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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1801 by gezelter, Mon Oct 1 18:21:15 2012 UTC vs.
Revision 1802 by gezelter, Wed Oct 3 14:07:28 2012 UTC

# Line 787 | Line 787 | namespace OpenMD {
787      int beginRigidBodyIndex;
788      int beginCutoffGroupIndex;
789      int nGlobalAtoms = info->getNGlobalAtoms();
790 +    int nGlobalRigidBodies = info->getNGlobalRigidBodies();
791      
792      beginAtomIndex = 0;
793      //rigidbody's index begins right after atom's
# Line 862 | Line 863 | namespace OpenMD {
863   #endif
864      
865      //fill molMembership
866 <    std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
866 >    std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
867 >                                         info->getNGlobalRigidBodies(), 0);
868      
869 <    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
869 >    for(mol = info->beginMolecule(mi); mol != NULL;
870 >        mol = info->nextMolecule(mi)) {
871        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
872          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
873        }
874 +      for (rb = mol->beginRigidBody(ri); rb != NULL;
875 +           rb = mol->nextRigidBody(ri)) {
876 +        globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
877 +      }
878      }
879      
880   #ifdef IS_MPI
881 <    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
881 >    std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
882 >                                      info->getNGlobalRigidBodies(), 0);
883      MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
884 <                              nGlobalAtoms,
884 >                              nGlobalAtoms + nGlobalRigidBodies,
885                                MPI::INT, MPI::SUM);
886      
887      info->setGlobalMolMembership(tmpMolMembership);
# Line 885 | Line 893 | namespace OpenMD {
893      // here the molecules are listed by their global indices.
894  
895      std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
896 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
896 >    for (mol = info->beginMolecule(mi); mol != NULL;
897 >         mol = info->nextMolecule(mi)) {
898        nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
899      }
900      
# Line 906 | Line 915 | namespace OpenMD {
915      }
916      
917      std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
918 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
918 >    for (mol = info->beginMolecule(mi); mol != NULL;
919 >         mol = info->nextMolecule(mi)) {
920        int myGlobalIndex = mol->getGlobalIndex();
921        int globalIO = startingIOIndexForMol[myGlobalIndex];
922        for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;

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