| 108 |
|
|
| 109 |
|
Globals* simParams_ = info_->getSimParams(); |
| 110 |
|
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
| 111 |
+ |
int mdFileVersion; |
| 112 |
|
|
| 113 |
+ |
if (simParams_->haveMDfileVersion()) |
| 114 |
+ |
mdFileVersion = simParams_->getMDfileVersion(); |
| 115 |
+ |
else |
| 116 |
+ |
mdFileVersion = 0; |
| 117 |
+ |
|
| 118 |
+ |
|
| 119 |
|
if (simParams_->haveCutoffRadius()) { |
| 120 |
|
rCut_ = simParams_->getCutoffRadius(); |
| 121 |
|
} else { |
| 375 |
|
for(atom = mol->beginAtom(ai); atom != NULL; |
| 376 |
|
atom = mol->nextAtom(ai)) { |
| 377 |
|
atom->zeroForcesAndTorques(); |
| 371 |
– |
cerr << "apos = " << atom->getPos() << "\n"; |
| 378 |
|
} |
| 379 |
|
|
| 380 |
|
//change the positions of atoms which belong to the rigidbodies |
| 388 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 389 |
|
//calculate the center of mass of cutoff group |
| 390 |
|
cg->updateCOM(); |
| 385 |
– |
cerr << "cgpos = " << cg->getPos() << "\n"; |
| 391 |
|
} |
| 392 |
|
} |
| 393 |
|
} |
| 533 |
|
mol = info_->nextMolecule(mi)) { |
| 534 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 535 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 531 |
– |
cerr << "branch1\n"; |
| 532 |
– |
cerr << "globind = " << cg->getGlobalIndex() << "\n"; |
| 536 |
|
cg->updateCOM(); |
| 537 |
|
} |
| 538 |
|
} |
| 539 |
|
} else { |
| 540 |
|
// center of mass of the group is the same as position of the atom |
| 541 |
|
// if cutoff group does not exist |
| 539 |
– |
cerr << "branch2\n"; |
| 542 |
|
cgConfig->position = config->position; |
| 543 |
|
} |
| 544 |
|
|
| 589 |
|
bool update_nlist = fDecomp_->checkNeighborList(); |
| 590 |
|
if (update_nlist) |
| 591 |
|
neighborList = fDecomp_->buildNeighborList(); |
| 592 |
< |
} |
| 593 |
< |
|
| 592 |
> |
} |
| 593 |
> |
|
| 594 |
|
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 595 |
|
it != neighborList.end(); ++it) { |
| 596 |
|
|
| 600 |
|
cuts = fDecomp_->getGroupCutoffs(cg1, cg2); |
| 601 |
|
|
| 602 |
|
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 603 |
+ |
|
| 604 |
|
curSnapshot->wrapVector(d_grp); |
| 605 |
|
rgrpsq = d_grp.lengthSquare(); |
| 603 |
– |
|
| 606 |
|
rCutSq = cuts.second; |
| 607 |
|
|
| 608 |
|
if (rgrpsq < rCutSq) { |
| 617 |
|
|
| 618 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 619 |
|
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 620 |
+ |
|
| 621 |
|
|
| 622 |
|
for (vector<int>::iterator ia = atomListRow.begin(); |
| 623 |
|
ia != atomListRow.end(); ++ia) { |
| 641 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 642 |
|
idat.d = &d_grp; |
| 643 |
|
idat.r2 = &rgrpsq; |
| 641 |
– |
cerr << "dgrp = " << d_grp << "\n"; |
| 644 |
|
} else { |
| 645 |
|
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 646 |
|
curSnapshot->wrapVector( d ); |
| 647 |
|
r2 = d.lengthSquare(); |
| 646 |
– |
cerr << "datm = " << d<< "\n"; |
| 648 |
|
idat.d = &d; |
| 649 |
|
idat.r2 = &r2; |
| 650 |
|
} |
| 651 |
< |
|
| 651 |
< |
cerr << "idat.d = " << *(idat.d) << "\n"; |
| 651 |
> |
|
| 652 |
|
r = sqrt( *(idat.r2) ); |
| 653 |
|
idat.rij = &r; |
| 654 |
|
|
| 658 |
|
interactionMan_->doPair(idat); |
| 659 |
|
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 660 |
|
|
| 661 |
– |
cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n"; |
| 661 |
|
vij += vpair; |
| 662 |
|
fij += f1; |
| 663 |
|
tau -= outProduct( *(idat.d), f1); |
| 713 |
|
} |
| 714 |
|
} |
| 715 |
|
} |
| 716 |
< |
//if (!SIM_uses_AtomicVirial) { |
| 716 |
> |
//if (!info_->usesAtomicVirial()) { |
| 717 |
|
// tau -= outProduct(d_grp, fij); |
| 718 |
|
//} |
| 719 |
|
} |
| 734 |
|
|
| 735 |
|
} |
| 736 |
|
} |
| 738 |
– |
|
| 737 |
|
} |
| 738 |
|
|
| 739 |
|
fDecomp_->collectData(); |
