| 368 |
|
for(atom = mol->beginAtom(ai); atom != NULL; |
| 369 |
|
atom = mol->nextAtom(ai)) { |
| 370 |
|
atom->zeroForcesAndTorques(); |
| 371 |
– |
cerr << "apos = " << atom->getPos() << "\n"; |
| 371 |
|
} |
| 372 |
|
|
| 373 |
|
//change the positions of atoms which belong to the rigidbodies |
| 381 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 382 |
|
//calculate the center of mass of cutoff group |
| 383 |
|
cg->updateCOM(); |
| 385 |
– |
cerr << "cgpos = " << cg->getPos() << "\n"; |
| 384 |
|
} |
| 385 |
|
} |
| 386 |
|
} |
| 526 |
|
mol = info_->nextMolecule(mi)) { |
| 527 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 528 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 531 |
– |
cerr << "branch1\n"; |
| 532 |
– |
cerr << "globind = " << cg->getGlobalIndex() << "\n"; |
| 529 |
|
cg->updateCOM(); |
| 530 |
|
} |
| 531 |
|
} |
| 532 |
|
} else { |
| 533 |
|
// center of mass of the group is the same as position of the atom |
| 534 |
|
// if cutoff group does not exist |
| 539 |
– |
cerr << "branch2\n"; |
| 535 |
|
cgConfig->position = config->position; |
| 536 |
|
} |
| 537 |
|
|
| 633 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 634 |
|
idat.d = &d_grp; |
| 635 |
|
idat.r2 = &rgrpsq; |
| 641 |
– |
cerr << "dgrp = " << d_grp << "\n"; |
| 636 |
|
} else { |
| 637 |
|
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 638 |
|
curSnapshot->wrapVector( d ); |
| 639 |
|
r2 = d.lengthSquare(); |
| 646 |
– |
cerr << "datm = " << d<< "\n"; |
| 640 |
|
idat.d = &d; |
| 641 |
|
idat.r2 = &r2; |
| 642 |
|
} |
| 643 |
< |
|
| 651 |
< |
cerr << "idat.d = " << *(idat.d) << "\n"; |
| 643 |
> |
|
| 644 |
|
r = sqrt( *(idat.r2) ); |
| 645 |
|
idat.rij = &r; |
| 646 |
|
|
| 650 |
|
interactionMan_->doPair(idat); |
| 651 |
|
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 652 |
|
|
| 661 |
– |
cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n"; |
| 653 |
|
vij += vpair; |
| 654 |
|
fij += f1; |
| 655 |
|
tau -= outProduct( *(idat.d), f1); |
