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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC vs.
Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 UTC

# Line 103 | Line 103 | namespace OpenMD {
103        const int masterNode = 0;
104  
105        if (worldRank == masterNode) {
106 <        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
106 >        MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
107 >        // MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
108   #endif                
109          SimplePreprocessor preprocessor;
110 <        preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
110 >        preprocessor.preprocess(rawMetaDataStream, filename,
111 >                                startOfMetaDataBlock, ppStream);
112                  
113   #ifdef IS_MPI            
114 <        //brocasting the stream size
114 >        //broadcasting the stream size
115          streamSize = ppStream.str().size() +1;
116 <        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
117 <        MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
116 >        MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
117 >        MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
118 >                  streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
119 >
120 >        // MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
121 >        // MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
122 >        //                       streamSize, MPI::CHAR, masterNode);
123                            
124        } else {
118 –        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
125  
126 <        //get stream size
127 <        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
126 >        MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
127 >        // MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
128  
129 +        //get stream size
130 +        MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
131 +        // MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
132          char* buf = new char[streamSize];
133          assert(buf);
134                  
135          //receive file content
136 <        MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
137 <                
136 >        MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
137 >        // MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
138 >
139          ppStream.str(buf);
140          delete [] buf;
141        }
# Line 149 | Line 159 | namespace OpenMD {
159        parser.initializeASTFactory(factory);
160        parser.setASTFactory(&factory);
161        parser.mdfile();
152 –
162        // Create a tree parser that reads information into Globals
163        MDTreeParser treeParser;
164        treeParser.initializeASTFactory(factory);
# Line 520 | Line 529 | namespace OpenMD {
529                                                      // error
530                                                      // condition:
531      
532 <    nProcessors = MPI::COMM_WORLD.Get_size();
532 >    MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);    
533 >    //nProcessors = MPI::COMM_WORLD.Get_size();
534      
535      if (nProcessors > nGlobalMols) {
536        sprintf(painCave.errMsg,
# Line 639 | Line 649 | namespace OpenMD {
649        delete myRandom;
650  
651        // Spray out this nonsense to all other processors:
652 <      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
652 >      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
653 >      // MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
654      } else {
655        
656        // Listen to your marching orders from processor 0:
657 <      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
657 >      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
658 >      // MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
659  
660      }
661      
# Line 803 | Line 815 | namespace OpenMD {
815      Molecule::AtomIterator ai;
816      Molecule::RigidBodyIterator ri;
817      Molecule::CutoffGroupIterator ci;
818 +    Molecule::BondIterator boi;
819 +    Molecule::BendIterator bei;
820 +    Molecule::TorsionIterator ti;
821 +    Molecule::InversionIterator ii;
822      Molecule::IntegrableObjectIterator  ioi;
823 <    Molecule * mol;
824 <    Atom * atom;
825 <    RigidBody * rb;
826 <    CutoffGroup * cg;
823 >    Molecule* mol;
824 >    Atom* atom;
825 >    RigidBody* rb;
826 >    CutoffGroup* cg;
827 >    Bond* bond;
828 >    Bend* bend;
829 >    Torsion* torsion;
830 >    Inversion* inversion;
831      int beginAtomIndex;
832      int beginRigidBodyIndex;
833      int beginCutoffGroupIndex;
834 +    int beginBondIndex;
835 +    int beginBendIndex;
836 +    int beginTorsionIndex;
837 +    int beginInversionIndex;
838      int nGlobalAtoms = info->getNGlobalAtoms();
839      int nGlobalRigidBodies = info->getNGlobalRigidBodies();
840      
841      beginAtomIndex = 0;
842 <    //rigidbody's index begins right after atom's
842 >    // The rigid body indices begin immediately after the atom indices:
843      beginRigidBodyIndex = info->getNGlobalAtoms();
844      beginCutoffGroupIndex = 0;
845 <
845 >    beginBondIndex = 0;
846 >    beginBendIndex = 0;
847 >    beginTorsionIndex = 0;
848 >    beginInversionIndex = 0;
849 >  
850      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
851        
852   #ifdef IS_MPI      
# Line 827 | Line 855 | namespace OpenMD {
855          // stuff to do if I own this molecule
856          mol = info->getMoleculeByGlobalIndex(i);
857  
858 <        //local index(index in DataStorge) of atom is important
859 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
858 >        // The local index(index in DataStorge) of the atom is important:
859 >        for(atom = mol->beginAtom(ai); atom != NULL;
860 >            atom = mol->nextAtom(ai)) {
861            atom->setGlobalIndex(beginAtomIndex++);
862          }
863          
# Line 837 | Line 866 | namespace OpenMD {
866            rb->setGlobalIndex(beginRigidBodyIndex++);
867          }
868          
869 <        //local index of cutoff group is trivial, it only depends on
870 <        //the order of travesing
869 >        // The local index of other objects only depends on the order
870 >        // of traversal:
871          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
872              cg = mol->nextCutoffGroup(ci)) {
873            cg->setGlobalIndex(beginCutoffGroupIndex++);
874          }        
875 +        for(bond = mol->beginBond(boi); bond != NULL;
876 +            bond = mol->nextBond(boi)) {
877 +          bond->setGlobalIndex(beginBondIndex++);
878 +        }        
879 +        for(bend = mol->beginBend(bei); bend != NULL;
880 +            bend = mol->nextBend(bei)) {
881 +          bend->setGlobalIndex(beginBendIndex++);
882 +        }        
883 +        for(torsion = mol->beginTorsion(ti); torsion != NULL;
884 +            torsion = mol->nextTorsion(ti)) {
885 +          torsion->setGlobalIndex(beginTorsionIndex++);
886 +        }        
887 +        for(inversion = mol->beginInversion(ii); inversion != NULL;
888 +            inversion = mol->nextInversion(ii)) {
889 +          inversion->setGlobalIndex(beginInversionIndex++);
890 +        }        
891          
892   #ifdef IS_MPI        
893        }  else {
# Line 855 | Line 900 | namespace OpenMD {
900          beginAtomIndex += stamp->getNAtoms();
901          beginRigidBodyIndex += stamp->getNRigidBodies();
902          beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
903 +        beginBondIndex += stamp->getNBonds();
904 +        beginBendIndex += stamp->getNBends();
905 +        beginTorsionIndex += stamp->getNTorsions();
906 +        beginInversionIndex += stamp->getNInversions();
907        }
908   #endif          
909  
# Line 862 | Line 911 | namespace OpenMD {
911  
912      //fill globalGroupMembership
913      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
914 <    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
915 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
916 <        
914 >    for(mol = info->beginMolecule(mi); mol != NULL;
915 >        mol = info->nextMolecule(mi)) {        
916 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
917 >           cg = mol->nextCutoffGroup(ci)) {        
918          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
919            globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
920          }
# Line 879 | Line 929 | namespace OpenMD {
929      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
930      // docs said we could.
931      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
932 <    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
933 <                              &tmpGroupMembership[0], nGlobalAtoms,
934 <                              MPI::INT, MPI::SUM);
932 >    MPI_Allreduce(&globalGroupMembership[0],
933 >                  &tmpGroupMembership[0], nGlobalAtoms,
934 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
935 >    // MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
936 >    //                           &tmpGroupMembership[0], nGlobalAtoms,
937 >    //                           MPI::INT, MPI::SUM);
938      info->setGlobalGroupMembership(tmpGroupMembership);
939   #else
940      info->setGlobalGroupMembership(globalGroupMembership);
# Line 905 | Line 958 | namespace OpenMD {
958   #ifdef IS_MPI
959      std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
960                                        info->getNGlobalRigidBodies(), 0);
961 <    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
962 <                              nGlobalAtoms + nGlobalRigidBodies,
963 <                              MPI::INT, MPI::SUM);
961 >    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
962 >                  nGlobalAtoms + nGlobalRigidBodies,
963 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
964 >    // MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
965 >    //                           nGlobalAtoms + nGlobalRigidBodies,
966 >    //                           MPI::INT, MPI::SUM);
967      
968      info->setGlobalMolMembership(tmpMolMembership);
969   #else
# Line 925 | Line 981 | namespace OpenMD {
981      
982   #ifdef IS_MPI
983      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
984 <    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
985 <                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
984 >    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
985 >      info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
986 >    // MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
987 >    //                           info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
988   #else
989      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
990   #endif    

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