*b+0] -= rmb * dx; |
633 |
< |
vel[3*b+1] -= rmb * dy; |
634 |
< |
vel[3*b+2] -= rmb * dz; |
632 |
> |
vel[bx] -= rmb * dx; |
633 |
> |
vel[by] -= rmb * dy; |
634 |
> |
vel[bz] -= rmb * dz; |
635 |
|
|
636 |
|
moving[a] = 1; |
637 |
|
moving[b] = 1; |