| 16 |
|
|
| 17 |
|
Molecule::~Molecule( void ){ |
| 18 |
|
int i; |
| 19 |
+ |
CutoffGroup* cg; |
| 20 |
+ |
vector<CutoffGroup*>::iterator iter; |
| 21 |
|
|
| 22 |
|
if( myAtoms != NULL ){ |
| 23 |
|
for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i]; |
| 39 |
|
delete[] myTorsions; |
| 40 |
|
} |
| 41 |
|
|
| 42 |
+ |
for(cg = beginCutoffGroup(iter); cg != NULL; cg = nextCutoffGroup(iter)) |
| 43 |
+ |
delete cg; |
| 44 |
+ |
myCutoffGroups.clear(); |
| 45 |
+ |
|
| 46 |
|
} |
| 47 |
|
|
| 48 |
|
|
| 61 |
|
nTorsions = theInit.nTorsions; |
| 62 |
|
nRigidBodies = theInit.nRigidBodies; |
| 63 |
|
nOriented = theInit.nOriented; |
| 58 |
– |
nCutoffGroups = theInit.nCutoffGroups; |
| 64 |
|
|
| 65 |
|
myAtoms = theInit.myAtoms; |
| 66 |
|
myBonds = theInit.myBonds; |
| 74 |
|
myRigidBodies[i]->calcRefCoords(); |
| 75 |
|
|
| 76 |
|
myCutoffGroups = theInit.myCutoffGroups; |
| 77 |
< |
|
| 73 |
< |
//creat a global index set of atoms which belong to cutoff group. |
| 74 |
< |
//it will be use to speed up the query whether an atom belongs to cutoff group or not |
| 75 |
< |
cutoffAtomSet.clear(); |
| 76 |
< |
|
| 77 |
< |
for(curCutoffGroup = beginCutoffGroup(iterCutoff); curCutoffGroup != NULL; |
| 78 |
< |
curCutoffGroup = nextCutoffGroup(iterCutoff)){ |
| 79 |
< |
|
| 80 |
< |
for(cutoffAtom = curCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
| 81 |
< |
cutoffAtom = curCutoffGroup->nextAtom(iterAtom)){ |
| 82 |
< |
#ifdef IS_MPI |
| 83 |
< |
atomIndex = cutoffAtom->getGlobalIndex(); |
| 84 |
< |
#else |
| 85 |
< |
atomIndex = cutoffAtom->getIndex(); |
| 86 |
< |
#endif |
| 87 |
< |
cutoffAtomSet.insert(atomIndex); |
| 88 |
< |
}// end for(cutoffAtom) |
| 89 |
< |
}//end for(curCutoffGroup) |
| 77 |
> |
nCutoffGroups = myCutoffGroups.size(); |
| 78 |
|
|
| 79 |
|
} |
| 80 |
|
|
