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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 1976 by gezelter, Wed Mar 12 20:01:15 2014 UTC

# Line 64 | Line 64
64   #include "brains/ForceField.hpp"
65   #include "utils/simError.h"
66   #include "utils/StringUtils.hpp"
67 + #include "utils/Revision.hpp"
68   #include "math/SeqRandNumGen.hpp"
69   #include "mdParser/MDLexer.hpp"
70   #include "mdParser/MDParser.hpp"
# Line 103 | Line 104 | namespace OpenMD {
104        const int masterNode = 0;
105  
106        if (worldRank == masterNode) {
107 <        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
107 >        MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
108 >        // MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
109   #endif                
110          SimplePreprocessor preprocessor;
111 <        preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
111 >        preprocessor.preprocess(rawMetaDataStream, filename,
112 >                                startOfMetaDataBlock, ppStream);
113                  
114   #ifdef IS_MPI            
115 <        //brocasting the stream size
115 >        //broadcasting the stream size
116          streamSize = ppStream.str().size() +1;
117 <        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
118 <        MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
117 >        MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
118 >        MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
119 >                  streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
120 >
121 >        // MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
122 >        // MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
123 >        //                       streamSize, MPI::CHAR, masterNode);
124                            
125        } else {
118 –        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
126  
127 <        //get stream size
128 <        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
127 >        MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
128 >        // MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
129  
130 +        //get stream size
131 +        MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
132 +        // MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
133          char* buf = new char[streamSize];
134          assert(buf);
135                  
136          //receive file content
137 <        MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
138 <                
137 >        MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
138 >        // MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
139 >
140          ppStream.str(buf);
141          delete [] buf;
142        }
# Line 149 | Line 160 | namespace OpenMD {
160        parser.initializeASTFactory(factory);
161        parser.setASTFactory(&factory);
162        parser.mdfile();
152 –
163        // Create a tree parser that reads information into Globals
164        MDTreeParser treeParser;
165        treeParser.initializeASTFactory(factory);
# Line 263 | Line 273 | namespace OpenMD {
273      version.append(".");
274      version.append(OPENMD_VERSION_MINOR);
275  
276 <    std::string svnrev;
276 >    std::string svnrev(g_REVISION, strnlen(g_REVISION, 20));
277      //convert a macro from compiler to a string in c++
278 <    STR_DEFINE(svnrev, SVN_REV );
278 >    // STR_DEFINE(svnrev, SVN_REV );
279      version.append(" Revision: ");
280      // If there's no SVN revision, just call this the RELEASE revision.
281      if (!svnrev.empty()) {
# Line 520 | Line 530 | namespace OpenMD {
530                                                      // error
531                                                      // condition:
532      
533 <    nProcessors = MPI::COMM_WORLD.Get_size();
533 >    MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);    
534 >    //nProcessors = MPI::COMM_WORLD.Get_size();
535      
536      if (nProcessors > nGlobalMols) {
537        sprintf(painCave.errMsg,
# Line 639 | Line 650 | namespace OpenMD {
650        delete myRandom;
651  
652        // Spray out this nonsense to all other processors:
653 <      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
653 >      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
654 >      // MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
655      } else {
656        
657        // Listen to your marching orders from processor 0:
658 <      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
658 >      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
659 >      // MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
660  
661      }
662      
# Line 803 | Line 816 | namespace OpenMD {
816      Molecule::AtomIterator ai;
817      Molecule::RigidBodyIterator ri;
818      Molecule::CutoffGroupIterator ci;
819 +    Molecule::BondIterator boi;
820 +    Molecule::BendIterator bei;
821 +    Molecule::TorsionIterator ti;
822 +    Molecule::InversionIterator ii;
823      Molecule::IntegrableObjectIterator  ioi;
824 <    Molecule * mol;
825 <    Atom * atom;
826 <    RigidBody * rb;
827 <    CutoffGroup * cg;
824 >    Molecule* mol;
825 >    Atom* atom;
826 >    RigidBody* rb;
827 >    CutoffGroup* cg;
828 >    Bond* bond;
829 >    Bend* bend;
830 >    Torsion* torsion;
831 >    Inversion* inversion;
832      int beginAtomIndex;
833      int beginRigidBodyIndex;
834      int beginCutoffGroupIndex;
835 +    int beginBondIndex;
836 +    int beginBendIndex;
837 +    int beginTorsionIndex;
838 +    int beginInversionIndex;
839      int nGlobalAtoms = info->getNGlobalAtoms();
840      int nGlobalRigidBodies = info->getNGlobalRigidBodies();
841      
842      beginAtomIndex = 0;
843 <    //rigidbody's index begins right after atom's
843 >    // The rigid body indices begin immediately after the atom indices:
844      beginRigidBodyIndex = info->getNGlobalAtoms();
845      beginCutoffGroupIndex = 0;
846 <
846 >    beginBondIndex = 0;
847 >    beginBendIndex = 0;
848 >    beginTorsionIndex = 0;
849 >    beginInversionIndex = 0;
850 >  
851      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
852        
853   #ifdef IS_MPI      
# Line 827 | Line 856 | namespace OpenMD {
856          // stuff to do if I own this molecule
857          mol = info->getMoleculeByGlobalIndex(i);
858  
859 <        //local index(index in DataStorge) of atom is important
860 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
859 >        // The local index(index in DataStorge) of the atom is important:
860 >        for(atom = mol->beginAtom(ai); atom != NULL;
861 >            atom = mol->nextAtom(ai)) {
862            atom->setGlobalIndex(beginAtomIndex++);
863          }
864          
# Line 837 | Line 867 | namespace OpenMD {
867            rb->setGlobalIndex(beginRigidBodyIndex++);
868          }
869          
870 <        //local index of cutoff group is trivial, it only depends on
871 <        //the order of travesing
870 >        // The local index of other objects only depends on the order
871 >        // of traversal:
872          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
873              cg = mol->nextCutoffGroup(ci)) {
874            cg->setGlobalIndex(beginCutoffGroupIndex++);
875          }        
876 +        for(bond = mol->beginBond(boi); bond != NULL;
877 +            bond = mol->nextBond(boi)) {
878 +          bond->setGlobalIndex(beginBondIndex++);
879 +        }        
880 +        for(bend = mol->beginBend(bei); bend != NULL;
881 +            bend = mol->nextBend(bei)) {
882 +          bend->setGlobalIndex(beginBendIndex++);
883 +        }        
884 +        for(torsion = mol->beginTorsion(ti); torsion != NULL;
885 +            torsion = mol->nextTorsion(ti)) {
886 +          torsion->setGlobalIndex(beginTorsionIndex++);
887 +        }        
888 +        for(inversion = mol->beginInversion(ii); inversion != NULL;
889 +            inversion = mol->nextInversion(ii)) {
890 +          inversion->setGlobalIndex(beginInversionIndex++);
891 +        }        
892          
893   #ifdef IS_MPI        
894        }  else {
# Line 855 | Line 901 | namespace OpenMD {
901          beginAtomIndex += stamp->getNAtoms();
902          beginRigidBodyIndex += stamp->getNRigidBodies();
903          beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
904 +        beginBondIndex += stamp->getNBonds();
905 +        beginBendIndex += stamp->getNBends();
906 +        beginTorsionIndex += stamp->getNTorsions();
907 +        beginInversionIndex += stamp->getNInversions();
908        }
909   #endif          
910  
# Line 862 | Line 912 | namespace OpenMD {
912  
913      //fill globalGroupMembership
914      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
915 <    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
916 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
917 <        
915 >    for(mol = info->beginMolecule(mi); mol != NULL;
916 >        mol = info->nextMolecule(mi)) {        
917 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
918 >           cg = mol->nextCutoffGroup(ci)) {        
919          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
920            globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
921          }
# Line 879 | Line 930 | namespace OpenMD {
930      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
931      // docs said we could.
932      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
933 <    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
934 <                              &tmpGroupMembership[0], nGlobalAtoms,
935 <                              MPI::INT, MPI::SUM);
933 >    MPI_Allreduce(&globalGroupMembership[0],
934 >                  &tmpGroupMembership[0], nGlobalAtoms,
935 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
936 >    // MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
937 >    //                           &tmpGroupMembership[0], nGlobalAtoms,
938 >    //                           MPI::INT, MPI::SUM);
939      info->setGlobalGroupMembership(tmpGroupMembership);
940   #else
941      info->setGlobalGroupMembership(globalGroupMembership);
# Line 905 | Line 959 | namespace OpenMD {
959   #ifdef IS_MPI
960      std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
961                                        info->getNGlobalRigidBodies(), 0);
962 <    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
963 <                              nGlobalAtoms + nGlobalRigidBodies,
964 <                              MPI::INT, MPI::SUM);
962 >    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
963 >                  nGlobalAtoms + nGlobalRigidBodies,
964 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
965 >    // MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
966 >    //                           nGlobalAtoms + nGlobalRigidBodies,
967 >    //                           MPI::INT, MPI::SUM);
968      
969      info->setGlobalMolMembership(tmpMolMembership);
970   #else
# Line 925 | Line 982 | namespace OpenMD {
982      
983   #ifdef IS_MPI
984      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
985 <    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
986 <                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
985 >    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
986 >      info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
987 >    // MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
988 >    //                           info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
989   #else
990      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
991   #endif    

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