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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1810 by gezelter, Thu Nov 8 14:23:43 2012 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

# Line 1 | Line 1
1   /*
2 < * copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
5   * non-exclusive, royalty free, license to use, modify and
# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 44 | Line 44
44   * @file SimCreator.cpp
45   * @author tlin
46   * @date 11/03/2004
47 – * @time 13:51am
47   * @version 1.0
48   */
49 +
50 + #ifdef IS_MPI
51 + #include "mpi.h"
52 + #include "math/ParallelRandNumGen.hpp"
53 + #endif
54 +
55   #include <exception>
56   #include <iostream>
57   #include <sstream>
# Line 84 | Line 89
89   #include "types/FixedChargeAdapter.hpp"
90   #include "types/FluctuatingChargeAdapter.hpp"
91  
87 – #ifdef IS_MPI
88 – #include "mpi.h"
89 – #include "math/ParallelRandNumGen.hpp"
90 – #endif
92  
93   namespace OpenMD {
94    
# Line 102 | 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,
111 <                                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())),
118 <                              streamSize, MPI::CHAR, masterNode);
119 <                
116 >        MPI_Bcast(&streamSize, 1, MPI_LONG, 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 {
125  
126 <        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, 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::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
131 <
130 >        MPI_Bcast(&streamSize, 1, MPI_LONG, 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;
133 –
141        }
142   #endif            
143        // Create a scanner that reads from the input stream
# Line 152 | Line 159 | namespace OpenMD {
159        parser.initializeASTFactory(factory);
160        parser.setASTFactory(&factory);
161        parser.mdfile();
155 –
162        // Create a tree parser that reads information into Globals
163        MDTreeParser treeParser;
164        treeParser.initializeASTFactory(factory);
# Line 256 | Line 262 | namespace OpenMD {
262      int metaDataBlockStart = -1;
263      int metaDataBlockEnd = -1;
264      int i, j;
265 <    streamoff mdOffset(0);
265 >    streamoff mdOffset;
266      int mdFileVersion;
267  
268      // Create a string for embedding the version information in the MetaData
# Line 515 | Line 521 | namespace OpenMD {
521    
522   #ifdef IS_MPI
523    void SimCreator::divideMolecules(SimInfo *info) {
518 –    RealType numerator;
519 –    RealType denominator;
520 –    RealType precast;
521 –    RealType x;
522 –    RealType y;
524      RealType a;
524 –    int old_atoms;
525 –    int add_atoms;
526 –    int new_atoms;
527 –    int nTarget;
528 –    int done;
529 –    int i;
530 –    int loops;
531 –    int which_proc;
525      int nProcessors;
526      std::vector<int> atomsPerProc;
527      int nGlobalMols = info->getNGlobalMolecules();
528 <    std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
528 >    std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
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 543 | Line 539 | namespace OpenMD {
539                "\tthe number of molecules.  This will not result in a \n"
540                "\tusable division of atoms for force decomposition.\n"
541                "\tEither try a smaller number of processors, or run the\n"
542 <              "\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
542 >              "\tsingle-processor version of OpenMD.\n", nProcessors,
543 >              nGlobalMols);
544        
545        painCave.isFatal = 1;
546        simError();
547      }
548      
552 –    int seedValue;
549      Globals * simParams = info->getSimParams();
550 <    SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
550 >    SeqRandNumGen* myRandom; //divide labor does not need Parallel
551 >                             //random number generator
552      if (simParams->haveSeed()) {
553 <      seedValue = simParams->getSeed();
553 >      int seedValue = simParams->getSeed();
554        myRandom = new SeqRandNumGen(seedValue);
555      }else {
556        myRandom = new SeqRandNumGen();
# Line 566 | Line 563 | namespace OpenMD {
563      atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
564      
565      if (worldRank == 0) {
566 <      numerator = info->getNGlobalAtoms();
567 <      denominator = nProcessors;
568 <      precast = numerator / denominator;
569 <      nTarget = (int)(precast + 0.5);
566 >      RealType numerator = info->getNGlobalAtoms();
567 >      RealType denominator = nProcessors;
568 >      RealType precast = numerator / denominator;
569 >      int nTarget = (int)(precast + 0.5);
570        
571 <      for(i = 0; i < nGlobalMols; i++) {
571 >      for(int i = 0; i < nGlobalMols; i++) {
572  
573 <        done = 0;
574 <        loops = 0;
573 >        int done = 0;
574 >        int loops = 0;
575          
576          while (!done) {
577            loops++;
578            
579            // Pick a processor at random
580            
581 <          which_proc = (int) (myRandom->rand() * nProcessors);
581 >          int which_proc = (int) (myRandom->rand() * nProcessors);
582            
583            //get the molecule stamp first
584            int stampId = info->getMoleculeStampId(i);
585            MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
586            
587            // How many atoms does this processor have so far?
588 <          old_atoms = atomsPerProc[which_proc];
589 <          add_atoms = moleculeStamp->getNAtoms();
590 <          new_atoms = old_atoms + add_atoms;
588 >          int old_atoms = atomsPerProc[which_proc];
589 >          int add_atoms = moleculeStamp->getNAtoms();
590 >          int new_atoms = old_atoms + add_atoms;
591            
592            // If we've been through this loop too many times, we need
593            // to just give up and assign the molecule to this processor
# Line 634 | Line 631 | namespace OpenMD {
631            //           Pacc(x) = exp(- a * x)
632            // where a = penalty / (average atoms per molecule)
633            
634 <          x = (RealType)(new_atoms - nTarget);
635 <          y = myRandom->rand();
634 >          RealType x = (RealType)(new_atoms - nTarget);
635 >          RealType y = myRandom->rand();
636            
637            if (y < exp(- a * x)) {
638              molToProcMap[i] = which_proc;
# Line 652 | 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 704 | Line 703 | namespace OpenMD {
703      set<AtomType*>::iterator i;
704      bool hasDirectionalAtoms = false;
705      bool hasFixedCharge = false;
706 <    bool hasMultipoles = false;    
706 >    bool hasDipoles = false;    
707 >    bool hasQuadrupoles = false;    
708      bool hasPolarizable = false;    
709      bool hasFluctuatingCharge = false;    
710      bool hasMetallic = false;
# Line 726 | Line 726 | namespace OpenMD {
726        if (da.isDirectional()){
727          hasDirectionalAtoms = true;
728        }
729 <      if (ma.isMultipole()){
730 <        hasMultipoles = true;
729 >      if (ma.isDipole()){
730 >        hasDipoles = true;
731        }
732 +      if (ma.isQuadrupole()){
733 +        hasQuadrupoles = true;
734 +      }
735        if (ea.isEAM() || sca.isSuttonChen()){
736          hasMetallic = true;
737        }
# Line 752 | Line 755 | namespace OpenMD {
755          storageLayout |= DataStorage::dslTorque;
756        }
757      }
758 <    if (hasMultipoles) {
759 <      storageLayout |= DataStorage::dslElectroFrame;
758 >    if (hasDipoles) {
759 >      storageLayout |= DataStorage::dslDipole;
760      }
761 +    if (hasQuadrupoles) {
762 +      storageLayout |= DataStorage::dslQuadrupole;
763 +    }
764      if (hasFixedCharge || hasFluctuatingCharge) {
765        storageLayout |= DataStorage::dslSkippedCharge;
766      }
# Line 789 | Line 795 | namespace OpenMD {
795        }
796      }
797  
798 <    if (simParams->getOutputElectricField()) {
798 >    if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
799        storageLayout |= DataStorage::dslElectricField;
800      }
801 +
802      if (simParams->getOutputFluctuatingCharges()) {
803        storageLayout |= DataStorage::dslFlucQPosition;
804        storageLayout |= DataStorage::dslFlucQVelocity;
805        storageLayout |= DataStorage::dslFlucQForce;
806      }
807  
808 +    info->setStorageLayout(storageLayout);
809 +
810      return storageLayout;
811    }
812  
# Line 806 | 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 830 | 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 840 | 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 858 | 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 865 | 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 882 | 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 908 | 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 928 | 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    
# Line 960 | Line 1015 | namespace OpenMD {
1015    }
1016    
1017    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
1018 <
1018 >    
1019      DumpReader reader(info, mdFileName);
1020      int nframes = reader.getNFrames();
1021 <
1021 >    
1022      if (nframes > 0) {
1023        reader.readFrame(nframes - 1);
1024      } else {

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