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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1214 by gezelter, Tue Jun 1 18:42:58 2004 UTC vs.
Revision 1229 by gezelter, Thu Jun 3 20:02:25 2004 UTC

# Line 516 | Line 516 | void SimSetup::makeMolecules(void){
516          myCutoffGroup = new CutoffGroup();
517          
518   #ifdef IS_MPI
519 <        myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
519 >        myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
520   #else
521 <        myCutoffGroup->setGlobalIndex(j + groupOffset);
521 >        myCutoffGroup->setGlobalIndex(groupOffset);
522   #endif
523          
524          for (int cg = 0; cg < nMembers; cg++) {
# Line 531 | Line 531 | void SimSetup::makeMolecules(void){
531  
532   #ifdef IS_MPI
533            globalID = info[k].atoms[tempI]->getGlobalIndex();
534 <          info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
534 >          info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
535   #else
536            globalID = info[k].atoms[tempI]->getIndex();
537 <          info[k].globalGroupMembership[globalID] = j + groupOffset;
538 < #endif
539 <          
540 <
541 <          
542 <          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
543 <          
537 >          info[k].globalGroupMembership[globalID] = groupOffset;
538 > #endif                    
539 >          myCutoffGroup->addAtom(info[k].atoms[tempI]);
540            cutoffAtomSet.insert(tempI);
541          }
542          
# Line 549 | Line 545 | void SimSetup::makeMolecules(void){
545  
546        }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
547        
552 –      //creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
548        
549 +      // create a cutoff group for every atom in current molecule which
550 +      // does not belong to cutoffgroup defined at mdl file
551 +      
552        for(j = 0; j < molInfo.nAtoms; j++){
553          
554          if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
555            myCutoffGroup = new CutoffGroup();
556            myCutoffGroup->addAtom(molInfo.myAtoms[j]);
557 <
557 >          
558   #ifdef IS_MPI
559 <          myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
559 >          myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
560            globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
561 <          info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
561 >          info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
562   #else
563 <          myCutoffGroup->setGlobalIndex(j + groupOffset);
563 >          myCutoffGroup->setGlobalIndex(groupOffset);
564            globalID = info[k].atoms[atomOffset + j]->getIndex();
565 <          info[k].globalGroupMembership[globalID] = j+groupOffset;
565 >          info[k].globalGroupMembership[globalID] = groupOffset;
566   #endif
567            molInfo.myCutoffGroups.push_back(myCutoffGroup);
568            groupOffset++;
569 <        }
572 <          
569 >        }          
570        }
571  
572        // After this is all set up, scan through the atoms to

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