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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 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC vs.
Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/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 –
63   #ifdef IS_MPI
64 < #include "UseTheForce/mpiComponentPlan.h"
65 < #include "UseTheForce/DarkSide/simParallel_interface.h"
69 < #endif
64 > #include <mpi.h>
65 > #endif
66  
67   using namespace std;
68   namespace OpenMD {
# Line 78 | Line 74 | namespace OpenMD {
74      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
76      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
77 <    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
77 >    nConstraints_(0), sman_(NULL), topologyDone_(false),
78      calcBoxDipole_(false), useAtomicVirial_(true) {    
79      
80      MoleculeStamp* molStamp;
# Line 132 | Line 128 | namespace OpenMD {
128      //equal to the total number of atoms minus number of atoms belong to
129      //cutoff group defined in meta-data file plus the number of cutoff
130      //groups defined in meta-data file
131 +
132      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133      
134      //every free atom (atom does not belong to rigid bodies) is an
# Line 274 | Line 271 | namespace OpenMD {
271      fdf_ = fdf_local;
272   #endif
273      return fdf_;
274 +  }
275 +  
276 +  unsigned int SimInfo::getNLocalCutoffGroups(){
277 +    int nLocalCutoffAtoms = 0;
278 +    Molecule* mol;
279 +    MoleculeIterator mi;
280 +    CutoffGroup* cg;
281 +    Molecule::CutoffGroupIterator ci;
282 +    
283 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
284 +      
285 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
286 +           cg = mol->nextCutoffGroup(ci)) {
287 +        nLocalCutoffAtoms += cg->getNumAtom();
288 +        
289 +      }        
290 +    }
291 +    
292 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
293    }
294      
295    void SimInfo::calcNdfRaw() {
# Line 656 | Line 672 | namespace OpenMD {
672    /**
673     * update
674     *
675 <   *  Performs the global checks and variable settings after the objects have been
676 <   *  created.
675 >   *  Performs the global checks and variable settings after the
676 >   *  objects have been created.
677     *
678     */
679 <  void SimInfo::update() {
664 <    
679 >  void SimInfo::update() {  
680      setupSimVariables();
666 –    setupCutoffs();
667 –    setupSwitching();
668 –    setupElectrostatics();
669 –    setupNeighborlists();
670 –
671 – #ifdef IS_MPI
672 –    setupFortranParallel();
673 – #endif
674 –    setupFortranSim();
675 –    fortranInitialized_ = true;
676 –
681      calcNdf();
682      calcNdfRaw();
683      calcNdfTrans();
684    }
685    
686 +  /**
687 +   * getSimulatedAtomTypes
688 +   *
689 +   * Returns an STL set of AtomType* that are actually present in this
690 +   * simulation.  Must query all processors to assemble this information.
691 +   *
692 +   */
693    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
694      SimInfo::MoleculeIterator mi;
695      Molecule* mol;
# Line 686 | Line 697 | namespace OpenMD {
697      Atom* atom;
698      set<AtomType*> atomTypes;
699      
700 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
701 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
700 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
701 >      for(atom = mol->beginAtom(ai); atom != NULL;
702 >          atom = mol->nextAtom(ai)) {
703          atomTypes.insert(atom->getAtomType());
704        }      
705      }    
706 <    return atomTypes;        
707 <  }
706 >    
707 > #ifdef IS_MPI
708  
709 <  /**
710 <   * setupCutoffs
699 <   *
700 <   * Sets the values of cutoffRadius and cutoffMethod
701 <   *
702 <   * cutoffRadius : realType
703 <   *  If the cutoffRadius was explicitly set, use that value.
704 <   *  If the cutoffRadius was not explicitly set:
705 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
706 <   *      No electrostatic atoms?  Poll the atom types present in the
707 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
708 <   *      Use the maximum suggested value that was found.
709 <   *
710 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
711 <   *      If cutoffMethod was explicitly set, use that choice.
712 <   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
713 <   */
714 <  void SimInfo::setupCutoffs() {
709 >    // loop over the found atom types on this processor, and add their
710 >    // numerical idents to a vector:
711      
712 <    if (simParams_->haveCutoffRadius()) {
713 <      cutoffRadius_ = simParams_->getCutoffRadius();
714 <    } else {      
715 <      if (usesElectrostaticAtoms_) {
720 <        sprintf(painCave.errMsg,
721 <                "SimInfo: No value was set for the cutoffRadius.\n"
722 <                "\tOpenMD will use a default value of 12.0 angstroms"
723 <                "\tfor the cutoffRadius.\n");
724 <        painCave.isFatal = 0;
725 <        painCave.severity = OPENMD_INFO;
726 <        simError();
727 <        cutoffRadius_ = 12.0;
728 <      } else {
729 <        RealType thisCut;
730 <        set<AtomType*>::iterator i;
731 <        set<AtomType*> atomTypes;
732 <        atomTypes = getSimulatedAtomTypes();        
733 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
735 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
736 <        }
737 <        sprintf(painCave.errMsg,
738 <                "SimInfo: No value was set for the cutoffRadius.\n"
739 <                "\tOpenMD will use %lf angstroms.\n",
740 <                cutoffRadius_);
741 <        painCave.isFatal = 0;
742 <        painCave.severity = OPENMD_INFO;
743 <        simError();
744 <      }            
745 <    }
712 >    vector<int> foundTypes;
713 >    set<AtomType*>::iterator i;
714 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
715 >      foundTypes.push_back( (*i)->getIdent() );
716  
717 <    map<string, CutoffMethod> stringToCutoffMethod;
718 <    stringToCutoffMethod["HARD"] = HARD;
719 <    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
720 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
721 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
717 >    // count_local holds the number of found types on this processor
718 >    int count_local = foundTypes.size();
719 >
720 >    int nproc = MPI::COMM_WORLD.Get_size();
721 >
722 >    // we need arrays to hold the counts and displacement vectors for
723 >    // all processors
724 >    vector<int> counts(nproc, 0);
725 >    vector<int> disps(nproc, 0);
726 >
727 >    // fill the counts array
728 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
729 >                              1, MPI::INT);
730    
731 <    if (simParams_->haveCutoffMethod()) {
732 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
733 <      map<string, CutoffMethod>::iterator i;
734 <      i = stringToCutoffMethod.find(cutMeth);
735 <      if (i == stringToCutoffMethod.end()) {
736 <        sprintf(painCave.errMsg,
759 <                "SimInfo: Could not find chosen cutoffMethod %s\n"
760 <                "\tShould be one of: "
761 <                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
762 <                cutMeth.c_str());
763 <        painCave.isFatal = 1;
764 <        painCave.severity = OPENMD_ERROR;
765 <        simError();
766 <      } else {
767 <        cutoffMethod_ = i->second;
768 <      }
769 <    } else {
770 <      sprintf(painCave.errMsg,
771 <              "SimInfo: No value was set for the cutoffMethod.\n"
772 <              "\tOpenMD will use SHIFTED_FORCE.\n");
773 <        painCave.isFatal = 0;
774 <        painCave.severity = OPENMD_INFO;
775 <        simError();
776 <        cutoffMethod_ = SHIFTED_FORCE;        
731 >    // use the processor counts to compute the displacement array
732 >    disps[0] = 0;    
733 >    int totalCount = counts[0];
734 >    for (int iproc = 1; iproc < nproc; iproc++) {
735 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
736 >      totalCount += counts[iproc];
737      }
738 <  }
739 <  
740 <  /**
781 <   * setupSwitching
782 <   *
783 <   * Sets the values of switchingRadius and
784 <   *  If the switchingRadius was explicitly set, use that value (but check it)
785 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
786 <   */
787 <  void SimInfo::setupSwitching() {
738 >
739 >    // we need a (possibly redundant) set of all found types:
740 >    vector<int> ftGlobal(totalCount);
741      
742 <    if (simParams_->haveSwitchingRadius()) {
743 <      switchingRadius_ = simParams_->getSwitchingRadius();
744 <      if (switchingRadius_ > cutoffRadius_) {        
745 <        sprintf(painCave.errMsg,
746 <                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
747 <                switchingRadius_, cutoffRadius_);
748 <        painCave.isFatal = 1;
749 <        painCave.severity = OPENMD_ERROR;
750 <        simError();
751 <      }
752 <    } else {      
753 <      switchingRadius_ = 0.85 * cutoffRadius_;
754 <      sprintf(painCave.errMsg,
802 <              "SimInfo: No value was set for the switchingRadius.\n"
803 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
804 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
805 <      painCave.isFatal = 0;
806 <      painCave.severity = OPENMD_WARNING;
807 <      simError();
808 <    }          
742 >    // now spray out the foundTypes to all the other processors:    
743 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
744 >                               &ftGlobal[0], &counts[0], &disps[0],
745 >                               MPI::INT);
746 >
747 >    vector<int>::iterator j;
748 >
749 >    // foundIdents is a stl set, so inserting an already found ident
750 >    // will have no effect.
751 >    set<int> foundIdents;
752 >
753 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
754 >      foundIdents.insert((*j));
755      
756 <    if (simParams_->haveSwitchingFunctionType()) {
757 <      string funcType = simParams_->getSwitchingFunctionType();
758 <      toUpper(funcType);
759 <      if (funcType == "CUBIC") {
760 <        sft_ = cubic;
761 <      } else {
762 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
817 <          sft_ = fifth_order_poly;
818 <        } else {
819 <          // throw error        
820 <          sprintf( painCave.errMsg,
821 <                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
822 <                   "\tswitchingFunctionType must be one of: "
823 <                   "\"cubic\" or \"fifth_order_polynomial\".",
824 <                   funcType.c_str() );
825 <          painCave.isFatal = 1;
826 <          painCave.severity = OPENMD_ERROR;
827 <          simError();
828 <        }          
829 <      }
830 <    }
831 <  }
756 >    // now iterate over the foundIdents and get the actual atom types
757 >    // that correspond to these:
758 >    set<int>::iterator it;
759 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
760 >      atomTypes.insert( forceField_->getAtomType((*it)) );
761 >
762 > #endif
763  
764 <  /**
834 <   * setupNeighborlists
835 <   *
836 <   *  If the skinThickness was explicitly set, use that value (but check it)
837 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
838 <   */
839 <  void SimInfo::setupNeighborlists() {    
840 <    if (simParams_->haveSkinThickness()) {
841 <      skinThickness_ = simParams_->getSkinThickness();
842 <    } else {      
843 <      skinThickness_ = 1.0;
844 <      sprintf(painCave.errMsg,
845 <              "SimInfo: No value was set for the skinThickness.\n"
846 <              "\tOpenMD will use a default value of %f Angstroms\n"
847 <              "\tfor this simulation\n", skinThickness_);
848 <      painCave.severity = OPENMD_INFO;
849 <      painCave.isFatal = 0;
850 <      simError();
851 <    }            
764 >    return atomTypes;        
765    }
766  
767    void SimInfo::setupSimVariables() {
# Line 859 | Line 772 | namespace OpenMD {
772        if ( simParams_->getAccumulateBoxDipole() ) {
773          calcBoxDipole_ = true;      
774        }
775 <
775 >    
776      set<AtomType*>::iterator i;
777      set<AtomType*> atomTypes;
778      atomTypes = getSimulatedAtomTypes();    
# Line 872 | Line 785 | namespace OpenMD {
785        usesMetallic |= (*i)->isMetal();
786        usesDirectional |= (*i)->isDirectional();
787      }
788 <
788 >    
789   #ifdef IS_MPI    
790      int temp;
791      temp = usesDirectional;
792      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
793 <
793 >    
794      temp = usesMetallic;
795      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
796 <
796 >    
797      temp = usesElectrostatic;
798      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799 + #else
800 +
801 +    usesDirectionalAtoms_ = usesDirectional;
802 +    usesMetallicAtoms_ = usesMetallic;
803 +    usesElectrostaticAtoms_ = usesElectrostatic;
804 +
805   #endif
806 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
807 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
808 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
809 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
891 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
806 >    
807 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
808 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
809 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
810    }
811  
812 <  void SimInfo::setupFortranSim() {
813 <    int isError;
814 <    int nExclude, nOneTwo, nOneThree, nOneFour;
815 <    vector<int> fortranGlobalGroupMembership;
812 >
813 >  vector<int> SimInfo::getGlobalAtomIndices() {
814 >    SimInfo::MoleculeIterator mi;
815 >    Molecule* mol;
816 >    Molecule::AtomIterator ai;
817 >    Atom* atom;
818 >
819 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
820      
821 <    notifyFortranSkinThickness(&skinThickness_);
821 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
822 >      
823 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
824 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
825 >      }
826 >    }
827 >    return GlobalAtomIndices;
828 >  }
829  
902 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
903 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
904 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
830  
831 <    isError = 0;
831 >  vector<int> SimInfo::getGlobalGroupIndices() {
832 >    SimInfo::MoleculeIterator mi;
833 >    Molecule* mol;
834 >    Molecule::CutoffGroupIterator ci;
835 >    CutoffGroup* cg;
836  
837 <    //globalGroupMembership_ is filled by SimCreator    
838 <    for (int i = 0; i < nGlobalAtoms_; i++) {
839 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
837 >    vector<int> GlobalGroupIndices;
838 >    
839 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840 >      
841 >      //local index of cutoff group is trivial, it only depends on the
842 >      //order of travesing
843 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
844 >           cg = mol->nextCutoffGroup(ci)) {
845 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
846 >      }        
847      }
848 +    return GlobalGroupIndices;
849 +  }
850  
851 +
852 +  void SimInfo::prepareTopology() {
853 +    int nExclude, nOneTwo, nOneThree, nOneFour;
854 +
855      //calculate mass ratio of cutoff group
914 –    vector<RealType> mfact;
856      SimInfo::MoleculeIterator mi;
857      Molecule* mol;
858      Molecule::CutoffGroupIterator ci;
# Line 920 | Line 861 | namespace OpenMD {
861      Atom* atom;
862      RealType totalMass;
863  
864 <    //to avoid memory reallocation, reserve enough space for mfact
865 <    mfact.reserve(getNCutoffGroups());
864 >    /**
865 >     * The mass factor is the relative mass of an atom to the total
866 >     * mass of the cutoff group it belongs to.  By default, all atoms
867 >     * are their own cutoff groups, and therefore have mass factors of
868 >     * 1.  We need some special handling for massless atoms, which
869 >     * will be treated as carrying the entire mass of the cutoff
870 >     * group.
871 >     */
872 >    massFactors_.clear();
873 >    massFactors_.resize(getNAtoms(), 1.0);
874      
875      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
876 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
876 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
877 >           cg = mol->nextCutoffGroup(ci)) {
878  
879          totalMass = cg->getMass();
880          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
881            // Check for massless groups - set mfact to 1 if true
882 <          if (totalMass != 0)
883 <            mfact.push_back(atom->getMass()/totalMass);
882 >          if (totalMass != 0)
883 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
884            else
885 <            mfact.push_back( 1.0 );
885 >            massFactors_[atom->getLocalIndex()] = 1.0;
886          }
887        }      
888      }
889  
890 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
941 <    vector<int> identArray;
890 >    // Build the identArray_
891  
892 <    //to avoid memory reallocation, reserve enough space identArray
893 <    identArray.reserve(getNAtoms());
945 <    
892 >    identArray_.clear();
893 >    identArray_.reserve(getNAtoms());    
894      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
895        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896 <        identArray.push_back(atom->getIdent());
896 >        identArray_.push_back(atom->getIdent());
897        }
898      }    
951 –
952 –    //fill molMembershipArray
953 –    //molMembershipArray is filled by SimCreator    
954 –    vector<int> molMembershipArray(nGlobalAtoms_);
955 –    for (int i = 0; i < nGlobalAtoms_; i++) {
956 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
957 –    }
899      
900 <    //setup fortran simulation
900 >    //scan topology
901  
902      nExclude = excludedInteractions_.getSize();
903      nOneTwo = oneTwoInteractions_.getSize();
# Line 968 | Line 909 | namespace OpenMD {
909      int* oneThreeList = oneThreeInteractions_.getPairList();
910      int* oneFourList = oneFourInteractions_.getPairList();
911  
912 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
972 <                   &nExclude, excludeList,
973 <                   &nOneTwo, oneTwoList,
974 <                   &nOneThree, oneThreeList,
975 <                   &nOneFour, oneFourList,
976 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
977 <                   &fortranGlobalGroupMembership[0], &isError);
978 <    
979 <    if( isError ){
980 <      
981 <      sprintf( painCave.errMsg,
982 <               "There was an error setting the simulation information in fortran.\n" );
983 <      painCave.isFatal = 1;
984 <      painCave.severity = OPENMD_ERROR;
985 <      simError();
986 <    }
987 <    
988 <    
989 <    sprintf( checkPointMsg,
990 <             "succesfully sent the simulation information to fortran.\n");
991 <    
992 <    errorCheckPoint();
993 <    
994 <    // Setup number of neighbors in neighbor list if present
995 <    if (simParams_->haveNeighborListNeighbors()) {
996 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
997 <      setNeighbors(&nlistNeighbors);
998 <    }
999 <  
1000 <
1001 <  }
1002 <
1003 <
1004 <  void SimInfo::setupFortranParallel() {
1005 < #ifdef IS_MPI    
1006 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1007 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008 <    vector<int> localToGlobalCutoffGroupIndex;
1009 <    SimInfo::MoleculeIterator mi;
1010 <    Molecule::AtomIterator ai;
1011 <    Molecule::CutoffGroupIterator ci;
1012 <    Molecule* mol;
1013 <    Atom* atom;
1014 <    CutoffGroup* cg;
1015 <    mpiSimData parallelData;
1016 <    int isError;
1017 <
1018 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1019 <
1020 <      //local index(index in DataStorge) of atom is important
1021 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1022 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1023 <      }
1024 <
1025 <      //local index of cutoff group is trivial, it only depends on the order of travesing
1026 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1027 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1028 <      }        
1029 <        
1030 <    }
1031 <
1032 <    //fill up mpiSimData struct
1033 <    parallelData.nMolGlobal = getNGlobalMolecules();
1034 <    parallelData.nMolLocal = getNMolecules();
1035 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
1036 <    parallelData.nAtomsLocal = getNAtoms();
1037 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1038 <    parallelData.nGroupsLocal = getNCutoffGroups();
1039 <    parallelData.myNode = worldRank;
1040 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1041 <
1042 <    //pass mpiSimData struct and index arrays to fortran
1043 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1044 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1045 <                    &localToGlobalCutoffGroupIndex[0], &isError);
1046 <
1047 <    if (isError) {
1048 <      sprintf(painCave.errMsg,
1049 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1050 <      painCave.isFatal = 1;
1051 <      simError();
1052 <    }
1053 <
1054 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1055 <    errorCheckPoint();
1056 <
1057 < #endif
912 >    topologyDone_ = true;
913    }
914  
1060 –
1061 –  void SimInfo::setupAccumulateBoxDipole() {    
1062 –
1063 –
1064 –  }
1065 –
915    void SimInfo::addProperty(GenericData* genData) {
916      properties_.addProperty(genData);  
917    }
# Line 1097 | Line 946 | namespace OpenMD {
946      Molecule* mol;
947      RigidBody* rb;
948      Atom* atom;
949 +    CutoffGroup* cg;
950      SimInfo::MoleculeIterator mi;
951      Molecule::RigidBodyIterator rbIter;
952 <    Molecule::AtomIterator atomIter;;
952 >    Molecule::AtomIterator atomIter;
953 >    Molecule::CutoffGroupIterator cgIter;
954  
955      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956          
# Line 1109 | Line 960 | namespace OpenMD {
960          
961        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
962          rb->setSnapshotManager(sman_);
963 +      }
964 +
965 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
966 +        cg->setSnapshotManager(sman_);
967        }
968      }    
969      

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