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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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 54 | Line 55
55   #include "math/Vector3.hpp"
56   #include "primitives/Molecule.hpp"
57   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/doForces_interface.h"
58 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
58   #include "utils/MemoryUtils.hpp"
59   #include "utils/simError.h"
60   #include "selection/SelectionManager.hpp"
61   #include "io/ForceFieldOptions.hpp"
62   #include "UseTheForce/ForceField.hpp"
63   #include "nonbonded/SwitchingFunction.hpp"
65 –
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
69 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 78 | Line 75 | namespace OpenMD {
75      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78 <    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
78 >    nConstraints_(0), sman_(NULL), topologyDone_(false),
79      calcBoxDipole_(false), useAtomicVirial_(true) {    
80      
81      MoleculeStamp* molStamp;
# Line 132 | Line 129 | namespace OpenMD {
129      //equal to the total number of atoms minus number of atoms belong to
130      //cutoff group defined in meta-data file plus the number of cutoff
131      //groups defined in meta-data file
132 +
133      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134      
135      //every free atom (atom does not belong to rigid bodies) is an
# Line 275 | Line 273 | namespace OpenMD {
273   #endif
274      return fdf_;
275    }
276 +  
277 +  unsigned int SimInfo::getNLocalCutoffGroups(){
278 +    int nLocalCutoffAtoms = 0;
279 +    Molecule* mol;
280 +    MoleculeIterator mi;
281 +    CutoffGroup* cg;
282 +    Molecule::CutoffGroupIterator ci;
283      
284 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
285 +      
286 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
287 +           cg = mol->nextCutoffGroup(ci)) {
288 +        nLocalCutoffAtoms += cg->getNumAtom();
289 +        
290 +      }        
291 +    }
292 +    
293 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
294 +  }
295 +    
296    void SimInfo::calcNdfRaw() {
297      int ndfRaw_local;
298  
# Line 656 | Line 673 | namespace OpenMD {
673    /**
674     * update
675     *
676 <   *  Performs the global checks and variable settings after the objects have been
677 <   *  created.
676 >   *  Performs the global checks and variable settings after the
677 >   *  objects have been created.
678     *
679     */
680 <  void SimInfo::update() {
664 <    
680 >  void SimInfo::update() {  
681      setupSimVariables();
666 –    setupCutoffs();
667 –    setupSwitching();
668 –    setupElectrostatics();
669 –    setupNeighborlists();
670 –
671 – #ifdef IS_MPI
672 –    setupFortranParallel();
673 – #endif
674 –    setupFortranSim();
675 –    fortranInitialized_ = true;
676 –
682      calcNdf();
683      calcNdfRaw();
684      calcNdfTrans();
685    }
686    
687 +  /**
688 +   * getSimulatedAtomTypes
689 +   *
690 +   * Returns an STL set of AtomType* that are actually present in this
691 +   * simulation.  Must query all processors to assemble this information.
692 +   *
693 +   */
694    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
695      SimInfo::MoleculeIterator mi;
696      Molecule* mol;
# Line 686 | Line 698 | namespace OpenMD {
698      Atom* atom;
699      set<AtomType*> atomTypes;
700      
701 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
702 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
701 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
702 >      for(atom = mol->beginAtom(ai); atom != NULL;
703 >          atom = mol->nextAtom(ai)) {
704          atomTypes.insert(atom->getAtomType());
705        }      
706      }    
707 <    return atomTypes;        
708 <  }
707 >    
708 > #ifdef IS_MPI
709  
710 <  /**
711 <   * 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() {
710 >    // loop over the found atom types on this processor, and add their
711 >    // numerical idents to a vector:
712      
713 <    if (simParams_->haveCutoffRadius()) {
714 <      cutoffRadius_ = simParams_->getCutoffRadius();
715 <    } else {      
716 <      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 <    }
713 >    vector<int> foundTypes;
714 >    set<AtomType*>::iterator i;
715 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
716 >      foundTypes.push_back( (*i)->getIdent() );
717  
718 <    map<string, CutoffMethod> stringToCutoffMethod;
719 <    stringToCutoffMethod["HARD"] = HARD;
720 <    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
721 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
722 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
718 >    // count_local holds the number of found types on this processor
719 >    int count_local = foundTypes.size();
720 >
721 >    int nproc = MPI::COMM_WORLD.Get_size();
722 >
723 >    // we need arrays to hold the counts and displacement vectors for
724 >    // all processors
725 >    vector<int> counts(nproc, 0);
726 >    vector<int> disps(nproc, 0);
727 >
728 >    // fill the counts array
729 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
730 >                              1, MPI::INT);
731    
732 <    if (simParams_->haveCutoffMethod()) {
733 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
734 <      map<string, CutoffMethod>::iterator i;
735 <      i = stringToCutoffMethod.find(cutMeth);
736 <      if (i == stringToCutoffMethod.end()) {
737 <        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;        
732 >    // use the processor counts to compute the displacement array
733 >    disps[0] = 0;    
734 >    int totalCount = counts[0];
735 >    for (int iproc = 1; iproc < nproc; iproc++) {
736 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
737 >      totalCount += counts[iproc];
738      }
739 <  }
740 <  
741 <  /**
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() {
739 >
740 >    // we need a (possibly redundant) set of all found types:
741 >    vector<int> ftGlobal(totalCount);
742      
743 <    if (simParams_->haveSwitchingRadius()) {
744 <      switchingRadius_ = simParams_->getSwitchingRadius();
745 <      if (switchingRadius_ > cutoffRadius_) {        
746 <        sprintf(painCave.errMsg,
747 <                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
748 <                switchingRadius_, cutoffRadius_);
749 <        painCave.isFatal = 1;
750 <        painCave.severity = OPENMD_ERROR;
751 <        simError();
752 <      }
753 <    } else {      
754 <      switchingRadius_ = 0.85 * cutoffRadius_;
755 <      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 <    }          
743 >    // now spray out the foundTypes to all the other processors:    
744 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
745 >                               &ftGlobal[0], &counts[0], &disps[0],
746 >                               MPI::INT);
747 >
748 >    vector<int>::iterator j;
749 >
750 >    // foundIdents is a stl set, so inserting an already found ident
751 >    // will have no effect.
752 >    set<int> foundIdents;
753 >
754 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
755 >      foundIdents.insert((*j));
756      
757 <    if (simParams_->haveSwitchingFunctionType()) {
758 <      string funcType = simParams_->getSwitchingFunctionType();
759 <      toUpper(funcType);
760 <      if (funcType == "CUBIC") {
761 <        sft_ = cubic;
762 <      } else {
763 <        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 <  }
757 >    // now iterate over the foundIdents and get the actual atom types
758 >    // that correspond to these:
759 >    set<int>::iterator it;
760 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
761 >      atomTypes.insert( forceField_->getAtomType((*it)) );
762 >
763 > #endif
764  
765 <  /**
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 <    }            
765 >    return atomTypes;        
766    }
767  
768    void SimInfo::setupSimVariables() {
# Line 859 | Line 773 | namespace OpenMD {
773        if ( simParams_->getAccumulateBoxDipole() ) {
774          calcBoxDipole_ = true;      
775        }
776 <
776 >    
777      set<AtomType*>::iterator i;
778      set<AtomType*> atomTypes;
779      atomTypes = getSimulatedAtomTypes();    
# Line 872 | Line 786 | namespace OpenMD {
786        usesMetallic |= (*i)->isMetal();
787        usesDirectional |= (*i)->isDirectional();
788      }
789 <
789 >    
790   #ifdef IS_MPI    
791      int temp;
792      temp = usesDirectional;
793      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
794 <
794 >    
795      temp = usesMetallic;
796      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
797 <
797 >    
798      temp = usesElectrostatic;
799      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800 + #else
801 +
802 +    usesDirectionalAtoms_ = usesDirectional;
803 +    usesMetallicAtoms_ = usesMetallic;
804 +    usesElectrostaticAtoms_ = usesElectrostatic;
805 +
806   #endif
807 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
808 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
809 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
810 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
891 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
807 >    
808 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
809 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
810 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
811    }
812  
813 <  void SimInfo::setupFortranSim() {
814 <    int isError;
815 <    int nExclude, nOneTwo, nOneThree, nOneFour;
816 <    vector<int> fortranGlobalGroupMembership;
813 >
814 >  vector<int> SimInfo::getGlobalAtomIndices() {
815 >    SimInfo::MoleculeIterator mi;
816 >    Molecule* mol;
817 >    Molecule::AtomIterator ai;
818 >    Atom* atom;
819 >
820 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
821      
822 <    notifyFortranSkinThickness(&skinThickness_);
822 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
823 >      
824 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
826 >      }
827 >    }
828 >    return GlobalAtomIndices;
829 >  }
830  
902 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
903 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
904 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
831  
832 <    isError = 0;
832 >  vector<int> SimInfo::getGlobalGroupIndices() {
833 >    SimInfo::MoleculeIterator mi;
834 >    Molecule* mol;
835 >    Molecule::CutoffGroupIterator ci;
836 >    CutoffGroup* cg;
837  
838 <    //globalGroupMembership_ is filled by SimCreator    
839 <    for (int i = 0; i < nGlobalAtoms_; i++) {
840 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
838 >    vector<int> GlobalGroupIndices;
839 >    
840 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
841 >      
842 >      //local index of cutoff group is trivial, it only depends on the
843 >      //order of travesing
844 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
845 >           cg = mol->nextCutoffGroup(ci)) {
846 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
847 >      }        
848      }
849 +    return GlobalGroupIndices;
850 +  }
851  
852 +
853 +  void SimInfo::prepareTopology() {
854 +    int nExclude, nOneTwo, nOneThree, nOneFour;
855 +
856      //calculate mass ratio of cutoff group
914 –    vector<RealType> mfact;
857      SimInfo::MoleculeIterator mi;
858      Molecule* mol;
859      Molecule::CutoffGroupIterator ci;
# Line 920 | Line 862 | namespace OpenMD {
862      Atom* atom;
863      RealType totalMass;
864  
865 <    //to avoid memory reallocation, reserve enough space for mfact
866 <    mfact.reserve(getNCutoffGroups());
865 >    /**
866 >     * The mass factor is the relative mass of an atom to the total
867 >     * mass of the cutoff group it belongs to.  By default, all atoms
868 >     * are their own cutoff groups, and therefore have mass factors of
869 >     * 1.  We need some special handling for massless atoms, which
870 >     * will be treated as carrying the entire mass of the cutoff
871 >     * group.
872 >     */
873 >    massFactors_.clear();
874 >    massFactors_.resize(getNAtoms(), 1.0);
875      
876      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
877 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
877 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
878 >           cg = mol->nextCutoffGroup(ci)) {
879  
880          totalMass = cg->getMass();
881          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
882            // Check for massless groups - set mfact to 1 if true
883 <          if (totalMass != 0)
884 <            mfact.push_back(atom->getMass()/totalMass);
883 >          if (totalMass != 0)
884 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
885            else
886 <            mfact.push_back( 1.0 );
886 >            massFactors_[atom->getLocalIndex()] = 1.0;
887          }
888        }      
889      }
890  
891 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
941 <    vector<int> identArray;
891 >    // Build the identArray_
892  
893 <    //to avoid memory reallocation, reserve enough space identArray
894 <    identArray.reserve(getNAtoms());
945 <    
893 >    identArray_.clear();
894 >    identArray_.reserve(getNAtoms());    
895      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
896        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897 <        identArray.push_back(atom->getIdent());
897 >        identArray_.push_back(atom->getIdent());
898        }
899      }    
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 –    }
900      
901 <    //setup fortran simulation
901 >    //scan topology
902  
903      nExclude = excludedInteractions_.getSize();
904      nOneTwo = oneTwoInteractions_.getSize();
# Line 968 | Line 910 | namespace OpenMD {
910      int* oneThreeList = oneThreeInteractions_.getPairList();
911      int* oneFourList = oneFourInteractions_.getPairList();
912  
913 <    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
913 >    topologyDone_ = true;
914    }
915  
1060 –
1061 –  void SimInfo::setupAccumulateBoxDipole() {    
1062 –
1063 –
1064 –  }
1065 –
916    void SimInfo::addProperty(GenericData* genData) {
917      properties_.addProperty(genData);  
918    }
# Line 1097 | Line 947 | namespace OpenMD {
947      Molecule* mol;
948      RigidBody* rb;
949      Atom* atom;
950 +    CutoffGroup* cg;
951      SimInfo::MoleculeIterator mi;
952      Molecule::RigidBodyIterator rbIter;
953 <    Molecule::AtomIterator atomIter;;
953 >    Molecule::AtomIterator atomIter;
954 >    Molecule::CutoffGroupIterator cgIter;
955  
956      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
957          
# Line 1109 | Line 961 | namespace OpenMD {
961          
962        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
963          rb->setSnapshotManager(sman_);
964 +      }
965 +
966 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
967 +        cg->setSnapshotManager(sman_);
968        }
969      }    
970      

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