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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 1586 by gezelter, Tue Jun 21 06:34:35 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 79 | 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 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 +
129      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130      
131      //every free atom (atom does not belong to rigid bodies) is an
# Line 276 | Line 269 | namespace OpenMD {
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() {
293      int ndfRaw_local;
294  
# Line 657 | 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() {
665 <    
676 >  void SimInfo::update() {  
677      setupSimVariables();
667 –    setupCutoffs();
668 –    setupSwitching();
669 –    setupElectrostatics();
670 –    setupNeighborlists();
671 –
672 – #ifdef IS_MPI
673 –    setupFortranParallel();
674 – #endif
675 –    setupFortranSim();
676 –    fortranInitialized_ = true;
677 –
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 692 | Line 699 | namespace OpenMD {
699          atomTypes.insert(atom->getAtomType());
700        }      
701      }    
695 –    return atomTypes;        
696 –  }
702  
703 <  /**
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 <    }
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;    
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 <    }
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 <  }
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_);
713 >    // count_local holds the number of found types on this processor
714 >    int count_local = foundTypes.size();
715  
716 <    SwitchingFunctionType ft;
717 <    
718 <    if (simParams_->haveSwitchingFunctionType()) {
719 <      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 <    }
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 <    InteractionManager::Instance()->setSwitchingFunctionType(ft);
722 <  }
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 <  /**
727 <   * setupSkinThickness
728 <   *
729 <   *  If the skinThickness was explicitly set, use that value (but check it)
730 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
731 <   */
732 <  void SimInfo::setupSkinThickness() {    
733 <    if (simParams_->haveSkinThickness()) {
734 <      skinThickness_ = simParams_->getSkinThickness();
735 <    } else {      
736 <      skinThickness_ = 1.0;
737 <      sprintf(painCave.errMsg,
738 <              "SimInfo Warning: No value was set for the skinThickness.\n"
739 <              "\tOpenMD will use a default value of %f Angstroms\n"
740 <              "\tfor this simulation\n", skinThickness_);
741 <      painCave.isFatal = 0;
742 <      simError();
743 <    }            
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 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
734 >                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
735 >
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 <  void SimInfo::setupSimType() {
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 >    
763      set<AtomType*>::iterator i;
764      set<AtomType*> atomTypes;
765 <    atomTypes = getSimulatedAtomTypes();
868 <
869 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
870 <
765 >    atomTypes = getSimulatedAtomTypes();    
766      int usesElectrostatic = 0;
767      int usesMetallic = 0;
768      int usesDirectional = 0;
# Line 877 | Line 772 | namespace OpenMD {
772        usesMetallic |= (*i)->isMetal();
773        usesDirectional |= (*i)->isDirectional();
774      }
775 <
775 >    
776   #ifdef IS_MPI    
777      int temp;
778      temp = usesDirectional;
779      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
780 <
780 >    
781      temp = usesMetallic;
782      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
783 <
783 >    
784      temp = usesElectrostatic;
785      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786 + #else
787 +
788 +    usesDirectionalAtoms_ = usesDirectional;
789 +    usesMetallicAtoms_ = usesMetallic;
790 +    usesElectrostaticAtoms_ = usesElectrostatic;
791 +
792   #endif
793 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
794 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
795 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
796 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
793 >    
794 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
795 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
796 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
797    }
798  
799 <  void SimInfo::setupFortranSim() {
800 <    int isError;
801 <    int nExclude, nOneTwo, nOneThree, nOneFour;
802 <    vector<int> fortranGlobalGroupMembership;
799 >
800 >  vector<int> SimInfo::getGlobalAtomIndices() {
801 >    SimInfo::MoleculeIterator mi;
802 >    Molecule* mol;
803 >    Molecule::AtomIterator ai;
804 >    Atom* atom;
805 >
806 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
807      
808 <    notifyFortranSkinThickness(&skinThickness_);
808 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
809 >      
810 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
811 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
812 >      }
813 >    }
814 >    return GlobalAtomIndices;
815 >  }
816  
907 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
817  
818 <    isError = 0;
818 >  vector<int> SimInfo::getGlobalGroupIndices() {
819 >    SimInfo::MoleculeIterator mi;
820 >    Molecule* mol;
821 >    Molecule::CutoffGroupIterator ci;
822 >    CutoffGroup* cg;
823  
824 <    //globalGroupMembership_ is filled by SimCreator    
825 <    for (int i = 0; i < nGlobalAtoms_; i++) {
826 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
824 >    vector<int> GlobalGroupIndices;
825 >    
826 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
827 >      
828 >      //local index of cutoff group is trivial, it only depends on the
829 >      //order of travesing
830 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
831 >           cg = mol->nextCutoffGroup(ci)) {
832 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
833 >      }        
834      }
835 +    return GlobalGroupIndices;
836 +  }
837  
838 +
839 +  void SimInfo::prepareTopology() {
840 +    int nExclude, nOneTwo, nOneThree, nOneFour;
841 +
842      //calculate mass ratio of cutoff group
919 –    vector<RealType> mfact;
843      SimInfo::MoleculeIterator mi;
844      Molecule* mol;
845      Molecule::CutoffGroupIterator ci;
# Line 925 | Line 848 | namespace OpenMD {
848      Atom* atom;
849      RealType totalMass;
850  
851 <    //to avoid memory reallocation, reserve enough space for mfact
852 <    mfact.reserve(getNCutoffGroups());
851 >    /**
852 >     * The mass factor is the relative mass of an atom to the total
853 >     * mass of the cutoff group it belongs to.  By default, all atoms
854 >     * are their own cutoff groups, and therefore have mass factors of
855 >     * 1.  We need some special handling for massless atoms, which
856 >     * will be treated as carrying the entire mass of the cutoff
857 >     * group.
858 >     */
859 >    massFactors_.clear();
860 >    massFactors_.resize(getNAtoms(), 1.0);
861      
862 +    cerr << "mfs in si = " << massFactors_.size() << "\n";
863      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
864 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
864 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865 >           cg = mol->nextCutoffGroup(ci)) {
866  
867          totalMass = cg->getMass();
868          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
869            // Check for massless groups - set mfact to 1 if true
870 <          if (totalMass != 0)
871 <            mfact.push_back(atom->getMass()/totalMass);
870 >          if (totalMass != 0)
871 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
872            else
873 <            mfact.push_back( 1.0 );
873 >            massFactors_[atom->getLocalIndex()] = 1.0;
874          }
875        }      
876      }
877  
878 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946 <    vector<int> identArray;
878 >    // Build the identArray_
879  
880 <    //to avoid memory reallocation, reserve enough space identArray
881 <    identArray.reserve(getNAtoms());
950 <    
880 >    identArray_.clear();
881 >    identArray_.reserve(getNAtoms());    
882      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
883        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
884 <        identArray.push_back(atom->getIdent());
884 >        identArray_.push_back(atom->getIdent());
885        }
886      }    
956 –
957 –    //fill molMembershipArray
958 –    //molMembershipArray is filled by SimCreator    
959 –    vector<int> molMembershipArray(nGlobalAtoms_);
960 –    for (int i = 0; i < nGlobalAtoms_; i++) {
961 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
962 –    }
887      
888 <    //setup fortran simulation
888 >    //scan topology
889  
890      nExclude = excludedInteractions_.getSize();
891      nOneTwo = oneTwoInteractions_.getSize();
# Line 973 | Line 897 | namespace OpenMD {
897      int* oneThreeList = oneThreeInteractions_.getPairList();
898      int* oneFourList = oneFourInteractions_.getPairList();
899  
900 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
977 <                   &nExclude, excludeList,
978 <                   &nOneTwo, oneTwoList,
979 <                   &nOneThree, oneThreeList,
980 <                   &nOneFour, oneFourList,
981 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
982 <                   &fortranGlobalGroupMembership[0], &isError);
983 <    
984 <    if( isError ){
985 <      
986 <      sprintf( painCave.errMsg,
987 <               "There was an error setting the simulation information in fortran.\n" );
988 <      painCave.isFatal = 1;
989 <      painCave.severity = OPENMD_ERROR;
990 <      simError();
991 <    }
992 <    
993 <    
994 <    sprintf( checkPointMsg,
995 <             "succesfully sent the simulation information to fortran.\n");
996 <    
997 <    errorCheckPoint();
998 <    
999 <    // Setup number of neighbors in neighbor list if present
1000 <    if (simParams_->haveNeighborListNeighbors()) {
1001 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
1002 <      setNeighbors(&nlistNeighbors);
1003 <    }
1004 <  
1005 <
1006 <  }
1007 <
1008 <
1009 <  void SimInfo::setupFortranParallel() {
1010 < #ifdef IS_MPI    
1011 <    //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;
1022 <
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 <
1037 <    //fill up mpiSimData struct
1038 <    parallelData.nMolGlobal = getNGlobalMolecules();
1039 <    parallelData.nMolLocal = getNMolecules();
1040 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
1041 <    parallelData.nAtomsLocal = getNAtoms();
1042 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1043 <    parallelData.nGroupsLocal = getNCutoffGroups();
1044 <    parallelData.myNode = worldRank;
1045 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1046 <
1047 <    //pass mpiSimData struct and index arrays to fortran
1048 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1049 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1050 <                    &localToGlobalCutoffGroupIndex[0], &isError);
1051 <
1052 <    if (isError) {
1053 <      sprintf(painCave.errMsg,
1054 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1055 <      painCave.isFatal = 1;
1056 <      simError();
1057 <    }
1058 <
1059 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1060 <    errorCheckPoint();
1061 <
1062 < #endif
1063 <  }
1064 <
1065 <
1066 <  void SimInfo::setupSwitchingFunction() {    
1067 <
1068 <  }
1069 <
1070 <  void SimInfo::setupAccumulateBoxDipole() {    
1071 <
1072 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073 <    if ( simParams_->haveAccumulateBoxDipole() )
1074 <      if ( simParams_->getAccumulateBoxDipole() ) {
1075 <        calcBoxDipole_ = true;
1076 <      }
1077 <
900 >    topologyDone_ = true;
901    }
902  
903    void SimInfo::addProperty(GenericData* genData) {
# Line 1111 | Line 934 | namespace OpenMD {
934      Molecule* mol;
935      RigidBody* rb;
936      Atom* atom;
937 +    CutoffGroup* cg;
938      SimInfo::MoleculeIterator mi;
939      Molecule::RigidBodyIterator rbIter;
940 <    Molecule::AtomIterator atomIter;;
940 >    Molecule::AtomIterator atomIter;
941 >    Molecule::CutoffGroupIterator cgIter;
942  
943      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
944          
# Line 1124 | Line 949 | namespace OpenMD {
949        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
950          rb->setSnapshotManager(sman_);
951        }
952 +
953 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
954 +        cg->setSnapshotManager(sman_);
955 +      }
956      }    
957      
958    }

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