| 62 |
|
useReactionField = 0; |
| 63 |
|
useGB = 0; |
| 64 |
|
useEAM = 0; |
| 65 |
< |
|
| 65 |
> |
useSolidThermInt = 0; |
| 66 |
> |
useLiquidThermInt = 0; |
| 67 |
> |
|
| 68 |
|
haveCutoffGroups = false; |
| 69 |
|
|
| 70 |
|
excludes = Exclude::Instance(); |
| 446 |
|
excl = excludes->getFortranArray(); |
| 447 |
|
|
| 448 |
|
#ifdef IS_MPI |
| 449 |
< |
n_global = mpiSim->getTotAtoms(); |
| 449 |
> |
n_global = mpiSim->getNAtomsGlobal(); |
| 450 |
|
#else |
| 451 |
|
n_global = n_atoms; |
| 452 |
|
#endif |
| 453 |
|
|
| 454 |
|
isError = 0; |
| 455 |
|
|
| 456 |
< |
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
| 456 |
> |
getFortranGroupArrays(this, FglobalGroupMembership, mfact); |
| 457 |
|
//it may not be a good idea to pass the address of first element in vector |
| 458 |
< |
//since c++ standard does not require vector to be stored continously in meomory |
| 459 |
< |
//Most of the compilers will organize the memory of vector continously |
| 458 |
> |
//since c++ standard does not require vector to be stored continuously in meomory |
| 459 |
> |
//Most of the compilers will organize the memory of vector continuously |
| 460 |
|
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 461 |
|
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 462 |
< |
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
| 462 |
> |
&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); |
| 463 |
|
|
| 464 |
|
if( isError ){ |
| 465 |
|
|
| 567 |
|
} |
| 568 |
|
|
| 569 |
|
|
| 570 |
< |
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
| 571 |
< |
vector<int>& groupList, vector<int>& groupStart){ |
| 570 |
> |
void SimInfo::getFortranGroupArrays(SimInfo* info, |
| 571 |
> |
vector<int>& FglobalGroupMembership, |
| 572 |
> |
vector<double>& mfact){ |
| 573 |
> |
|
| 574 |
|
Molecule* myMols; |
| 575 |
|
Atom** myAtoms; |
| 576 |
|
int numAtom; |
| 573 |
– |
int curIndex; |
| 577 |
|
double mtot; |
| 578 |
|
int numMol; |
| 579 |
|
int numCutoffGroups; |
| 585 |
|
double totalMass; |
| 586 |
|
|
| 587 |
|
mfact.clear(); |
| 588 |
< |
groupList.clear(); |
| 586 |
< |
groupStart.clear(); |
| 588 |
> |
FglobalGroupMembership.clear(); |
| 589 |
|
|
| 588 |
– |
//Be careful, fortran array begin at 1 |
| 589 |
– |
curIndex = 1; |
| 590 |
|
|
| 591 |
< |
myMols = info->molecules; |
| 592 |
< |
numMol = info->n_mol; |
| 593 |
< |
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(); |
| 591 |
> |
// Fix the silly fortran indexing problem |
| 592 |
> |
#ifdef IS_MPI |
| 593 |
> |
numAtom = mpiSim->getNAtomsGlobal(); |
| 594 |
|
#else |
| 595 |
< |
atomIndex = myAtoms[j]->getIndex(); |
| 595 |
> |
numAtom = n_atoms; |
| 596 |
|
#endif |
| 597 |
+ |
for (int i = 0; i < numAtom; i++) |
| 598 |
+ |
FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
| 599 |
|
|
| 600 |
< |
if(myMols[i].belongToCutoffGroup(atomIndex)) |
| 601 |
< |
continue; |
| 602 |
< |
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 |
< |
|
| 600 |
> |
myMols = info->molecules; |
| 601 |
> |
numMol = info->n_mol; |
| 602 |
> |
for(int i = 0; i < numMol; i++){ |
| 603 |
|
numCutoffGroups = myMols[i].getNCutoffGroups(); |
| 604 |
< |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
| 605 |
< |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 604 |
> |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); |
| 605 |
> |
myCutoffGroup != NULL; |
| 606 |
> |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 607 |
|
|
| 608 |
|
totalMass = myCutoffGroup->getMass(); |
| 609 |
|
|
| 610 |
< |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
| 611 |
< |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
| 610 |
> |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
| 611 |
> |
cutoffAtom != NULL; |
| 612 |
> |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
| 613 |
|
mfact.push_back(cutoffAtom->getMass()/totalMass); |
| 626 |
– |
groupList.push_back(cutoffAtom->getIndex() + 1); |
| 614 |
|
} |
| 615 |
< |
|
| 616 |
< |
groupStart.push_back(curIndex); |
| 630 |
< |
curIndex += myCutoffGroup->getNumAtom(); |
| 615 |
> |
} |
| 616 |
> |
} |
| 617 |
|
|
| 632 |
– |
}//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff)) |
| 633 |
– |
|
| 634 |
– |
}//end for(int i = 0; i < numMol; i++) |
| 635 |
– |
|
| 636 |
– |
ngroup = groupStart.size(); |
| 618 |
|
} |
