| 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 { |
| 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(); |
| 598 |
– |
|
| 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) { |
| 713 |
|
} |
| 714 |
|
} |
| 715 |
|
} |
| 716 |
< |
//if (!SIM_uses_AtomicVirial) { |
| 716 |
> |
//if (!info_->usesAtomicVirial()) { |
| 717 |
|
// tau -= outProduct(d_grp, fij); |
| 718 |
|
//} |
| 719 |
|
} |
| 734 |
|
|
| 735 |
|
} |
| 736 |
|
} |
| 729 |
– |
|
| 737 |
|
} |
| 738 |
|
|
| 739 |
|
fDecomp_->collectData(); |
