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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC vs.
Revision 1825 by gezelter, Wed Jan 9 19:27:52 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 56 | Line 55
55   #include "brains/SimCreator.hpp"
56   #include "brains/SimSnapshotManager.hpp"
57   #include "io/DumpReader.hpp"
58 < #include "UseTheForce/ForceFieldFactory.hpp"
58 > #include "brains/ForceField.hpp"
59   #include "utils/simError.h"
60   #include "utils/StringUtils.hpp"
61   #include "math/SeqRandNumGen.hpp"
# 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 371 | Line 400 | namespace OpenMD {
400                                     metaDataBlockStart + 1);
401      
402      //create the force field
403 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
403 >    ForceField * ff = new ForceField(simParams->getForceField());
404  
405      if (ff == NULL) {
406        sprintf(painCave.errMsg,
# Line 426 | Line 455 | namespace OpenMD {
455  
456      int storageLayout = computeStorageLayout(info);
457  
429 –    cerr << "computed Storage Layout = " << storageLayout << "\n";
430 –
458      //allocate memory for DataStorage(circular reference, need to
459      //break it)
460      info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
# Line 507 | Line 534 | namespace OpenMD {
534      int nGlobalMols = info->getNGlobalMolecules();
535      std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
536      
537 <    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
537 >    nProcessors = MPI::COMM_WORLD.Get_size();
538      
539      if (nProcessors > nGlobalMols) {
540        sprintf(painCave.errMsg,
# Line 545 | Line 572 | namespace OpenMD {
572        nTarget = (int)(precast + 0.5);
573        
574        for(i = 0; i < nGlobalMols; i++) {
575 +
576          done = 0;
577          loops = 0;
578          
# Line 569 | Line 597 | namespace OpenMD {
597            // and be done with it.
598            
599            if (loops > 100) {
600 +
601              sprintf(painCave.errMsg,
602 <                    "I've tried 100 times to assign molecule %d to a "
603 <                    " processor, but can't find a good spot.\n"
604 <                    "I'm assigning it at random to processor %d.\n",
602 >                    "There have been 100 attempts to assign molecule %d to an\n"
603 >                    "\tunderworked processor, but there's no good place to\n"
604 >                    "\tleave it.  OpenMD is assigning it at random to processor %d.\n",
605                      i, which_proc);
606 <            
606 >          
607              painCave.isFatal = 0;
608 +            painCave.severity = OPENMD_INFO;
609              simError();
610              
611              molToProcMap[i] = which_proc;
# Line 620 | Line 650 | namespace OpenMD {
650        }
651        
652        delete myRandom;
653 <      
653 >
654        // Spray out this nonsense to all other processors:
655 <      
626 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
655 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
656      } else {
657        
658        // Listen to your marching orders from processor 0:
659 <      
660 <      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      
663      info->setMolToProcMap(molToProcMap);
# Line 669 | Line 698 | namespace OpenMD {
698      
699    int SimCreator::computeStorageLayout(SimInfo* info) {
700  
701 +    Globals* simParams = info->getSimParams();
702      int nRigidBodies = info->getNGlobalRigidBodies();
703      set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
704      set<AtomType*>::iterator i;
705      bool hasDirectionalAtoms = false;
706      bool hasFixedCharge = false;
707 <    bool hasMultipoles = false;    
707 >    bool hasDipoles = false;    
708 >    bool hasQuadrupoles = false;    
709      bool hasPolarizable = false;    
710      bool hasFluctuatingCharge = false;    
711      bool hasMetallic = false;
# Line 696 | Line 727 | namespace OpenMD {
727        if (da.isDirectional()){
728          hasDirectionalAtoms = true;
729        }
730 <      if (ma.isMultipole()){
731 <        hasMultipoles = true;
730 >      if (ma.isDipole()){
731 >        hasDipoles = true;
732        }
733 +      if (ma.isQuadrupole()){
734 +        hasQuadrupoles = true;
735 +      }
736        if (ea.isEAM() || sca.isSuttonChen()){
737          hasMetallic = true;
738        }
# Line 722 | Line 756 | namespace OpenMD {
756          storageLayout |= DataStorage::dslTorque;
757        }
758      }
759 <    if (hasMultipoles) {
760 <      storageLayout |= DataStorage::dslElectroFrame;
759 >    if (hasDipoles) {
760 >      storageLayout |= DataStorage::dslDipole;
761      }
762 +    if (hasQuadrupoles) {
763 +      storageLayout |= DataStorage::dslQuadrupole;
764 +    }
765      if (hasFixedCharge || hasFluctuatingCharge) {
766        storageLayout |= DataStorage::dslSkippedCharge;
767      }
# Line 745 | Line 782 | namespace OpenMD {
782          storageLayout |= DataStorage::dslFlucQForce;
783        }
784      }
785 +    
786 +    // if the user has asked for them, make sure we've got the memory for the
787 +    // objects defined.
788 +
789 +    if (simParams->getOutputParticlePotential()) {
790 +      storageLayout |= DataStorage::dslParticlePot;
791 +    }
792 +
793 +    if (simParams->havePrintHeatFlux()) {
794 +      if (simParams->getPrintHeatFlux()) {
795 +        storageLayout |= DataStorage::dslParticlePot;
796 +      }
797 +    }
798 +
799 +    if (simParams->getOutputElectricField()) {
800 +      storageLayout |= DataStorage::dslElectricField;
801 +    }
802 +
803 +    if (simParams->getOutputFluctuatingCharges()) {
804 +      storageLayout |= DataStorage::dslFlucQPosition;
805 +      storageLayout |= DataStorage::dslFlucQVelocity;
806 +      storageLayout |= DataStorage::dslFlucQForce;
807 +    }
808 +
809      return storageLayout;
810    }
811  
# Line 762 | Line 823 | namespace OpenMD {
823      int beginRigidBodyIndex;
824      int beginCutoffGroupIndex;
825      int nGlobalAtoms = info->getNGlobalAtoms();
826 +    int nGlobalRigidBodies = info->getNGlobalRigidBodies();
827      
828      beginAtomIndex = 0;
829 <    beginRigidBodyIndex = 0;
829 >    //rigidbody's index begins right after atom's
830 >    beginRigidBodyIndex = info->getNGlobalAtoms();
831      beginCutoffGroupIndex = 0;
832  
833      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
# Line 827 | Line 890 | namespace OpenMD {
890      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
891      // docs said we could.
892      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
893 <    MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
894 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
893 >    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
894 >                              &tmpGroupMembership[0], nGlobalAtoms,
895 >                              MPI::INT, MPI::SUM);
896      info->setGlobalGroupMembership(tmpGroupMembership);
897   #else
898      info->setGlobalGroupMembership(globalGroupMembership);
899   #endif
900      
901      //fill molMembership
902 <    std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
902 >    std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
903 >                                         info->getNGlobalRigidBodies(), 0);
904      
905 <    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
905 >    for(mol = info->beginMolecule(mi); mol != NULL;
906 >        mol = info->nextMolecule(mi)) {
907        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
908          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
909        }
910 +      for (rb = mol->beginRigidBody(ri); rb != NULL;
911 +           rb = mol->nextRigidBody(ri)) {
912 +        globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
913 +      }
914      }
915      
916   #ifdef IS_MPI
917 <    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
917 >    std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
918 >                                      info->getNGlobalRigidBodies(), 0);
919 >    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
920 >                              nGlobalAtoms + nGlobalRigidBodies,
921 >                              MPI::INT, MPI::SUM);
922      
849 –    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
850 –                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
851 –    
923      info->setGlobalMolMembership(tmpMolMembership);
924   #else
925      info->setGlobalMolMembership(globalMolMembership);
# Line 858 | Line 929 | namespace OpenMD {
929      // here the molecules are listed by their global indices.
930  
931      std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
932 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
932 >    for (mol = info->beginMolecule(mi); mol != NULL;
933 >         mol = info->nextMolecule(mi)) {
934        nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
935      }
936      
937   #ifdef IS_MPI
938      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
939 <    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
940 <                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
939 >    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
940 >                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
941   #else
942      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
943   #endif    
# Line 879 | Line 951 | namespace OpenMD {
951      }
952      
953      std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
954 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
954 >    for (mol = info->beginMolecule(mi); mol != NULL;
955 >         mol = info->nextMolecule(mi)) {
956        int myGlobalIndex = mol->getGlobalIndex();
957        int globalIO = startingIOIndexForMol[myGlobalIndex];
958 <      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
959 <           integrableObject = mol->nextIntegrableObject(ioi)) {
960 <        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
961 <        IOIndexToIntegrableObject[globalIO] = integrableObject;
958 >      for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
959 >           sd = mol->nextIntegrableObject(ioi)) {
960 >        sd->setGlobalIntegrableObjectIndex(globalIO);
961 >        IOIndexToIntegrableObject[globalIO] = sd;
962          globalIO++;
963        }
964      }
# Line 895 | Line 968 | namespace OpenMD {
968    }
969    
970    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
898 –    Globals* simParams;
899 –
900 –    simParams = info->getSimParams();
971      
972      DumpReader reader(info, mdFileName);
973      int nframes = reader.getNFrames();
974 <
974 >    
975      if (nframes > 0) {
976        reader.readFrame(nframes - 1);
977      } else {

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