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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 1158 by tim, Tue May 11 21:14:26 2004 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC

# Line 62 | Line 62 | SimInfo::SimInfo(){
62    useReactionField = 0;
63    useGB = 0;
64    useEAM = 0;
65 <  
65 >  useThermInt = 0;
66 >
67    haveCutoffGroups = false;
68  
69    excludes = Exclude::Instance();
# Line 453 | Line 454 | void SimInfo::refreshSim(){
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);
# Line 591 | Line 592 | void getFortranGroupArray(SimInfo* info, vector<double
592    myMols = info->molecules;
593    numMol = info->n_mol;
594    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();
603 #else
604      atomIndex = myAtoms[j]->getIndex();
605 #endif
606
607      if(myMols[i].belongToCutoffGroup(atomIndex))
608        continue;
609      else{
610        mfact.push_back(myAtoms[j]->getMass());
611        groupList.push_back(myAtoms[j]->getIndex() + 1);
612        groupStart.push_back(curIndex++);  
613      }
614    }
615      
595      numCutoffGroups = myMols[i].getNCutoffGroups();
596      for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
597                                                    myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
# Line 631 | Line 610 | void getFortranGroupArray(SimInfo* info, vector<double
610      }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
611  
612    }//end for(int i  = 0; i < numMol; i++)
613 <  
614 <  ngroup = groupStart.size();
613 >
614 >
615 >  //The last cutoff group need more element to indicate the end of the cutoff
616 >  groupStart.push_back(curIndex);
617 >  ngroup = groupStart.size() - 1;
618   }

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