| 62 |
|
useReactionField = 0; |
| 63 |
|
useGB = 0; |
| 64 |
|
useEAM = 0; |
| 65 |
< |
|
| 65 |
> |
useThermInt = 0; |
| 66 |
> |
|
| 67 |
|
haveCutoffGroups = false; |
| 68 |
|
|
| 69 |
|
excludes = Exclude::Instance(); |
| 445 |
|
excl = excludes->getFortranArray(); |
| 446 |
|
|
| 447 |
|
#ifdef IS_MPI |
| 448 |
< |
n_global = mpiSim->getTotAtoms(); |
| 448 |
> |
n_global = mpiSim->getNAtomsGlobal(); |
| 449 |
|
#else |
| 450 |
|
n_global = n_atoms; |
| 451 |
|
#endif |
| 454 |
|
|
| 455 |
|
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
| 456 |
|
//it may not be a good idea to pass the address of first element in vector |
| 457 |
< |
//since c++ standard does not require vector to be stored continously in meomory |
| 458 |
< |
//Most of the compilers will organize the memory of vector continously |
| 457 |
> |
//since c++ standard does not require vector to be stored continuously in meomory |
| 458 |
> |
//Most of the compilers will organize the memory of vector continuously |
| 459 |
|
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 460 |
|
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 461 |
|
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
| 580 |
|
Atom* cutoffAtom; |
| 581 |
|
vector<Atom*>::iterator iterAtom; |
| 582 |
|
int atomIndex; |
| 583 |
+ |
double totalMass; |
| 584 |
|
|
| 585 |
|
mfact.clear(); |
| 586 |
|
groupList.clear(); |
| 592 |
|
myMols = info->molecules; |
| 593 |
|
numMol = info->n_mol; |
| 594 |
|
for(int i = 0; i < numMol; i++){ |
| 593 |
– |
numAtom = myMols[i].getNAtoms(); |
| 594 |
– |
myAtoms = myMols[i].getMyAtoms(); |
| 595 |
– |
|
| 596 |
– |
|
| 597 |
– |
for(int j = 0; j < numAtom; j++){ |
| 598 |
– |
|
| 599 |
– |
|
| 600 |
– |
#ifdef IS_MPI |
| 601 |
– |
atomIndex = myAtoms[j]->getGlobalIndex(); |
| 602 |
– |
#else |
| 603 |
– |
atomIndex = myAtoms[j]->getIndex(); |
| 604 |
– |
#endif |
| 605 |
– |
|
| 606 |
– |
if(myMols[i].belongToCutoffGroup(atomIndex)) |
| 607 |
– |
continue; |
| 608 |
– |
else{ |
| 609 |
– |
mfact.push_back(myAtoms[j]->getMass()); |
| 610 |
– |
groupList.push_back(myAtoms[j]->getIndex() + 1); |
| 611 |
– |
groupStart.push_back(curIndex++); |
| 612 |
– |
} |
| 613 |
– |
} |
| 614 |
– |
|
| 595 |
|
numCutoffGroups = myMols[i].getNCutoffGroups(); |
| 596 |
|
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
| 597 |
|
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 598 |
+ |
|
| 599 |
+ |
totalMass = myCutoffGroup->getMass(); |
| 600 |
|
|
| 601 |
|
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
| 602 |
< |
cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){ |
| 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); |
| 612 |
|
curIndex += myCutoffGroup->getNumAtom(); |
| 626 |
– |
} |
| 627 |
– |
|
| 628 |
– |
} |
| 613 |
|
|
| 614 |
+ |
}//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff)) |
| 615 |
+ |
|
| 616 |
+ |
}//end for(int i = 0; i < numMol; i++) |
| 617 |
+ |
|
| 618 |
+ |
|
| 619 |
+ |
//The last cutoff group need more element to indicate the end of the cutoff |
| 620 |
|
ngroup = groupStart.size(); |
| 621 |
|
} |
