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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC vs.
Revision 1826 by gezelter, Wed Jan 9 19:41:48 2013 UTC

# 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 255 | Line 254 | namespace OpenMD {
254      std::string mdRawData;
255      int metaDataBlockStart = -1;
256      int metaDataBlockEnd = -1;
257 <    int i;
258 <    int mdOffset;
257 >    int i, j;
258 >    streamoff mdOffset;
259      int mdFileVersion;
260 +
261 +    // Create a string for embedding the version information in the MetaData
262 +    std::string version;
263 +    version.assign("## Last run using OpenMD Version: ");
264 +    version.append(OPENMD_VERSION_MAJOR);
265 +    version.append(".");
266 +    version.append(OPENMD_VERSION_MINOR);
267  
268 +    std::string svnrev;
269 +    //convert a macro from compiler to a string in c++
270 +    STR_DEFINE(svnrev, SVN_REV );
271 +    version.append(" Revision: ");
272 +    // If there's no SVN revision, just call this the RELEASE revision.
273 +    if (!svnrev.empty()) {
274 +      version.append(svnrev);
275 +    } else {
276 +      version.append("RELEASE");
277 +    }
278 +  
279   #ifdef IS_MPI            
280      const int masterNode = 0;
281      if (worldRank == masterNode) {
282   #endif
283  
284 <      std::ifstream mdFile_(mdFileName.c_str());
284 >      std::ifstream mdFile_;
285 >      mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
286        
287        if (mdFile_.fail()) {
288          sprintf(painCave.errMsg,
# Line 352 | Line 370 | namespace OpenMD {
370  
371        mdRawData.clear();
372  
373 +      bool foundVersion = false;
374 +
375        for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
376          mdFile_.getline(buffer, bufferSize);
377 <        mdRawData += buffer;
377 >        std::string line = trimLeftCopy(buffer);
378 >        j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
379 >        if (static_cast<size_t>(j) != string::npos) {
380 >          foundVersion = true;
381 >          mdRawData += version;
382 >        } else {
383 >          mdRawData += buffer;
384 >        }
385          mdRawData += "\n";
386        }
387 <
387 >      
388 >      if (!foundVersion) mdRawData += version + "\n";
389 >      
390        mdFile_.close();
391  
392   #ifdef IS_MPI
# Line 497 | Line 526 | namespace OpenMD {
526      int nTarget;
527      int done;
528      int i;
500 –    int j;
529      int loops;
530      int which_proc;
531      int nProcessors;
# Line 505 | Line 533 | namespace OpenMD {
533      int nGlobalMols = info->getNGlobalMolecules();
534      std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
535      
536 <    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
536 >    nProcessors = MPI::COMM_WORLD.Get_size();
537      
538      if (nProcessors > nGlobalMols) {
539        sprintf(painCave.errMsg,
# Line 543 | Line 571 | namespace OpenMD {
571        nTarget = (int)(precast + 0.5);
572        
573        for(i = 0; i < nGlobalMols; i++) {
574 +
575          done = 0;
576          loops = 0;
577          
# Line 567 | Line 596 | namespace OpenMD {
596            // and be done with it.
597            
598            if (loops > 100) {
599 +
600              sprintf(painCave.errMsg,
601 <                    "I've tried 100 times to assign molecule %d to a "
602 <                    " processor, but can't find a good spot.\n"
603 <                    "I'm assigning it at random to processor %d.\n",
601 >                    "There have been 100 attempts to assign molecule %d to an\n"
602 >                    "\tunderworked processor, but there's no good place to\n"
603 >                    "\tleave it.  OpenMD is assigning it at random to processor %d.\n",
604                      i, which_proc);
605 <            
605 >          
606              painCave.isFatal = 0;
607 +            painCave.severity = OPENMD_INFO;
608              simError();
609              
610              molToProcMap[i] = which_proc;
# Line 618 | Line 649 | namespace OpenMD {
649        }
650        
651        delete myRandom;
652 <      
652 >
653        // Spray out this nonsense to all other processors:
654 <      
624 <      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 <      
659 <      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      
662      info->setMolToProcMap(molToProcMap);
# Line 673 | 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 695 | 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 721 | 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 761 | Line 798 | namespace OpenMD {
798      if (simParams->getOutputElectricField()) {
799        storageLayout |= DataStorage::dslElectricField;
800      }
801 +
802      if (simParams->getOutputFluctuatingCharges()) {
803        storageLayout |= DataStorage::dslFlucQPosition;
804        storageLayout |= DataStorage::dslFlucQVelocity;
# Line 784 | Line 822 | namespace OpenMD {
822      int beginRigidBodyIndex;
823      int beginCutoffGroupIndex;
824      int nGlobalAtoms = info->getNGlobalAtoms();
825 +    int nGlobalRigidBodies = info->getNGlobalRigidBodies();
826      
827      beginAtomIndex = 0;
828 <    beginRigidBodyIndex = 0;
828 >    //rigidbody's index begins right after atom's
829 >    beginRigidBodyIndex = info->getNGlobalAtoms();
830      beginCutoffGroupIndex = 0;
831  
832      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
# Line 849 | Line 889 | namespace OpenMD {
889      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
890      // docs said we could.
891      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
892 <    MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
893 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
892 >    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
893 >                              &tmpGroupMembership[0], nGlobalAtoms,
894 >                              MPI::INT, MPI::SUM);
895      info->setGlobalGroupMembership(tmpGroupMembership);
896   #else
897      info->setGlobalGroupMembership(globalGroupMembership);
898   #endif
899      
900      //fill molMembership
901 <    std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
901 >    std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
902 >                                         info->getNGlobalRigidBodies(), 0);
903      
904 <    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
904 >    for(mol = info->beginMolecule(mi); mol != NULL;
905 >        mol = info->nextMolecule(mi)) {
906        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
908        }
909 +      for (rb = mol->beginRigidBody(ri); rb != NULL;
910 +           rb = mol->nextRigidBody(ri)) {
911 +        globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
912 +      }
913      }
914      
915   #ifdef IS_MPI
916 <    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
916 >    std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
917 >                                      info->getNGlobalRigidBodies(), 0);
918 >    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
919 >                              nGlobalAtoms + nGlobalRigidBodies,
920 >                              MPI::INT, MPI::SUM);
921      
871 –    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
872 –                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
873 –    
922      info->setGlobalMolMembership(tmpMolMembership);
923   #else
924      info->setGlobalMolMembership(globalMolMembership);
# Line 880 | Line 928 | namespace OpenMD {
928      // here the molecules are listed by their global indices.
929  
930      std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
931 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
931 >    for (mol = info->beginMolecule(mi); mol != NULL;
932 >         mol = info->nextMolecule(mi)) {
933        nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
934      }
935      
936   #ifdef IS_MPI
937      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
938 <    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
939 <                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
938 >    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
939 >                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
940   #else
941      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
942   #endif    
# Line 901 | Line 950 | namespace OpenMD {
950      }
951      
952      std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
953 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
953 >    for (mol = info->beginMolecule(mi); mol != NULL;
954 >         mol = info->nextMolecule(mi)) {
955        int myGlobalIndex = mol->getGlobalIndex();
956        int globalIO = startingIOIndexForMol[myGlobalIndex];
957 <      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
958 <           integrableObject = mol->nextIntegrableObject(ioi)) {
959 <        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
960 <        IOIndexToIntegrableObject[globalIO] = integrableObject;
957 >      for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
958 >           sd = mol->nextIntegrableObject(ioi)) {
959 >        sd->setGlobalIntegrableObjectIndex(globalIO);
960 >        IOIndexToIntegrableObject[globalIO] = sd;
961          globalIO++;
962        }
963      }
# Line 917 | Line 967 | namespace OpenMD {
967    }
968    
969    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
920 –    Globals* simParams;
921 –
922 –    simParams = info->getSimParams();
970      
971      DumpReader reader(info, mdFileName);
972      int nframes = reader.getNFrames();
973 <
973 >    
974      if (nframes > 0) {
975        reader.readFrame(nframes - 1);
976      } else {

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