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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 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/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"
60   #include "io/ForceFieldOptions.hpp"
61   #include "UseTheForce/ForceField.hpp"
62   #include "nonbonded/SwitchingFunction.hpp"
66 –
67 –
68 – #ifdef IS_MPI
69 – #include "UseTheForce/mpiComponentPlan.h"
70 – #include "UseTheForce/DarkSide/simParallel_interface.h"
71 – #endif
63  
64   using namespace std;
65   namespace OpenMD {
# 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 +
129      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130      
131      //every free atom (atom does not belong to rigid bodies) is an
# Line 276 | Line 268 | namespace OpenMD {
268      fdf_ = fdf_local;
269   #endif
270      return fdf_;
271 +  }
272 +  
273 +  unsigned int SimInfo::getNLocalCutoffGroups(){
274 +    int nLocalCutoffAtoms = 0;
275 +    Molecule* mol;
276 +    MoleculeIterator mi;
277 +    CutoffGroup* cg;
278 +    Molecule::CutoffGroupIterator ci;
279 +    
280 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
281 +      
282 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
283 +           cg = mol->nextCutoffGroup(ci)) {
284 +        nLocalCutoffAtoms += cg->getNumAtom();
285 +        
286 +      }        
287 +    }
288 +    
289 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
290    }
291      
292    void SimInfo::calcNdfRaw() {
# Line 658 | Line 669 | namespace OpenMD {
669    /**
670     * update
671     *
672 <   *  Performs the global checks and variable settings after the objects have been
673 <   *  created.
672 >   *  Performs the global checks and variable settings after the
673 >   *  objects have been created.
674     *
675     */
676 <  void SimInfo::update() {
666 <    
676 >  void SimInfo::update() {  
677      setupSimVariables();
668 –    setupCutoffs();
669 –    setupSwitching();
670 –    setupElectrostatics();
671 –    setupNeighborlists();
672 –
673 – #ifdef IS_MPI
674 –    setupFortranParallel();
675 – #endif
676 –    setupFortranSim();
677 –    fortranInitialized_ = true;
678 –
678      calcNdf();
679      calcNdfRaw();
680      calcNdfTrans();
681    }
682    
683 +  /**
684 +   * getSimulatedAtomTypes
685 +   *
686 +   * Returns an STL set of AtomType* that are actually present in this
687 +   * simulation.  Must query all processors to assemble this information.
688 +   *
689 +   */
690    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
691      SimInfo::MoleculeIterator mi;
692      Molecule* mol;
# Line 693 | Line 699 | namespace OpenMD {
699          atomTypes.insert(atom->getAtomType());
700        }      
701      }    
696 –    return atomTypes;        
697 –  }
702  
703 <  /**
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 <    }
703 > #ifdef IS_MPI
704  
705 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
705 >    // loop over the found atom types on this processor, and add their
706 >    // numerical idents to a vector:
707  
708 <    map<string, CutoffMethod> stringToCutoffMethod;
709 <    stringToCutoffMethod["HARD"] = HARD;
710 <    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
711 <    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 <    }
708 >    vector<int> foundTypes;
709 >    set<AtomType*>::iterator i;
710 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
711 >      foundTypes.push_back( (*i)->getIdent() );
712  
713 <    InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
714 <  }
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_);
713 >    // count_local holds the number of found types on this processor
714 >    int count_local = foundTypes.size();
715  
716 <    SwitchingFunctionType ft;
716 >    // count holds the total number of found types on all processors
717 >    // (some will be redundant with the ones found locally):
718 >    int count;
719 >    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
720 >
721 >    // create a vector to hold the globally found types, and resize it:
722 >    vector<int> ftGlobal;
723 >    ftGlobal.resize(count);
724 >    vector<int> counts;
725 >
726 >    int nproc = MPI::COMM_WORLD.Get_size();
727 >    counts.resize(nproc);
728 >    vector<int> disps;
729 >    disps.resize(nproc);
730 >
731 >    // now spray out the foundTypes to all the other processors:
732      
733 <    if (simParams_->haveSwitchingFunctionType()) {
734 <      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 <    }
733 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
734 >                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
735  
736 <    InteractionManager::Instance()->setSwitchingFunctionType(ft);
736 >    // foundIdents is a stl set, so inserting an already found ident
737 >    // will have no effect.
738 >    set<int> foundIdents;
739 >    vector<int>::iterator j;
740 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
741 >      foundIdents.insert((*j));
742 >    
743 >    // now iterate over the foundIdents and get the actual atom types
744 >    // that correspond to these:
745 >    set<int>::iterator it;
746 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
747 >      atomTypes.insert( forceField_->getAtomType((*it)) );
748 >
749 > #endif
750 >    
751 >    return atomTypes;        
752    }
753  
754 <  /**
755 <   * setupSkinThickness
756 <   *
757 <   *  If the skinThickness was explicitly set, use that value (but check it)
758 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
759 <   */
760 <  void SimInfo::setupSkinThickness() {    
761 <    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 <  }
754 >  void SimInfo::setupSimVariables() {
755 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
756 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
757 >    calcBoxDipole_ = false;
758 >    if ( simParams_->haveAccumulateBoxDipole() )
759 >      if ( simParams_->getAccumulateBoxDipole() ) {
760 >        calcBoxDipole_ = true;      
761 >      }
762  
865 –  void SimInfo::setupSimType() {
763      set<AtomType*>::iterator i;
764      set<AtomType*> atomTypes;
765 <    atomTypes = getSimulatedAtomTypes();
869 <
870 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
871 <
765 >    atomTypes = getSimulatedAtomTypes();    
766      int usesElectrostatic = 0;
767      int usesMetallic = 0;
768      int usesDirectional = 0;
# Line 890 | Line 784 | namespace OpenMD {
784      temp = usesElectrostatic;
785      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786   #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_;
787    }
788  
789 <  void SimInfo::setupFortranSim() {
790 <    int isError;
791 <    int nExclude, nOneTwo, nOneThree, nOneFour;
792 <    vector<int> fortranGlobalGroupMembership;
789 >
790 >  vector<int> SimInfo::getGlobalAtomIndices() {
791 >    SimInfo::MoleculeIterator mi;
792 >    Molecule* mol;
793 >    Molecule::AtomIterator ai;
794 >    Atom* atom;
795 >
796 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
797      
798 <    notifyFortranSkinThickness(&skinThickness_);
798 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
799 >      
800 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
801 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
802 >      }
803 >    }
804 >    return GlobalAtomIndices;
805 >  }
806  
908 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
909 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
910 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
807  
808 <    isError = 0;
808 >  vector<int> SimInfo::getGlobalGroupIndices() {
809 >    SimInfo::MoleculeIterator mi;
810 >    Molecule* mol;
811 >    Molecule::CutoffGroupIterator ci;
812 >    CutoffGroup* cg;
813  
814 <    //globalGroupMembership_ is filled by SimCreator    
815 <    for (int i = 0; i < nGlobalAtoms_; i++) {
816 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
814 >    vector<int> GlobalGroupIndices;
815 >    
816 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
817 >      
818 >      //local index of cutoff group is trivial, it only depends on the
819 >      //order of travesing
820 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
821 >           cg = mol->nextCutoffGroup(ci)) {
822 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
823 >      }        
824      }
825 +    return GlobalGroupIndices;
826 +  }
827  
828 +
829 +  void SimInfo::prepareTopology() {
830 +    int nExclude, nOneTwo, nOneThree, nOneFour;
831 +
832      //calculate mass ratio of cutoff group
920 –    vector<RealType> mfact;
833      SimInfo::MoleculeIterator mi;
834      Molecule* mol;
835      Molecule::CutoffGroupIterator ci;
# Line 926 | Line 838 | namespace OpenMD {
838      Atom* atom;
839      RealType totalMass;
840  
841 <    //to avoid memory reallocation, reserve enough space for mfact
842 <    mfact.reserve(getNCutoffGroups());
841 >    /**
842 >     * The mass factor is the relative mass of an atom to the total
843 >     * mass of the cutoff group it belongs to.  By default, all atoms
844 >     * are their own cutoff groups, and therefore have mass factors of
845 >     * 1.  We need some special handling for massless atoms, which
846 >     * will be treated as carrying the entire mass of the cutoff
847 >     * group.
848 >     */
849 >    massFactors_.clear();
850 >    massFactors_.resize(getNAtoms(), 1.0);
851      
852      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
853 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
853 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
854 >           cg = mol->nextCutoffGroup(ci)) {
855  
856          totalMass = cg->getMass();
857          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
858            // Check for massless groups - set mfact to 1 if true
859 <          if (totalMass != 0)
860 <            mfact.push_back(atom->getMass()/totalMass);
859 >          if (totalMass != 0)
860 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
861            else
862 <            mfact.push_back( 1.0 );
862 >            massFactors_[atom->getLocalIndex()] = 1.0;
863          }
864        }      
865      }
866  
867 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
947 <    vector<int> identArray;
867 >    // Build the identArray_
868  
869 <    //to avoid memory reallocation, reserve enough space identArray
870 <    identArray.reserve(getNAtoms());
951 <    
869 >    identArray_.clear();
870 >    identArray_.reserve(getNAtoms());    
871      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
872        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
873 <        identArray.push_back(atom->getIdent());
873 >        identArray_.push_back(atom->getIdent());
874        }
875      }    
876 <
877 <    //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 <    }
964 <    
965 <    //setup fortran simulation
876 >    
877 >    //scan topology
878  
879      nExclude = excludedInteractions_.getSize();
880      nOneTwo = oneTwoInteractions_.getSize();
# Line 974 | Line 886 | namespace OpenMD {
886      int* oneThreeList = oneThreeInteractions_.getPairList();
887      int* oneFourList = oneFourInteractions_.getPairList();
888  
889 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
978 <                   &nExclude, excludeList,
979 <                   &nOneTwo, oneTwoList,
980 <                   &nOneThree, oneThreeList,
981 <                   &nOneFour, oneFourList,
982 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
983 <                   &fortranGlobalGroupMembership[0], &isError);
984 <    
985 <    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 <
889 >    topologyDone_ = true;
890    }
891  
892    void SimInfo::addProperty(GenericData* genData) {
# Line 1112 | Line 923 | namespace OpenMD {
923      Molecule* mol;
924      RigidBody* rb;
925      Atom* atom;
926 +    CutoffGroup* cg;
927      SimInfo::MoleculeIterator mi;
928      Molecule::RigidBodyIterator rbIter;
929 <    Molecule::AtomIterator atomIter;;
929 >    Molecule::AtomIterator atomIter;
930 >    Molecule::CutoffGroupIterator cgIter;
931  
932      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
933          
# Line 1124 | Line 937 | namespace OpenMD {
937          
938        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
939          rb->setSnapshotManager(sman_);
940 +      }
941 +
942 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
943 +        cg->setSnapshotManager(sman_);
944        }
945      }    
946      

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