| 12 |
|
myBonds = NULL; |
| 13 |
|
myBends = NULL; |
| 14 |
|
myTorsions = NULL; |
| 15 |
– |
|
| 15 |
|
} |
| 16 |
|
|
| 17 |
|
Molecule::~Molecule( void ){ |
| 41 |
|
|
| 42 |
|
|
| 43 |
|
void Molecule::initialize( molInit &theInit ){ |
| 44 |
< |
double totMass; |
| 44 |
> |
|
| 45 |
> |
CutoffGroup* curCutoffGroup; |
| 46 |
> |
vector<CutoffGroup*>::iterator iterCutoff; |
| 47 |
> |
Atom* cutoffAtom; |
| 48 |
> |
vector<Atom*>::iterator iterAtom; |
| 49 |
> |
int atomIndex; |
| 50 |
|
|
| 51 |
|
nAtoms = theInit.nAtoms; |
| 52 |
|
nMembers = nAtoms; |
| 55 |
|
nTorsions = theInit.nTorsions; |
| 56 |
|
nRigidBodies = theInit.nRigidBodies; |
| 57 |
|
nOriented = theInit.nOriented; |
| 58 |
+ |
nCutoffGroups = theInit.nCutoffGroups; |
| 59 |
|
|
| 60 |
|
myAtoms = theInit.myAtoms; |
| 61 |
|
myBonds = theInit.myBonds; |
| 68 |
|
for (int i = 0; i < myRigidBodies.size(); i++) |
| 69 |
|
myRigidBodies[i]->calcRefCoords(); |
| 70 |
|
|
| 71 |
+ |
myCutoffGroups = theInit.myCutoffGroups; |
| 72 |
|
|
| 73 |
< |
//the mass ratio will never change during the simulation. Thus, we could |
| 74 |
< |
//just calculate it at the begining of the simulation |
| 75 |
< |
totMass = getTotalMass(); |
| 76 |
< |
for(int i = 0; i < nAtoms; i ++) |
| 77 |
< |
myAtoms[i]->setMassRatio(myAtoms[i]->getMass()/totMass); |
| 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) |
| 90 |
> |
|
| 91 |
|
} |
| 92 |
|
|
| 93 |
|
void Molecule::calcForces( void ){ |
| 100 |
|
} |
| 101 |
|
|
| 102 |
|
//calculate the center of mass of the molecule |
| 103 |
< |
getCOM(com); |
| 104 |
< |
for(int i = 0; i < nAtoms; i ++) |
| 105 |
< |
myAtoms[i]->setRc(com); |
| 103 |
> |
//getCOM(com); |
| 104 |
> |
//for(int i = 0; i < nAtoms; i ++) |
| 105 |
> |
// myAtoms[i]->setRc(com); |
| 106 |
|
|
| 107 |
|
|
| 108 |
|
for(i=0; i<nBonds; i++){ |
