| 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 |
|
|
