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root/OpenMD/branches/development/src/brains/SimInfo.cpp
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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
Revision 1553 by gezelter, Fri Apr 29 17:25:12 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/doForces_interface.h"
58 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
57   #include "utils/MemoryUtils.hpp"
58   #include "utils/simError.h"
59   #include "selection/SelectionManager.hpp"
60   #include "io/ForceFieldOptions.hpp"
61   #include "UseTheForce/ForceField.hpp"
62   #include "nonbonded/SwitchingFunction.hpp"
65 –
66 –
67 – #ifdef IS_MPI
68 – #include "UseTheForce/mpiComponentPlan.h"
69 – #include "UseTheForce/DarkSide/simParallel_interface.h"
70 – #endif
63  
64   using namespace std;
65   namespace OpenMD {
# Line 133 | Line 125 | namespace OpenMD {
125      //equal to the total number of atoms minus number of atoms belong to
126      //cutoff group defined in meta-data file plus the number of cutoff
127      //groups defined in meta-data file
128 +    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129 +    std::cerr << "nCA = " << nCutoffAtoms << "\n";
130 +    std::cerr << "nG = " << nGroups << "\n";
131 +
132      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133 +
134 +    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135      
136      //every free atom (atom does not belong to rigid bodies) is an
137      //integrable object therefore the total number of integrable objects
# Line 657 | Line 655 | namespace OpenMD {
655    /**
656     * update
657     *
658 <   *  Performs the global checks and variable settings after the objects have been
659 <   *  created.
658 >   *  Performs the global checks and variable settings after the
659 >   *  objects have been created.
660     *
661     */
662 <  void SimInfo::update() {
665 <    
662 >  void SimInfo::update() {  
663      setupSimVariables();
667 –    setupCutoffs();
668 –    setupSwitching();
669 –    setupElectrostatics();
670 –    setupNeighborlists();
671 –
672 – #ifdef IS_MPI
673 –    setupFortranParallel();
674 – #endif
675 –    setupFortranSim();
676 –    fortranInitialized_ = true;
677 –
664      calcNdf();
665      calcNdfRaw();
666      calcNdfTrans();
667    }
668    
669 +  /**
670 +   * getSimulatedAtomTypes
671 +   *
672 +   * Returns an STL set of AtomType* that are actually present in this
673 +   * simulation.  Must query all processors to assemble this information.
674 +   *
675 +   */
676    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677      SimInfo::MoleculeIterator mi;
678      Molecule* mol;
# Line 692 | Line 685 | namespace OpenMD {
685          atomTypes.insert(atom->getAtomType());
686        }      
687      }    
695 –    return atomTypes;        
696 –  }
688  
689 <  /**
699 <   * setupCutoffs
700 <   *
701 <   * Sets the values of cutoffRadius and cutoffMethod
702 <   *
703 <   * cutoffRadius : realType
704 <   *  If the cutoffRadius was explicitly set, use that value.
705 <   *  If the cutoffRadius was not explicitly set:
706 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
707 <   *      No electrostatic atoms?  Poll the atom types present in the
708 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709 <   *      Use the maximum suggested value that was found.
710 <   *
711 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712 <   *      If cutoffMethod was explicitly set, use that choice.
713 <   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714 <   */
715 <  void SimInfo::setupCutoffs() {
716 <    
717 <    if (simParams_->haveCutoffRadius()) {
718 <      cutoffRadius_ = simParams_->getCutoffRadius();
719 <    } else {      
720 <      if (usesElectrostaticAtoms_) {
721 <        sprintf(painCave.errMsg,
722 <                "SimInfo: No value was set for the cutoffRadius.\n"
723 <                "\tOpenMD will use a default value of 12.0 angstroms"
724 <                "\tfor the cutoffRadius.\n");
725 <        painCave.isFatal = 0;
726 <        painCave.severity = OPENMD_INFO;
727 <        simError();
728 <        cutoffRadius_ = 12.0;
729 <      } else {
730 <        RealType thisCut;
731 <        set<AtomType*>::iterator i;
732 <        set<AtomType*> atomTypes;
733 <        atomTypes = getSimulatedAtomTypes();        
734 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
737 <        }
738 <        sprintf(painCave.errMsg,
739 <                "SimInfo: No value was set for the cutoffRadius.\n"
740 <                "\tOpenMD will use %lf angstroms.\n",
741 <                cutoffRadius_);
742 <        painCave.isFatal = 0;
743 <        painCave.severity = OPENMD_INFO;
744 <        simError();
745 <      }            
746 <    }
689 > #ifdef IS_MPI
690  
691 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
691 >    // loop over the found atom types on this processor, and add their
692 >    // numerical idents to a vector:
693  
694 <    map<string, CutoffMethod> stringToCutoffMethod;
695 <    stringToCutoffMethod["HARD"] = HARD;
696 <    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
697 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
754 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
755 <  
756 <    if (simParams_->haveCutoffMethod()) {
757 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
758 <      map<string, CutoffMethod>::iterator i;
759 <      i = stringToCutoffMethod.find(cutMeth);
760 <      if (i == stringToCutoffMethod.end()) {
761 <        sprintf(painCave.errMsg,
762 <                "SimInfo: Could not find chosen cutoffMethod %s\n"
763 <                "\tShould be one of: "
764 <                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765 <                cutMeth.c_str());
766 <        painCave.isFatal = 1;
767 <        painCave.severity = OPENMD_ERROR;
768 <        simError();
769 <      } else {
770 <        cutoffMethod_ = i->second;
771 <      }
772 <    } else {
773 <      sprintf(painCave.errMsg,
774 <              "SimInfo: No value was set for the cutoffMethod.\n"
775 <              "\tOpenMD will use SHIFTED_FORCE.\n");
776 <        painCave.isFatal = 0;
777 <        painCave.severity = OPENMD_INFO;
778 <        simError();
779 <        cutoffMethod_ = SHIFTED_FORCE;        
780 <    }
694 >    vector<int> foundTypes;
695 >    set<AtomType*>::iterator i;
696 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697 >      foundTypes.push_back( (*i)->getIdent() );
698  
699 <    InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
700 <  }
784 <  
785 <  /**
786 <   * setupSwitching
787 <   *
788 <   * Sets the values of switchingRadius and
789 <   *  If the switchingRadius was explicitly set, use that value (but check it)
790 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791 <   */
792 <  void SimInfo::setupSwitching() {
793 <    
794 <    if (simParams_->haveSwitchingRadius()) {
795 <      switchingRadius_ = simParams_->getSwitchingRadius();
796 <      if (switchingRadius_ > cutoffRadius_) {        
797 <        sprintf(painCave.errMsg,
798 <                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799 <                switchingRadius_, cutoffRadius_);
800 <        painCave.isFatal = 1;
801 <        painCave.severity = OPENMD_ERROR;
802 <        simError();
803 <      }
804 <    } else {      
805 <      switchingRadius_ = 0.85 * cutoffRadius_;
806 <      sprintf(painCave.errMsg,
807 <              "SimInfo: No value was set for the switchingRadius.\n"
808 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810 <      painCave.isFatal = 0;
811 <      painCave.severity = OPENMD_WARNING;
812 <      simError();
813 <    }          
814 <  
815 <    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
699 >    // count_local holds the number of found types on this processor
700 >    int count_local = foundTypes.size();
701  
702 <    SwitchingFunctionType ft;
702 >    // count holds the total number of found types on all processors
703 >    // (some will be redundant with the ones found locally):
704 >    int count;
705 >    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706 >
707 >    // create a vector to hold the globally found types, and resize it:
708 >    vector<int> ftGlobal;
709 >    ftGlobal.resize(count);
710 >    vector<int> counts;
711 >
712 >    int nproc = MPI::COMM_WORLD.Get_size();
713 >    counts.resize(nproc);
714 >    vector<int> disps;
715 >    disps.resize(nproc);
716 >
717 >    // now spray out the foundTypes to all the other processors:
718      
719 <    if (simParams_->haveSwitchingFunctionType()) {
720 <      string funcType = simParams_->getSwitchingFunctionType();
821 <      toUpper(funcType);
822 <      if (funcType == "CUBIC") {
823 <        ft = cubic;
824 <      } else {
825 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826 <          ft = fifth_order_poly;
827 <        } else {
828 <          // throw error        
829 <          sprintf( painCave.errMsg,
830 <                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831 <                   "\tswitchingFunctionType must be one of: "
832 <                   "\"cubic\" or \"fifth_order_polynomial\".",
833 <                   funcType.c_str() );
834 <          painCave.isFatal = 1;
835 <          painCave.severity = OPENMD_ERROR;
836 <          simError();
837 <        }          
838 <      }
839 <    }
719 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720 >                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721  
722 <    InteractionManager::Instance()->setSwitchingFunctionType(ft);
722 >    // foundIdents is a stl set, so inserting an already found ident
723 >    // will have no effect.
724 >    set<int> foundIdents;
725 >    vector<int>::iterator j;
726 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727 >      foundIdents.insert((*j));
728 >    
729 >    // now iterate over the foundIdents and get the actual atom types
730 >    // that correspond to these:
731 >    set<int>::iterator it;
732 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733 >      atomTypes.insert( forceField_->getAtomType((*it)) );
734 >
735 > #endif
736 >    
737 >    return atomTypes;        
738    }
739  
740 <  /**
741 <   * setupSkinThickness
742 <   *
743 <   *  If the skinThickness was explicitly set, use that value (but check it)
744 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
745 <   */
746 <  void SimInfo::setupSkinThickness() {    
747 <    if (simParams_->haveSkinThickness()) {
852 <      skinThickness_ = simParams_->getSkinThickness();
853 <    } else {      
854 <      skinThickness_ = 1.0;
855 <      sprintf(painCave.errMsg,
856 <              "SimInfo Warning: No value was set for the skinThickness.\n"
857 <              "\tOpenMD will use a default value of %f Angstroms\n"
858 <              "\tfor this simulation\n", skinThickness_);
859 <      painCave.isFatal = 0;
860 <      simError();
861 <    }            
862 <  }
740 >  void SimInfo::setupSimVariables() {
741 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
742 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743 >    calcBoxDipole_ = false;
744 >    if ( simParams_->haveAccumulateBoxDipole() )
745 >      if ( simParams_->getAccumulateBoxDipole() ) {
746 >        calcBoxDipole_ = true;      
747 >      }
748  
864 –  void SimInfo::setupSimType() {
749      set<AtomType*>::iterator i;
750      set<AtomType*> atomTypes;
751 <    atomTypes = getSimulatedAtomTypes();
868 <
869 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
870 <
751 >    atomTypes = getSimulatedAtomTypes();    
752      int usesElectrostatic = 0;
753      int usesMetallic = 0;
754      int usesDirectional = 0;
# Line 889 | Line 770 | namespace OpenMD {
770      temp = usesElectrostatic;
771      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772   #endif
892 –    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
893 –    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
894 –    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
895 –    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896 –    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897 –    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
773    }
774  
775 <  void SimInfo::setupFortranSim() {
775 >
776 >  vector<int> SimInfo::getGlobalAtomIndices() {
777 >    SimInfo::MoleculeIterator mi;
778 >    Molecule* mol;
779 >    Molecule::AtomIterator ai;
780 >    Atom* atom;
781 >
782 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
783 >    
784 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
785 >      
786 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
787 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
788 >      }
789 >    }
790 >    return GlobalAtomIndices;
791 >  }
792 >
793 >
794 >  vector<int> SimInfo::getGlobalGroupIndices() {
795 >    SimInfo::MoleculeIterator mi;
796 >    Molecule* mol;
797 >    Molecule::CutoffGroupIterator ci;
798 >    CutoffGroup* cg;
799 >
800 >    vector<int> GlobalGroupIndices;
801 >    
802 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
803 >      
804 >      //local index of cutoff group is trivial, it only depends on the
805 >      //order of travesing
806 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
807 >           cg = mol->nextCutoffGroup(ci)) {
808 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
809 >      }        
810 >    }
811 >    return GlobalGroupIndices;
812 >  }
813 >
814 >
815 >  void SimInfo::setupFortran() {
816      int isError;
817      int nExclude, nOneTwo, nOneThree, nOneFour;
818      vector<int> fortranGlobalGroupMembership;
819      
905 –    notifyFortranSkinThickness(&skinThickness_);
906 –
907 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
910 –
820      isError = 0;
821  
822      //globalGroupMembership_ is filled by SimCreator    
# Line 942 | Line 851 | namespace OpenMD {
851        }      
852      }
853  
854 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946 <    vector<int> identArray;
854 >    // Build the identArray_
855  
856 <    //to avoid memory reallocation, reserve enough space identArray
857 <    identArray.reserve(getNAtoms());
950 <    
856 >    identArray_.clear();
857 >    identArray_.reserve(getNAtoms());    
858      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
859        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
860 <        identArray.push_back(atom->getIdent());
860 >        identArray_.push_back(atom->getIdent());
861        }
862      }    
863  
# Line 973 | Line 880 | namespace OpenMD {
880      int* oneThreeList = oneThreeInteractions_.getPairList();
881      int* oneFourList = oneFourInteractions_.getPairList();
882  
883 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
884 <                   &nExclude, excludeList,
885 <                   &nOneTwo, oneTwoList,
886 <                   &nOneThree, oneThreeList,
887 <                   &nOneFour, oneFourList,
888 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
889 <                   &fortranGlobalGroupMembership[0], &isError);
883 >    //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
884 >    //               &nExclude, excludeList,
885 >    //               &nOneTwo, oneTwoList,
886 >    //               &nOneThree, oneThreeList,
887 >    //               &nOneFour, oneFourList,
888 >    //               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
889 >    //               &fortranGlobalGroupMembership[0], &isError);
890      
891 <    if( isError ){
892 <      
893 <      sprintf( painCave.errMsg,
894 <               "There was an error setting the simulation information in fortran.\n" );
895 <      painCave.isFatal = 1;
896 <      painCave.severity = OPENMD_ERROR;
897 <      simError();
898 <    }
891 >    // if( isError ){
892 >    //  
893 >    //  sprintf( painCave.errMsg,
894 >    //         "There was an error setting the simulation information in fortran.\n" );
895 >    //  painCave.isFatal = 1;
896 >    //  painCave.severity = OPENMD_ERROR;
897 >    //  simError();
898 >    //}
899      
900      
901 <    sprintf( checkPointMsg,
902 <             "succesfully sent the simulation information to fortran.\n");
901 >    // sprintf( checkPointMsg,
902 >    //          "succesfully sent the simulation information to fortran.\n");
903      
904 <    errorCheckPoint();
904 >    // errorCheckPoint();
905      
906      // Setup number of neighbors in neighbor list if present
907 <    if (simParams_->haveNeighborListNeighbors()) {
908 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
909 <      setNeighbors(&nlistNeighbors);
910 <    }
911 <  
1005 <
1006 <  }
1007 <
1008 <
1009 <  void SimInfo::setupFortranParallel() {
907 >    //if (simParams_->haveNeighborListNeighbors()) {
908 >    //  int nlistNeighbors = simParams_->getNeighborListNeighbors();
909 >    //  setNeighbors(&nlistNeighbors);
910 >    //}
911 >  
912   #ifdef IS_MPI    
913 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013 <    vector<int> localToGlobalCutoffGroupIndex;
1014 <    SimInfo::MoleculeIterator mi;
1015 <    Molecule::AtomIterator ai;
1016 <    Molecule::CutoffGroupIterator ci;
1017 <    Molecule* mol;
1018 <    Atom* atom;
1019 <    CutoffGroup* cg;
1020 <    mpiSimData parallelData;
1021 <    int isError;
913 >    // mpiSimData parallelData;
914  
1023 –    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1024 –
1025 –      //local index(index in DataStorge) of atom is important
1026 –      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1027 –        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1028 –      }
1029 –
1030 –      //local index of cutoff group is trivial, it only depends on the order of travesing
1031 –      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1032 –        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1033 –      }        
1034 –        
1035 –    }
1036 –
915      //fill up mpiSimData struct
916 <    parallelData.nMolGlobal = getNGlobalMolecules();
917 <    parallelData.nMolLocal = getNMolecules();
918 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
919 <    parallelData.nAtomsLocal = getNAtoms();
920 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
921 <    parallelData.nGroupsLocal = getNCutoffGroups();
922 <    parallelData.myNode = worldRank;
923 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
916 >    // parallelData.nMolGlobal = getNGlobalMolecules();
917 >    // parallelData.nMolLocal = getNMolecules();
918 >    // parallelData.nAtomsGlobal = getNGlobalAtoms();
919 >    // parallelData.nAtomsLocal = getNAtoms();
920 >    // parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
921 >    // parallelData.nGroupsLocal = getNCutoffGroups();
922 >    // parallelData.myNode = worldRank;
923 >    // MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
924  
925      //pass mpiSimData struct and index arrays to fortran
926 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
927 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
928 <                    &localToGlobalCutoffGroupIndex[0], &isError);
926 >    //setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
927 >    //                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
928 >    //                &localToGlobalCutoffGroupIndex[0], &isError);
929  
930 <    if (isError) {
931 <      sprintf(painCave.errMsg,
932 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
933 <      painCave.isFatal = 1;
934 <      simError();
935 <    }
930 >    // if (isError) {
931 >    //   sprintf(painCave.errMsg,
932 >    //           "mpiRefresh errror: fortran didn't like something we gave it.\n");
933 >    //   painCave.isFatal = 1;
934 >    //   simError();
935 >    // }
936  
937 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
938 <    errorCheckPoint();
1061 <
937 >    // sprintf(checkPointMsg, " mpiRefresh successful.\n");
938 >    // errorCheckPoint();
939   #endif
1063 –  }
940  
941 <
942 <  void SimInfo::setupSwitchingFunction() {    
943 <
944 <  }
945 <
946 <  void SimInfo::setupAccumulateBoxDipole() {    
947 <
948 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073 <    if ( simParams_->haveAccumulateBoxDipole() )
1074 <      if ( simParams_->getAccumulateBoxDipole() ) {
1075 <        calcBoxDipole_ = true;
1076 <      }
1077 <
941 >    // initFortranFF(&isError);
942 >    // if (isError) {
943 >    //   sprintf(painCave.errMsg,
944 >    //           "initFortranFF errror: fortran didn't like something we gave it.\n");
945 >    //   painCave.isFatal = 1;
946 >    //   simError();
947 >    // }
948 >    // fortranInitialized_ = true;
949    }
950  
951    void SimInfo::addProperty(GenericData* genData) {
# Line 1111 | Line 982 | namespace OpenMD {
982      Molecule* mol;
983      RigidBody* rb;
984      Atom* atom;
985 +    CutoffGroup* cg;
986      SimInfo::MoleculeIterator mi;
987      Molecule::RigidBodyIterator rbIter;
988 <    Molecule::AtomIterator atomIter;;
988 >    Molecule::AtomIterator atomIter;
989 >    Molecule::CutoffGroupIterator cgIter;
990  
991      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
992          
# Line 1124 | Line 997 | namespace OpenMD {
997        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
998          rb->setSnapshotManager(sman_);
999        }
1000 +
1001 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1002 +        cg->setSnapshotManager(sman_);
1003 +      }
1004      }    
1005      
1006    }

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