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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC vs.
Revision 1880 by gezelter, Mon Jun 17 18:28:30 2013 UTC

# 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   #include <exception>
# Line 100 | Line 99 | namespace OpenMD {
99   #ifdef IS_MPI            
100        int streamSize;
101        const int masterNode = 0;
102 <      int commStatus;
102 >
103        if (worldRank == masterNode) {
104 <        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
104 >        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
105   #endif                
106          SimplePreprocessor preprocessor;
107          preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
# Line 110 | Line 109 | namespace OpenMD {
109   #ifdef IS_MPI            
110          //brocasting the stream size
111          streamSize = ppStream.str().size() +1;
112 <        commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);                  
113 <
114 <        commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
116 <            
117 <                
112 >        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
113 >        MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
114 >                          
115        } else {
116 +        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
117  
120 –        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121 –
118          //get stream size
119 <        commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
119 >        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
120  
121          char* buf = new char[streamSize];
122          assert(buf);
123                  
124          //receive file content
125 <        commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
125 >        MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
126                  
127          ppStream.str(buf);
128          delete [] buf;
133 –
129        }
130   #endif            
131        // Create a scanner that reads from the input stream
# Line 255 | Line 250 | namespace OpenMD {
250      std::string mdRawData;
251      int metaDataBlockStart = -1;
252      int metaDataBlockEnd = -1;
253 <    int i;
254 <    streamoff mdOffset(0);
253 >    int i, j;
254 >    streamoff mdOffset;
255      int mdFileVersion;
256  
257 +    // Create a string for embedding the version information in the MetaData
258 +    std::string version;
259 +    version.assign("## Last run using OpenMD Version: ");
260 +    version.append(OPENMD_VERSION_MAJOR);
261 +    version.append(".");
262 +    version.append(OPENMD_VERSION_MINOR);
263  
264 +    std::string svnrev;
265 +    //convert a macro from compiler to a string in c++
266 +    STR_DEFINE(svnrev, SVN_REV );
267 +    version.append(" Revision: ");
268 +    // If there's no SVN revision, just call this the RELEASE revision.
269 +    if (!svnrev.empty()) {
270 +      version.append(svnrev);
271 +    } else {
272 +      version.append("RELEASE");
273 +    }
274 +  
275   #ifdef IS_MPI            
276      const int masterNode = 0;
277      if (worldRank == masterNode) {
# Line 354 | Line 366 | namespace OpenMD {
366  
367        mdRawData.clear();
368  
369 +      bool foundVersion = false;
370 +
371        for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
372          mdFile_.getline(buffer, bufferSize);
373 <        mdRawData += buffer;
373 >        std::string line = trimLeftCopy(buffer);
374 >        j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
375 >        if (static_cast<size_t>(j) != string::npos) {
376 >          foundVersion = true;
377 >          mdRawData += version;
378 >        } else {
379 >          mdRawData += buffer;
380 >        }
381          mdRawData += "\n";
382        }
383 <
383 >      
384 >      if (!foundVersion) mdRawData += version + "\n";
385 >      
386        mdFile_.close();
387  
388   #ifdef IS_MPI
# Line 487 | Line 510 | namespace OpenMD {
510    
511   #ifdef IS_MPI
512    void SimCreator::divideMolecules(SimInfo *info) {
490 –    RealType numerator;
491 –    RealType denominator;
492 –    RealType precast;
493 –    RealType x;
494 –    RealType y;
513      RealType a;
496 –    int old_atoms;
497 –    int add_atoms;
498 –    int new_atoms;
499 –    int nTarget;
500 –    int done;
501 –    int i;
502 –    int j;
503 –    int loops;
504 –    int which_proc;
514      int nProcessors;
515      std::vector<int> atomsPerProc;
516      int nGlobalMols = info->getNGlobalMolecules();
517 <    std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
517 >    std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
518 >                                                    // error
519 >                                                    // condition:
520      
521 <    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
521 >    nProcessors = MPI::COMM_WORLD.Get_size();
522      
523      if (nProcessors > nGlobalMols) {
524        sprintf(painCave.errMsg,
# Line 516 | Line 527 | namespace OpenMD {
527                "\tthe number of molecules.  This will not result in a \n"
528                "\tusable division of atoms for force decomposition.\n"
529                "\tEither try a smaller number of processors, or run the\n"
530 <              "\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
530 >              "\tsingle-processor version of OpenMD.\n", nProcessors,
531 >              nGlobalMols);
532        
533        painCave.isFatal = 1;
534        simError();
535      }
536      
525 –    int seedValue;
537      Globals * simParams = info->getSimParams();
538 <    SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
538 >    SeqRandNumGen* myRandom; //divide labor does not need Parallel
539 >                             //random number generator
540      if (simParams->haveSeed()) {
541 <      seedValue = simParams->getSeed();
541 >      int seedValue = simParams->getSeed();
542        myRandom = new SeqRandNumGen(seedValue);
543      }else {
544        myRandom = new SeqRandNumGen();
# Line 539 | Line 551 | namespace OpenMD {
551      atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
552      
553      if (worldRank == 0) {
554 <      numerator = info->getNGlobalAtoms();
555 <      denominator = nProcessors;
556 <      precast = numerator / denominator;
557 <      nTarget = (int)(precast + 0.5);
554 >      RealType numerator = info->getNGlobalAtoms();
555 >      RealType denominator = nProcessors;
556 >      RealType precast = numerator / denominator;
557 >      int nTarget = (int)(precast + 0.5);
558        
559 <      for(i = 0; i < nGlobalMols; i++) {
560 <        done = 0;
561 <        loops = 0;
559 >      for(int i = 0; i < nGlobalMols; i++) {
560 >
561 >        int done = 0;
562 >        int loops = 0;
563          
564          while (!done) {
565            loops++;
566            
567            // Pick a processor at random
568            
569 <          which_proc = (int) (myRandom->rand() * nProcessors);
569 >          int which_proc = (int) (myRandom->rand() * nProcessors);
570            
571            //get the molecule stamp first
572            int stampId = info->getMoleculeStampId(i);
573            MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
574            
575            // How many atoms does this processor have so far?
576 <          old_atoms = atomsPerProc[which_proc];
577 <          add_atoms = moleculeStamp->getNAtoms();
578 <          new_atoms = old_atoms + add_atoms;
576 >          int old_atoms = atomsPerProc[which_proc];
577 >          int add_atoms = moleculeStamp->getNAtoms();
578 >          int new_atoms = old_atoms + add_atoms;
579            
580            // If we've been through this loop too many times, we need
581            // to just give up and assign the molecule to this processor
582            // and be done with it.
583            
584            if (loops > 100) {
585 +
586              sprintf(painCave.errMsg,
587 <                    "I've tried 100 times to assign molecule %d to a "
588 <                    " processor, but can't find a good spot.\n"
589 <                    "I'm assigning it at random to processor %d.\n",
587 >                    "There have been 100 attempts to assign molecule %d to an\n"
588 >                    "\tunderworked processor, but there's no good place to\n"
589 >                    "\tleave it.  OpenMD is assigning it at random to processor %d.\n",
590                      i, which_proc);
591 <            
591 >          
592              painCave.isFatal = 0;
593 +            painCave.severity = OPENMD_INFO;
594              simError();
595              
596              molToProcMap[i] = which_proc;
# Line 604 | Line 619 | namespace OpenMD {
619            //           Pacc(x) = exp(- a * x)
620            // where a = penalty / (average atoms per molecule)
621            
622 <          x = (RealType)(new_atoms - nTarget);
623 <          y = myRandom->rand();
622 >          RealType x = (RealType)(new_atoms - nTarget);
623 >          RealType y = myRandom->rand();
624            
625            if (y < exp(- a * x)) {
626              molToProcMap[i] = which_proc;
# Line 620 | Line 635 | namespace OpenMD {
635        }
636        
637        delete myRandom;
638 <      
638 >
639        // Spray out this nonsense to all other processors:
640 <      
626 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
640 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
641      } else {
642        
643        // Listen to your marching orders from processor 0:
644 <      
645 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
644 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
645 >
646      }
647      
648      info->setMolToProcMap(molToProcMap);
# Line 675 | Line 689 | namespace OpenMD {
689      set<AtomType*>::iterator i;
690      bool hasDirectionalAtoms = false;
691      bool hasFixedCharge = false;
692 <    bool hasMultipoles = false;    
692 >    bool hasDipoles = false;    
693 >    bool hasQuadrupoles = false;    
694      bool hasPolarizable = false;    
695      bool hasFluctuatingCharge = false;    
696      bool hasMetallic = false;
# Line 697 | Line 712 | namespace OpenMD {
712        if (da.isDirectional()){
713          hasDirectionalAtoms = true;
714        }
715 <      if (ma.isMultipole()){
716 <        hasMultipoles = true;
715 >      if (ma.isDipole()){
716 >        hasDipoles = true;
717        }
718 +      if (ma.isQuadrupole()){
719 +        hasQuadrupoles = true;
720 +      }
721        if (ea.isEAM() || sca.isSuttonChen()){
722          hasMetallic = true;
723        }
# Line 723 | Line 741 | namespace OpenMD {
741          storageLayout |= DataStorage::dslTorque;
742        }
743      }
744 <    if (hasMultipoles) {
745 <      storageLayout |= DataStorage::dslElectroFrame;
744 >    if (hasDipoles) {
745 >      storageLayout |= DataStorage::dslDipole;
746      }
747 +    if (hasQuadrupoles) {
748 +      storageLayout |= DataStorage::dslQuadrupole;
749 +    }
750      if (hasFixedCharge || hasFluctuatingCharge) {
751        storageLayout |= DataStorage::dslSkippedCharge;
752      }
# Line 760 | Line 781 | namespace OpenMD {
781        }
782      }
783  
784 <    if (simParams->getOutputElectricField()) {
784 >    if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
785        storageLayout |= DataStorage::dslElectricField;
786      }
787 +
788      if (simParams->getOutputFluctuatingCharges()) {
789        storageLayout |= DataStorage::dslFlucQPosition;
790        storageLayout |= DataStorage::dslFlucQVelocity;
791        storageLayout |= DataStorage::dslFlucQForce;
792      }
793  
794 +    info->setStorageLayout(storageLayout);
795 +
796      return storageLayout;
797    }
798  
# Line 786 | Line 810 | namespace OpenMD {
810      int beginRigidBodyIndex;
811      int beginCutoffGroupIndex;
812      int nGlobalAtoms = info->getNGlobalAtoms();
813 +    int nGlobalRigidBodies = info->getNGlobalRigidBodies();
814      
815      beginAtomIndex = 0;
816      //rigidbody's index begins right after atom's
# Line 852 | Line 877 | namespace OpenMD {
877      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
878      // docs said we could.
879      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
880 <    MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
881 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
880 >    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
881 >                              &tmpGroupMembership[0], nGlobalAtoms,
882 >                              MPI::INT, MPI::SUM);
883      info->setGlobalGroupMembership(tmpGroupMembership);
884   #else
885      info->setGlobalGroupMembership(globalGroupMembership);
886   #endif
887      
888      //fill molMembership
889 <    std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
889 >    std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
890 >                                         info->getNGlobalRigidBodies(), 0);
891      
892 <    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
892 >    for(mol = info->beginMolecule(mi); mol != NULL;
893 >        mol = info->nextMolecule(mi)) {
894        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
896        }
897 +      for (rb = mol->beginRigidBody(ri); rb != NULL;
898 +           rb = mol->nextRigidBody(ri)) {
899 +        globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
900 +      }
901      }
902      
903   #ifdef IS_MPI
904 <    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
904 >    std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
905 >                                      info->getNGlobalRigidBodies(), 0);
906 >    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
907 >                              nGlobalAtoms + nGlobalRigidBodies,
908 >                              MPI::INT, MPI::SUM);
909      
874 –    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
875 –                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
876 –    
910      info->setGlobalMolMembership(tmpMolMembership);
911   #else
912      info->setGlobalMolMembership(globalMolMembership);
# Line 883 | Line 916 | namespace OpenMD {
916      // here the molecules are listed by their global indices.
917  
918      std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
919 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
919 >    for (mol = info->beginMolecule(mi); mol != NULL;
920 >         mol = info->nextMolecule(mi)) {
921        nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
922      }
923      
924   #ifdef IS_MPI
925      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
926 <    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
927 <                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
926 >    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
927 >                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
928   #else
929      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
930   #endif    
# Line 904 | Line 938 | namespace OpenMD {
938      }
939      
940      std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
941 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
941 >    for (mol = info->beginMolecule(mi); mol != NULL;
942 >         mol = info->nextMolecule(mi)) {
943        int myGlobalIndex = mol->getGlobalIndex();
944        int globalIO = startingIOIndexForMol[myGlobalIndex];
945        for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
# Line 920 | Line 955 | namespace OpenMD {
955    }
956    
957    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
923 –    Globals* simParams;
924 –
925 –    simParams = info->getSimParams();
958      
959      DumpReader reader(info, mdFileName);
960      int nframes = reader.getNFrames();
961 <
961 >    
962      if (nframes > 0) {
963        reader.readFrame(nframes - 1);
964      } else {

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