| 695 |
|
RealType vij; |
| 696 |
|
Vector3d fij, fg, f1; |
| 697 |
|
tuple3<RealType, RealType, RealType> cuts; |
| 698 |
< |
RealType rCutSq; |
| 698 |
> |
RealType rCut, rCutSq, rListSq; |
| 699 |
|
bool in_switching_region; |
| 700 |
|
RealType sw, dswdr, swderiv; |
| 701 |
|
vector<int> atomListColumn, atomListRow; |
| 713 |
|
vector<int>::iterator ia, jb; |
| 714 |
|
|
| 715 |
|
int loopStart, loopEnd; |
| 716 |
< |
|
| 716 |
> |
|
| 717 |
> |
idat.rcut = &rCut; |
| 718 |
|
idat.vdwMult = &vdwMult; |
| 719 |
|
idat.electroMult = &electroMult; |
| 720 |
|
idat.pot = &workPot; |
| 747 |
|
if (update_nlist) { |
| 748 |
|
if (!usePeriodicBoundaryConditions_) |
| 749 |
|
Mat3x3d bbox = thermo->getBoundingBox(); |
| 750 |
< |
neighborList = fDecomp_->buildNeighborList(); |
| 750 |
> |
fDecomp_->buildNeighborList(neighborList_); |
| 751 |
|
} |
| 752 |
|
} |
| 753 |
|
|
| 754 |
< |
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 755 |
< |
it != neighborList.end(); ++it) { |
| 754 |
> |
for (vector<pair<int, int> >::iterator it = neighborList_.begin(); |
| 755 |
> |
it != neighborList_.end(); ++it) { |
| 756 |
|
|
| 757 |
|
cg1 = (*it).first; |
| 758 |
|
cg2 = (*it).second; |
| 759 |
|
|
| 760 |
< |
cuts = fDecomp_->getGroupCutoffs(cg1, cg2); |
| 760 |
> |
fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq); |
| 761 |
|
|
| 762 |
|
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 763 |
|
|
| 764 |
< |
curSnapshot->wrapVector(d_grp); |
| 764 |
> |
// already wrapped in the getIntergroupVector call: |
| 765 |
> |
// curSnapshot->wrapVector(d_grp); |
| 766 |
|
rgrpsq = d_grp.lengthSquare(); |
| 765 |
– |
rCutSq = cuts.second; |
| 767 |
|
|
| 768 |
|
if (rgrpsq < rCutSq) { |
| 769 |
< |
idat.rcut = &cuts.first; |
| 769 |
> |
|
| 770 |
|
if (iLoop == PAIR_LOOP) { |
| 771 |
|
vij = 0.0; |
| 772 |
|
fij.zero(); |
