| 62 |
|
useReactionField = 0; |
| 63 |
|
useGB = 0; |
| 64 |
|
useEAM = 0; |
| 65 |
< |
|
| 65 |
> |
useThermInt = 0; |
| 66 |
> |
|
| 67 |
|
haveCutoffGroups = false; |
| 68 |
|
|
| 69 |
|
excludes = Exclude::Instance(); |
| 592 |
|
myMols = info->molecules; |
| 593 |
|
numMol = info->n_mol; |
| 594 |
|
for(int i = 0; i < numMol; i++){ |
| 594 |
– |
numAtom = myMols[i].getNAtoms(); |
| 595 |
– |
myAtoms = myMols[i].getMyAtoms(); |
| 596 |
– |
|
| 597 |
– |
|
| 598 |
– |
for(int j = 0; j < numAtom; j++){ |
| 599 |
– |
|
| 600 |
– |
|
| 601 |
– |
#ifdef IS_MPI |
| 602 |
– |
atomIndex = myAtoms[j]->getGlobalIndex(); |
| 603 |
– |
#else |
| 604 |
– |
atomIndex = myAtoms[j]->getIndex(); |
| 605 |
– |
#endif |
| 606 |
– |
|
| 607 |
– |
if(myMols[i].belongToCutoffGroup(atomIndex)) |
| 608 |
– |
continue; |
| 609 |
– |
else{ |
| 610 |
– |
// this is a fraction of the cutoff group's mass, not the mass itself! |
| 611 |
– |
mfact.push_back(1.0); |
| 612 |
– |
groupList.push_back(myAtoms[j]->getIndex() + 1); |
| 613 |
– |
groupStart.push_back(curIndex++); |
| 614 |
– |
} |
| 615 |
– |
} |
| 616 |
– |
|
| 595 |
|
numCutoffGroups = myMols[i].getNCutoffGroups(); |
| 596 |
|
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
| 597 |
|
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 601 |
|
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
| 602 |
|
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
| 603 |
|
mfact.push_back(cutoffAtom->getMass()/totalMass); |
| 604 |
+ |
#ifdef IS_MPI |
| 605 |
+ |
groupList.push_back(cutoffAtom->getGlobalIndex() + 1); |
| 606 |
+ |
#else |
| 607 |
|
groupList.push_back(cutoffAtom->getIndex() + 1); |
| 608 |
+ |
#endif |
| 609 |
|
} |
| 610 |
|
|
| 611 |
|
groupStart.push_back(curIndex); |
| 614 |
|
}//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff)) |
| 615 |
|
|
| 616 |
|
}//end for(int i = 0; i < numMol; i++) |
| 617 |
< |
|
| 617 |
> |
|
| 618 |
> |
|
| 619 |
> |
//The last cutoff group need more element to indicate the end of the cutoff |
| 620 |
|
ngroup = groupStart.size(); |
| 621 |
|
} |
