| 62 |
|
useReactionField = 0; |
| 63 |
|
useGB = 0; |
| 64 |
|
useEAM = 0; |
| 65 |
+ |
|
| 66 |
+ |
haveCutoffGroups = false; |
| 67 |
|
|
| 68 |
|
excludes = Exclude::Instance(); |
| 69 |
|
|
| 452 |
|
isError = 0; |
| 453 |
|
|
| 454 |
|
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
| 455 |
< |
|
| 455 |
> |
//it may not be a good idea to pass the address of first element in vector |
| 456 |
> |
//since c++ standard does not require vector to be stored continously in meomory |
| 457 |
> |
//Most of the compilers will organize the memory of vector continously |
| 458 |
|
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 459 |
|
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 460 |
|
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
| 567 |
|
|
| 568 |
|
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
| 569 |
|
vector<int>& groupList, vector<int>& groupStart){ |
| 570 |
< |
Molecule* mol; |
| 570 |
> |
Molecule* myMols; |
| 571 |
|
Atom** myAtoms; |
| 572 |
|
int numAtom; |
| 573 |
|
int curIndex; |
| 574 |
|
double mtot; |
| 575 |
< |
|
| 575 |
> |
int numMol; |
| 576 |
> |
int numCutoffGroups; |
| 577 |
> |
CutoffGroup* myCutoffGroup; |
| 578 |
> |
vector<CutoffGroup*>::iterator iterCutoff; |
| 579 |
> |
Atom* cutoffAtom; |
| 580 |
> |
vector<Atom*>::iterator iterAtom; |
| 581 |
> |
int atomIndex; |
| 582 |
> |
|
| 583 |
|
mfact.clear(); |
| 584 |
|
groupList.clear(); |
| 585 |
|
groupStart.clear(); |
| 586 |
|
|
| 587 |
|
//Be careful, fortran array begin at 1 |
| 588 |
|
curIndex = 1; |
| 589 |
< |
|
| 590 |
< |
if(info->useMolecularCutoffs){ |
| 591 |
< |
|
| 592 |
< |
#ifdef IS_MPI |
| 593 |
< |
ngroup = mpiSim->getMyNMol(); |
| 594 |
< |
#else |
| 595 |
< |
ngroup = info->n_mol; |
| 585 |
< |
#endif |
| 589 |
> |
|
| 590 |
> |
myMols = info->molecules; |
| 591 |
> |
numMol = info->n_mol; |
| 592 |
> |
for(int i = 0; i < numMol; i++){ |
| 593 |
> |
numAtom = myMols[i].getNAtoms(); |
| 594 |
> |
myAtoms = myMols[i].getMyAtoms(); |
| 595 |
> |
|
| 596 |
|
|
| 597 |
< |
for(int i = 0; i < ngroup; i ++){ |
| 588 |
< |
mol = &(info->molecules[i]); |
| 589 |
< |
numAtom = mol->getNAtoms(); |
| 590 |
< |
myAtoms = mol->getMyAtoms(); |
| 591 |
< |
mtot = 0.0; |
| 597 |
> |
for(int j = 0; j < numAtom; j++){ |
| 598 |
|
|
| 599 |
< |
for(int j=0; j < numAtom; j++) |
| 600 |
< |
mtot += myAtoms[j]->getMass(); |
| 601 |
< |
|
| 602 |
< |
for(int j=0; j < numAtom; j++){ |
| 603 |
< |
|
| 604 |
< |
// We want the local Index: |
| 599 |
< |
groupList.push_back(myAtoms[j]->getIndex() + 1); |
| 600 |
< |
mfact.push_back(myAtoms[j]->getMass() / mtot); |
| 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 |
|
|
| 615 |
< |
groupStart.push_back(curIndex); |
| 616 |
< |
curIndex += numAtom; |
| 615 |
> |
numCutoffGroups = myMols[i].getNCutoffGroups(); |
| 616 |
> |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
| 617 |
> |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 618 |
|
|
| 619 |
< |
} //end for(int i =0 ; i < ngroup; i++) |
| 620 |
< |
} |
| 621 |
< |
else{ |
| 622 |
< |
//using atomic cutoff, every single atom is just a group |
| 619 |
> |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
| 620 |
> |
cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){ |
| 621 |
> |
groupList.push_back(cutoffAtom->getIndex() + 1); |
| 622 |
> |
} |
| 623 |
> |
|
| 624 |
> |
groupStart.push_back(curIndex); |
| 625 |
> |
curIndex += myCutoffGroup->getNumAtom(); |
| 626 |
> |
} |
| 627 |
|
|
| 628 |
< |
#ifdef IS_MPI |
| 629 |
< |
ngroup = mpiSim->getMyNlocal(); |
| 630 |
< |
#else |
| 615 |
< |
ngroup = info->n_atoms; |
| 616 |
< |
#endif |
| 617 |
< |
|
| 618 |
< |
for(int i =0 ; i < ngroup; i++){ |
| 619 |
< |
groupStart.push_back(curIndex++); |
| 620 |
< |
groupList.push_back((info->atoms[i])->getIndex() + 1); |
| 621 |
< |
mfact.push_back(1.0); |
| 622 |
< |
|
| 623 |
< |
}//end for(int i =0 ; i < ngroup; i++) |
| 624 |
< |
|
| 625 |
< |
}//end if (info->useMolecularCutoffs) |
| 626 |
< |
|
| 628 |
> |
} |
| 629 |
> |
|
| 630 |
> |
ngroup = groupStart.size(); |
| 631 |
|
} |
