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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 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC vs.
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/fCutoffPolicy.h"
58 – #include "UseTheForce/doForces_interface.h"
59 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
57   #include "utils/MemoryUtils.hpp"
58   #include "utils/simError.h"
59   #include "selection/SelectionManager.hpp"
# Line 64 | Line 61
61   #include "UseTheForce/ForceField.hpp"
62   #include "nonbonded/SwitchingFunction.hpp"
63  
67 –
68 – #ifdef IS_MPI
69 – #include "UseTheForce/mpiComponentPlan.h"
70 – #include "UseTheForce/DarkSide/simParallel_interface.h"
71 – #endif
72 –
64   using namespace std;
65   namespace OpenMD {
66    
# Line 80 | Line 71 | namespace OpenMD {
71      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74 <    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
74 >    nConstraints_(0), sman_(NULL), topologyDone_(false),
75      calcBoxDipole_(false), useAtomicVirial_(true) {    
76      
77      MoleculeStamp* molStamp;
# Line 134 | 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 658 | 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() {
666 <    
662 >  void SimInfo::update() {  
663      setupSimVariables();
668 –    setupCutoffs();
669 –    setupSwitching();
670 –    setupElectrostatics();
671 –    setupNeighborlists();
672 –
673 – #ifdef IS_MPI
674 –    setupFortranParallel();
675 – #endif
676 –    setupFortranSim();
677 –    fortranInitialized_ = true;
678 –
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 693 | Line 685 | namespace OpenMD {
685          atomTypes.insert(atom->getAtomType());
686        }      
687      }    
696 –    return atomTypes;        
697 –  }
688  
689 <  /**
700 <   * setupCutoffs
701 <   *
702 <   * Sets the values of cutoffRadius and cutoffMethod
703 <   *
704 <   * cutoffRadius : realType
705 <   *  If the cutoffRadius was explicitly set, use that value.
706 <   *  If the cutoffRadius was not explicitly set:
707 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
708 <   *      No electrostatic atoms?  Poll the atom types present in the
709 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
710 <   *      Use the maximum suggested value that was found.
711 <   *
712 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
713 <   *      If cutoffMethod was explicitly set, use that choice.
714 <   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
715 <   */
716 <  void SimInfo::setupCutoffs() {
717 <    
718 <    if (simParams_->haveCutoffRadius()) {
719 <      cutoffRadius_ = simParams_->getCutoffRadius();
720 <    } else {      
721 <      if (usesElectrostaticAtoms_) {
722 <        sprintf(painCave.errMsg,
723 <                "SimInfo: No value was set for the cutoffRadius.\n"
724 <                "\tOpenMD will use a default value of 12.0 angstroms"
725 <                "\tfor the cutoffRadius.\n");
726 <        painCave.isFatal = 0;
727 <        painCave.severity = OPENMD_INFO;
728 <        simError();
729 <        cutoffRadius_ = 12.0;
730 <      } else {
731 <        RealType thisCut;
732 <        set<AtomType*>::iterator i;
733 <        set<AtomType*> atomTypes;
734 <        atomTypes = getSimulatedAtomTypes();        
735 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
736 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
737 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
738 <        }
739 <        sprintf(painCave.errMsg,
740 <                "SimInfo: No value was set for the cutoffRadius.\n"
741 <                "\tOpenMD will use %lf angstroms.\n",
742 <                cutoffRadius_);
743 <        painCave.isFatal = 0;
744 <        painCave.severity = OPENMD_INFO;
745 <        simError();
746 <      }            
747 <    }
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;    
755 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
756 <  
757 <    if (simParams_->haveCutoffMethod()) {
758 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
759 <      map<string, CutoffMethod>::iterator i;
760 <      i = stringToCutoffMethod.find(cutMeth);
761 <      if (i == stringToCutoffMethod.end()) {
762 <        sprintf(painCave.errMsg,
763 <                "SimInfo: Could not find chosen cutoffMethod %s\n"
764 <                "\tShould be one of: "
765 <                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
766 <                cutMeth.c_str());
767 <        painCave.isFatal = 1;
768 <        painCave.severity = OPENMD_ERROR;
769 <        simError();
770 <      } else {
771 <        cutoffMethod_ = i->second;
772 <      }
773 <    } else {
774 <      sprintf(painCave.errMsg,
775 <              "SimInfo: No value was set for the cutoffMethod.\n"
776 <              "\tOpenMD will use SHIFTED_FORCE.\n");
777 <        painCave.isFatal = 0;
778 <        painCave.severity = OPENMD_INFO;
779 <        simError();
780 <        cutoffMethod_ = SHIFTED_FORCE;        
781 <    }
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 <  }
785 <  
786 <  /**
787 <   * setupSwitching
788 <   *
789 <   * Sets the values of switchingRadius and
790 <   *  If the switchingRadius was explicitly set, use that value (but check it)
791 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
792 <   */
793 <  void SimInfo::setupSwitching() {
794 <    
795 <    if (simParams_->haveSwitchingRadius()) {
796 <      switchingRadius_ = simParams_->getSwitchingRadius();
797 <      if (switchingRadius_ > cutoffRadius_) {        
798 <        sprintf(painCave.errMsg,
799 <                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
800 <                switchingRadius_, cutoffRadius_);
801 <        painCave.isFatal = 1;
802 <        painCave.severity = OPENMD_ERROR;
803 <        simError();
804 <      }
805 <    } else {      
806 <      switchingRadius_ = 0.85 * cutoffRadius_;
807 <      sprintf(painCave.errMsg,
808 <              "SimInfo: No value was set for the switchingRadius.\n"
809 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
810 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
811 <      painCave.isFatal = 0;
812 <      painCave.severity = OPENMD_WARNING;
813 <      simError();
814 <    }          
815 <  
816 <    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();
822 <      toUpper(funcType);
823 <      if (funcType == "CUBIC") {
824 <        ft = cubic;
825 <      } else {
826 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
827 <          ft = fifth_order_poly;
828 <        } else {
829 <          // throw error        
830 <          sprintf( painCave.errMsg,
831 <                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
832 <                   "\tswitchingFunctionType must be one of: "
833 <                   "\"cubic\" or \"fifth_order_polynomial\".",
834 <                   funcType.c_str() );
835 <          painCave.isFatal = 1;
836 <          painCave.severity = OPENMD_ERROR;
837 <          simError();
838 <        }          
839 <      }
840 <    }
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()) {
853 <      skinThickness_ = simParams_->getSkinThickness();
854 <    } else {      
855 <      skinThickness_ = 1.0;
856 <      sprintf(painCave.errMsg,
857 <              "SimInfo Warning: No value was set for the skinThickness.\n"
858 <              "\tOpenMD will use a default value of %f Angstroms\n"
859 <              "\tfor this simulation\n", skinThickness_);
860 <      painCave.isFatal = 0;
861 <      simError();
862 <    }            
863 <  }
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  
865 –  void SimInfo::setupSimType() {
749      set<AtomType*>::iterator i;
750      set<AtomType*> atomTypes;
751 <    atomTypes = getSimulatedAtomTypes();
869 <
870 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
871 <
751 >    atomTypes = getSimulatedAtomTypes();    
752      int usesElectrostatic = 0;
753      int usesMetallic = 0;
754      int usesDirectional = 0;
# Line 890 | Line 770 | namespace OpenMD {
770      temp = usesElectrostatic;
771      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772   #endif
893 –    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
894 –    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
895 –    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
896 –    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
897 –    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
898 –    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
773    }
774  
775 <  void SimInfo::setupFortranSim() {
776 <    int isError;
777 <    int nExclude, nOneTwo, nOneThree, nOneFour;
778 <    vector<int> fortranGlobalGroupMembership;
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 <    notifyFortranSkinThickness(&skinThickness_);
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  
908 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
909 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
910 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
793  
794 <    isError = 0;
794 >  vector<int> SimInfo::getGlobalGroupIndices() {
795 >    SimInfo::MoleculeIterator mi;
796 >    Molecule* mol;
797 >    Molecule::CutoffGroupIterator ci;
798 >    CutoffGroup* cg;
799  
800 <    //globalGroupMembership_ is filled by SimCreator    
801 <    for (int i = 0; i < nGlobalAtoms_; i++) {
802 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
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::prepareTopology() {
816 +    int nExclude, nOneTwo, nOneThree, nOneFour;
817 +
818      //calculate mass ratio of cutoff group
920 –    vector<RealType> mfact;
819      SimInfo::MoleculeIterator mi;
820      Molecule* mol;
821      Molecule::CutoffGroupIterator ci;
# Line 926 | Line 824 | namespace OpenMD {
824      Atom* atom;
825      RealType totalMass;
826  
827 <    //to avoid memory reallocation, reserve enough space for mfact
828 <    mfact.reserve(getNCutoffGroups());
827 >    //to avoid memory reallocation, reserve enough space for massFactors_
828 >    massFactors_.clear();
829 >    massFactors_.reserve(getNCutoffGroups());
830      
831      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
832 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
832 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
833 >           cg = mol->nextCutoffGroup(ci)) {
834  
835          totalMass = cg->getMass();
836          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
837            // Check for massless groups - set mfact to 1 if true
838            if (totalMass != 0)
839 <            mfact.push_back(atom->getMass()/totalMass);
839 >            massFactors_.push_back(atom->getMass()/totalMass);
840            else
841 <            mfact.push_back( 1.0 );
841 >            massFactors_.push_back( 1.0 );
842          }
843        }      
844      }
845  
846 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
947 <    vector<int> identArray;
846 >    // Build the identArray_
847  
848 <    //to avoid memory reallocation, reserve enough space identArray
849 <    identArray.reserve(getNAtoms());
951 <    
848 >    identArray_.clear();
849 >    identArray_.reserve(getNAtoms());    
850      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
851        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
852 <        identArray.push_back(atom->getIdent());
852 >        identArray_.push_back(atom->getIdent());
853        }
854      }    
957 –
958 –    //fill molMembershipArray
959 –    //molMembershipArray is filled by SimCreator    
960 –    vector<int> molMembershipArray(nGlobalAtoms_);
961 –    for (int i = 0; i < nGlobalAtoms_; i++) {
962 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
963 –    }
855      
856 <    //setup fortran simulation
856 >    //scan topology
857  
858      nExclude = excludedInteractions_.getSize();
859      nOneTwo = oneTwoInteractions_.getSize();
# Line 974 | Line 865 | namespace OpenMD {
865      int* oneThreeList = oneThreeInteractions_.getPairList();
866      int* oneFourList = oneFourInteractions_.getPairList();
867  
868 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
869 <                   &nExclude, excludeList,
870 <                   &nOneTwo, oneTwoList,
871 <                   &nOneThree, oneThreeList,
872 <                   &nOneFour, oneFourList,
873 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874 <                   &fortranGlobalGroupMembership[0], &isError);
868 >    //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
869 >    //               &nExclude, excludeList,
870 >    //               &nOneTwo, oneTwoList,
871 >    //               &nOneThree, oneThreeList,
872 >    //               &nOneFour, oneFourList,
873 >    //               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874 >    //               &fortranGlobalGroupMembership[0], &isError);
875      
876 <    if( isError ){
986 <      
987 <      sprintf( painCave.errMsg,
988 <               "There was an error setting the simulation information in fortran.\n" );
989 <      painCave.isFatal = 1;
990 <      painCave.severity = OPENMD_ERROR;
991 <      simError();
992 <    }
993 <    
994 <    
995 <    sprintf( checkPointMsg,
996 <             "succesfully sent the simulation information to fortran.\n");
997 <    
998 <    errorCheckPoint();
999 <    
1000 <    // Setup number of neighbors in neighbor list if present
1001 <    if (simParams_->haveNeighborListNeighbors()) {
1002 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
1003 <      setNeighbors(&nlistNeighbors);
1004 <    }
1005 <  
1006 <
1007 <  }
1008 <
1009 <
1010 <  void SimInfo::setupFortranParallel() {
1011 < #ifdef IS_MPI    
1012 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1013 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014 <    vector<int> localToGlobalCutoffGroupIndex;
1015 <    SimInfo::MoleculeIterator mi;
1016 <    Molecule::AtomIterator ai;
1017 <    Molecule::CutoffGroupIterator ci;
1018 <    Molecule* mol;
1019 <    Atom* atom;
1020 <    CutoffGroup* cg;
1021 <    mpiSimData parallelData;
1022 <    int isError;
1023 <
1024 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1025 <
1026 <      //local index(index in DataStorge) of atom is important
1027 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1028 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1029 <      }
1030 <
1031 <      //local index of cutoff group is trivial, it only depends on the order of travesing
1032 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1033 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1034 <      }        
1035 <        
1036 <    }
1037 <
1038 <    //fill up mpiSimData struct
1039 <    parallelData.nMolGlobal = getNGlobalMolecules();
1040 <    parallelData.nMolLocal = getNMolecules();
1041 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
1042 <    parallelData.nAtomsLocal = getNAtoms();
1043 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1044 <    parallelData.nGroupsLocal = getNCutoffGroups();
1045 <    parallelData.myNode = worldRank;
1046 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1047 <
1048 <    //pass mpiSimData struct and index arrays to fortran
1049 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1050 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1051 <                    &localToGlobalCutoffGroupIndex[0], &isError);
1052 <
1053 <    if (isError) {
1054 <      sprintf(painCave.errMsg,
1055 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1056 <      painCave.isFatal = 1;
1057 <      simError();
1058 <    }
1059 <
1060 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1061 <    errorCheckPoint();
1062 <
1063 < #endif
1064 <  }
1065 <
1066 <
1067 <  void SimInfo::setupSwitchingFunction() {    
1068 <
1069 <  }
1070 <
1071 <  void SimInfo::setupAccumulateBoxDipole() {    
1072 <
1073 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1074 <    if ( simParams_->haveAccumulateBoxDipole() )
1075 <      if ( simParams_->getAccumulateBoxDipole() ) {
1076 <        calcBoxDipole_ = true;
1077 <      }
1078 <
876 >    topologyDone_ = true;
877    }
878  
879    void SimInfo::addProperty(GenericData* genData) {
# Line 1112 | Line 910 | namespace OpenMD {
910      Molecule* mol;
911      RigidBody* rb;
912      Atom* atom;
913 +    CutoffGroup* cg;
914      SimInfo::MoleculeIterator mi;
915      Molecule::RigidBodyIterator rbIter;
916 <    Molecule::AtomIterator atomIter;;
916 >    Molecule::AtomIterator atomIter;
917 >    Molecule::CutoffGroupIterator cgIter;
918  
919      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920          
# Line 1125 | Line 925 | namespace OpenMD {
925        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
926          rb->setSnapshotManager(sman_);
927        }
928 +
929 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
930 +        cg->setSnapshotManager(sman_);
931 +      }
932      }    
933      
934    }

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