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root/OpenMD/branches/development/src/brains/SimCreator.cpp
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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs.
Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

# Line 609 | Line 609 | namespace OpenMD {
609   #endif
610          
611          stampId = info->getMoleculeStampId(i);
612 <        Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
613 <                                                   stampId, i, info->getLocalIndexManager());
612 >        Molecule * mol = molCreator.createMolecule(info->getForceField(),
613 >                                                   info->getMoleculeStamp(stampId),
614 >                                                   stampId, i,
615 >                                                   info->getLocalIndexManager());
616          
617          info->addMolecule(mol);
618          
# Line 637 | Line 639 | namespace OpenMD {
639      int beginRigidBodyIndex;
640      int beginCutoffGroupIndex;
641      int nGlobalAtoms = info->getNGlobalAtoms();
640 –
641 –    /**@todo fixme */
642 – #ifndef IS_MPI
642      
643      beginAtomIndex = 0;
644      beginRigidBodyIndex = 0;
645      beginCutoffGroupIndex = 0;
646 <    
647 < #else
649 <    
650 <    int nproc;
651 <    int myNode;
652 <    
653 <    myNode = worldRank;
654 <    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
655 <    
656 <    std::vector < int > tmpAtomsInProc(nproc, 0);
657 <    std::vector < int > tmpRigidBodiesInProc(nproc, 0);
658 <    std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
659 <    std::vector < int > NumAtomsInProc(nproc, 0);
660 <    std::vector < int > NumRigidBodiesInProc(nproc, 0);
661 <    std::vector < int > NumCutoffGroupsInProc(nproc, 0);
662 <    
663 <    tmpAtomsInProc[myNode] = info->getNAtoms();
664 <    tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
665 <    tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
666 <    
667 <    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
668 <    MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
669 <                  MPI_SUM, MPI_COMM_WORLD);
670 <    MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
671 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
672 <    MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
673 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
674 <    
675 <    beginAtomIndex = 0;
676 <    beginRigidBodyIndex = 0;
677 <    beginCutoffGroupIndex = 0;
678 <    
679 <    for(int i = 0; i < myNode; i++) {
680 <      beginAtomIndex += NumAtomsInProc[i];
681 <      beginRigidBodyIndex += NumRigidBodiesInProc[i];
682 <      beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
683 <    }
684 <    
685 < #endif
686 <    
687 <    //rigidbody's index begins right after atom's
688 <    beginRigidBodyIndex += info->getNGlobalAtoms();
689 <    
690 <    for(mol = info->beginMolecule(mi); mol != NULL;
691 <        mol = info->nextMolecule(mi)) {
646 >
647 >    for(int i = 0; i < info->getNGlobalMolecules(); i++) {
648        
649 <      //local index(index in DataStorge) of atom is important
650 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
651 <        atom->setGlobalIndex(beginAtomIndex++);
649 > #ifdef IS_MPI      
650 >      if (info->getMolToProc(i) == worldRank) {
651 > #endif        
652 >        // stuff to do if I own this molecule
653 >        mol = info->getMoleculeByGlobalIndex(i);
654 >
655 >        //local index(index in DataStorge) of atom is important
656 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
657 >          atom->setGlobalIndex(beginAtomIndex++);
658 >        }
659 >        
660 >        for(rb = mol->beginRigidBody(ri); rb != NULL;
661 >            rb = mol->nextRigidBody(ri)) {
662 >          rb->setGlobalIndex(beginRigidBodyIndex++);
663 >        }
664 >        
665 >        //local index of cutoff group is trivial, it only depends on
666 >        //the order of travesing
667 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
668 >            cg = mol->nextCutoffGroup(ci)) {
669 >          cg->setGlobalIndex(beginCutoffGroupIndex++);
670 >        }        
671 >        
672 > #ifdef IS_MPI        
673 >      }  else {
674 >
675 >        // stuff to do if I don't own this molecule
676 >        
677 >        int stampId = info->getMoleculeStampId(i);
678 >        MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
679 >
680 >        beginAtomIndex += stamp->getNAtoms();
681 >        beginRigidBodyIndex += stamp->getNRigidBodies();
682 >        beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
683        }
684 <      
685 <      for(rb = mol->beginRigidBody(ri); rb != NULL;
686 <          rb = mol->nextRigidBody(ri)) {
687 <        rb->setGlobalIndex(beginRigidBodyIndex++);
701 <      }
702 <      
703 <      //local index of cutoff group is trivial, it only depends on the order of travesing
704 <      for(cg = mol->beginCutoffGroup(ci); cg != NULL;
705 <          cg = mol->nextCutoffGroup(ci)) {
706 <        cg->setGlobalIndex(beginCutoffGroupIndex++);
707 <      }
708 <    }
709 <    
684 > #endif          
685 >
686 >    } //end for(int i=0)  
687 >
688      //fill globalGroupMembership
689      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
690      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
# Line 788 | Line 766 | namespace OpenMD {
766          globalIO++;
767        }
768      }
769 <    
769 >      
770      info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
771      
772    }

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