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root/OpenMD/branches/development/src/brains/SimCreator.cpp
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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC vs.
Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 UTC

# Line 56 | Line 56
56   #include "brains/SimCreator.hpp"
57   #include "brains/SimSnapshotManager.hpp"
58   #include "io/DumpReader.hpp"
59 < #include "UseTheForce/ForceFieldFactory.hpp"
59 > #include "brains/ForceField.hpp"
60   #include "utils/simError.h"
61   #include "utils/StringUtils.hpp"
62   #include "math/SeqRandNumGen.hpp"
# Line 256 | Line 256 | namespace OpenMD {
256      int metaDataBlockStart = -1;
257      int metaDataBlockEnd = -1;
258      int i;
259 <    int mdOffset;
259 >    streamoff mdOffset;
260      int mdFileVersion;
261  
262 +
263   #ifdef IS_MPI            
264      const int masterNode = 0;
265      if (worldRank == masterNode) {
266   #endif
267  
268 <      std::ifstream mdFile_(mdFileName.c_str());
268 >      std::ifstream mdFile_;
269 >      mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
270        
271        if (mdFile_.fail()) {
272          sprintf(painCave.errMsg,
# Line 371 | Line 373 | namespace OpenMD {
373                                     metaDataBlockStart + 1);
374      
375      //create the force field
376 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
376 >    ForceField * ff = new ForceField(simParams->getForceField());
377  
378      if (ff == NULL) {
379        sprintf(painCave.errMsg,
# Line 426 | Line 428 | namespace OpenMD {
428  
429      int storageLayout = computeStorageLayout(info);
430  
429 –    cerr << "computed Storage Layout = " << storageLayout << "\n";
430 –
431      //allocate memory for DataStorage(circular reference, need to
432      //break it)
433      info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
# Line 507 | Line 507 | namespace OpenMD {
507      int nGlobalMols = info->getNGlobalMolecules();
508      std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
509      
510 <    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
510 >    nProcessors = MPI::COMM_WORLD.Get_size();
511      
512      if (nProcessors > nGlobalMols) {
513        sprintf(painCave.errMsg,
# Line 622 | Line 622 | namespace OpenMD {
622        delete myRandom;
623        
624        // Spray out this nonsense to all other processors:
625 <      
626 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
625 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
626      } else {
627        
628        // Listen to your marching orders from processor 0:
629 <      
631 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
629 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
630      }
631      
632      info->setMolToProcMap(molToProcMap);
# Line 675 | Line 673 | namespace OpenMD {
673      set<AtomType*>::iterator i;
674      bool hasDirectionalAtoms = false;
675      bool hasFixedCharge = false;
676 <    bool hasMultipoles = false;    
676 >    bool hasDipoles = false;    
677 >    bool hasQuadrupoles = false;    
678      bool hasPolarizable = false;    
679      bool hasFluctuatingCharge = false;    
680      bool hasMetallic = false;
# Line 697 | Line 696 | namespace OpenMD {
696        if (da.isDirectional()){
697          hasDirectionalAtoms = true;
698        }
699 <      if (ma.isMultipole()){
700 <        hasMultipoles = true;
699 >      if (ma.isDipole()){
700 >        hasDipoles = true;
701        }
702 +      if (ma.isQuadrupole()){
703 +        hasQuadrupoles = true;
704 +      }
705        if (ea.isEAM() || sca.isSuttonChen()){
706          hasMetallic = true;
707        }
# Line 723 | Line 725 | namespace OpenMD {
725          storageLayout |= DataStorage::dslTorque;
726        }
727      }
728 <    if (hasMultipoles) {
729 <      storageLayout |= DataStorage::dslElectroFrame;
728 >    if (hasDipoles) {
729 >      storageLayout |= DataStorage::dslDipole;
730      }
731 +    if (hasQuadrupoles) {
732 +      storageLayout |= DataStorage::dslQuadrupole;
733 +    }
734      if (hasFixedCharge || hasFluctuatingCharge) {
735        storageLayout |= DataStorage::dslSkippedCharge;
736      }
# Line 753 | Line 758 | namespace OpenMD {
758      if (simParams->getOutputParticlePotential()) {
759        storageLayout |= DataStorage::dslParticlePot;
760      }
761 +
762 +    if (simParams->havePrintHeatFlux()) {
763 +      if (simParams->getPrintHeatFlux()) {
764 +        storageLayout |= DataStorage::dslParticlePot;
765 +      }
766 +    }
767 +
768      if (simParams->getOutputElectricField()) {
769        storageLayout |= DataStorage::dslElectricField;
770      }
771 +
772      if (simParams->getOutputFluctuatingCharges()) {
773        storageLayout |= DataStorage::dslFlucQPosition;
774        storageLayout |= DataStorage::dslFlucQVelocity;
# Line 781 | Line 794 | namespace OpenMD {
794      int nGlobalAtoms = info->getNGlobalAtoms();
795      
796      beginAtomIndex = 0;
797 <    beginRigidBodyIndex = 0;
797 >    //rigidbody's index begins right after atom's
798 >    beginRigidBodyIndex = info->getNGlobalAtoms();
799      beginCutoffGroupIndex = 0;
800  
801      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
# Line 844 | Line 858 | namespace OpenMD {
858      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
859      // docs said we could.
860      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
861 <    MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
862 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
861 >    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
862 >                              &tmpGroupMembership[0], nGlobalAtoms,
863 >                              MPI::INT, MPI::SUM);
864      info->setGlobalGroupMembership(tmpGroupMembership);
865   #else
866      info->setGlobalGroupMembership(globalGroupMembership);
# Line 862 | Line 877 | namespace OpenMD {
877      
878   #ifdef IS_MPI
879      std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
880 +    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
881 +                              nGlobalAtoms,
882 +                              MPI::INT, MPI::SUM);
883      
866 –    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
867 –                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
868 –    
884      info->setGlobalMolMembership(tmpMolMembership);
885   #else
886      info->setGlobalMolMembership(globalMolMembership);
# Line 881 | Line 896 | namespace OpenMD {
896      
897   #ifdef IS_MPI
898      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
899 <    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
900 <                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
899 >    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
900 >                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
901   #else
902      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
903   #endif    
# Line 899 | Line 914 | namespace OpenMD {
914      for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
915        int myGlobalIndex = mol->getGlobalIndex();
916        int globalIO = startingIOIndexForMol[myGlobalIndex];
917 <      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
918 <           integrableObject = mol->nextIntegrableObject(ioi)) {
919 <        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
920 <        IOIndexToIntegrableObject[globalIO] = integrableObject;
917 >      for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
918 >           sd = mol->nextIntegrableObject(ioi)) {
919 >        sd->setGlobalIntegrableObjectIndex(globalIO);
920 >        IOIndexToIntegrableObject[globalIO] = sd;
921          globalIO++;
922        }
923      }

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