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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 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1597 by gezelter, Tue Jul 26 15:49:24 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/DarkSide/fSwitchingFunctionType.h"
59 – #include "UseTheForce/doForces_interface.h"
60 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
61 – #include "UseTheForce/DarkSide/switcheroo_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/InteractionManager.hpp"
68 <
69 <
70 < #ifdef IS_MPI
71 < #include "UseTheForce/mpiComponentPlan.h"
72 < #include "UseTheForce/DarkSide/simParallel_interface.h"
73 < #endif
62 > #include "nonbonded/SwitchingFunction.hpp"
63  
64   using namespace std;
65   namespace OpenMD {
# Line 82 | 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 136 | 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 278 | 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 656 | Line 665 | namespace OpenMD {
665      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666    }
667  
659 –  void SimInfo::update() {
668  
669 <    setupSimType();
670 <    setupCutoffRadius();
671 <    setupSwitchingRadius();
672 <    setupCutoffMethod();
673 <    setupSkinThickness();
674 <    setupSwitchingFunction();
675 <    setupAccumulateBoxDipole();
676 <
677 < #ifdef IS_MPI
670 <    setupFortranParallel();
671 < #endif
672 <    setupFortranSim();
673 <    fortranInitialized_ = true;
674 <
669 >  /**
670 >   * update
671 >   *
672 >   *  Performs the global checks and variable settings after the
673 >   *  objects have been created.
674 >   *
675 >   */
676 >  void SimInfo::update() {  
677 >    setupSimVariables();
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 685 | Line 695 | namespace OpenMD {
695      set<AtomType*> atomTypes;
696      
697      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698 <      
699 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
698 >      for(atom = mol->beginAtom(ai); atom != NULL;
699 >          atom = mol->nextAtom(ai)) {
700          atomTypes.insert(atom->getAtomType());
701 <      }
702 <      
693 <    }
701 >      }      
702 >    }    
703      
704 <    return atomTypes;        
696 <  }
704 > #ifdef IS_MPI
705  
706 <  /**
707 <   * setupCutoffRadius
700 <   *
701 <   *  If the cutoffRadius was explicitly set, use that value.
702 <   *  If the cutoffRadius was not explicitly set:
703 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
704 <   *      No electrostatic atoms?  Poll the atom types present in the
705 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
706 <   *      Use the maximum suggested value that was found.
707 <   */
708 <  void SimInfo::setupCutoffRadius() {
706 >    // loop over the found atom types on this processor, and add their
707 >    // numerical idents to a vector:
708      
709 <    if (simParams_->haveCutoffRadius()) {
710 <      cutoffRadius_ = simParams_->getCutoffRadius();
711 <    } else {      
712 <      if (usesElectrostaticAtoms_) {
714 <        sprintf(painCave.errMsg,
715 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
716 <                "\tOpenMD will use a default value of 12.0 angstroms"
717 <                "\tfor the cutoffRadius.\n");
718 <        painCave.isFatal = 0;
719 <        simError();
720 <        cutoffRadius_ = 12.0;
721 <      } else {
722 <        RealType thisCut;
723 <        set<AtomType*>::iterator i;
724 <        set<AtomType*> atomTypes;
725 <        atomTypes = getSimulatedAtomTypes();        
726 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
727 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
728 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
729 <        }
730 <        sprintf(painCave.errMsg,
731 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
732 <                "\tOpenMD will use %lf angstroms.\n",
733 <                cutoffRadius_);
734 <        painCave.isFatal = 0;
735 <        simError();
736 <      }            
737 <    }
709 >    vector<int> foundTypes;
710 >    set<AtomType*>::iterator i;
711 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
712 >      foundTypes.push_back( (*i)->getIdent() );
713  
714 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
715 <  }
714 >    // count_local holds the number of found types on this processor
715 >    int count_local = foundTypes.size();
716 >
717 >    int nproc = MPI::COMM_WORLD.Get_size();
718 >
719 >    // we need arrays to hold the counts and displacement vectors for
720 >    // all processors
721 >    vector<int> counts(nproc, 0);
722 >    vector<int> disps(nproc, 0);
723 >
724 >    // fill the counts array
725 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
726 >                              1, MPI::INT);
727    
728 <  /**
729 <   * setupSwitchingRadius
730 <   *
731 <   *  If the switchingRadius was explicitly set, use that value (but check it)
732 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
733 <   */
734 <  void SimInfo::setupSwitchingRadius() {
728 >    // use the processor counts to compute the displacement array
729 >    disps[0] = 0;    
730 >    int totalCount = counts[0];
731 >    for (int iproc = 1; iproc < nproc; iproc++) {
732 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
733 >      totalCount += counts[iproc];
734 >    }
735 >
736 >    // we need a (possibly redundant) set of all found types:
737 >    vector<int> ftGlobal(totalCount);
738      
739 <    if (simParams_->haveSwitchingRadius()) {
740 <      switchingRadius_ = simParams_->getSwitchingRadius();
741 <      if (switchingRadius_ > cutoffRadius_) {        
742 <        sprintf(painCave.errMsg,
754 <                "SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755 <                switchingRadius_, cutoffRadius_);
756 <        painCave.isFatal = 1;
757 <        simError();
739 >    // now spray out the foundTypes to all the other processors:    
740 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
741 >                               &ftGlobal[0], &counts[0], &disps[0],
742 >                               MPI::INT);
743  
744 <      }
760 <    } else {      
761 <      switchingRadius_ = 0.85 * cutoffRadius_;
762 <      sprintf(painCave.errMsg,
763 <              "SimInfo Warning: No value was set for the switchingRadius.\n"
764 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
765 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
766 <      painCave.isFatal = 0;
767 <      simError();
768 <    }            
769 <    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
770 <  }
744 >    vector<int>::iterator j;
745  
746 <  /**
747 <   * setupSkinThickness
748 <   *
749 <   *  If the skinThickness was explicitly set, use that value (but check it)
750 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
751 <   */
752 <  void SimInfo::setupSkinThickness() {    
753 <    if (simParams_->haveSkinThickness()) {
754 <      skinThickness_ = simParams_->getSkinThickness();
755 <    } else {      
756 <      skinThickness_ = 1.0;
757 <      sprintf(painCave.errMsg,
758 <              "SimInfo Warning: No value was set for the skinThickness.\n"
759 <              "\tOpenMD will use a default value of %f Angstroms\n"
760 <              "\tfor this simulation\n", skinThickness_);
761 <      painCave.isFatal = 0;
788 <      simError();
789 <    }            
746 >    // foundIdents is a stl set, so inserting an already found ident
747 >    // will have no effect.
748 >    set<int> foundIdents;
749 >
750 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
751 >      foundIdents.insert((*j));
752 >    
753 >    // now iterate over the foundIdents and get the actual atom types
754 >    // that correspond to these:
755 >    set<int>::iterator it;
756 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
757 >      atomTypes.insert( forceField_->getAtomType((*it)) );
758 >
759 > #endif
760 >
761 >    return atomTypes;        
762    }
763  
764 <  void SimInfo::setupSimType() {
764 >  void SimInfo::setupSimVariables() {
765 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
766 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
767 >    calcBoxDipole_ = false;
768 >    if ( simParams_->haveAccumulateBoxDipole() )
769 >      if ( simParams_->getAccumulateBoxDipole() ) {
770 >        calcBoxDipole_ = true;      
771 >      }
772 >    
773      set<AtomType*>::iterator i;
774      set<AtomType*> atomTypes;
775 <    atomTypes = getSimulatedAtomTypes();
796 <
797 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
798 <
775 >    atomTypes = getSimulatedAtomTypes();    
776      int usesElectrostatic = 0;
777      int usesMetallic = 0;
778      int usesDirectional = 0;
# Line 805 | Line 782 | namespace OpenMD {
782        usesMetallic |= (*i)->isMetal();
783        usesDirectional |= (*i)->isDirectional();
784      }
785 <
785 >    
786   #ifdef IS_MPI    
787      int temp;
788      temp = usesDirectional;
789      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
790 <
790 >    
791      temp = usesMetallic;
792      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
793 <
793 >    
794      temp = usesElectrostatic;
795      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796 + #else
797 +
798 +    usesDirectionalAtoms_ = usesDirectional;
799 +    usesMetallicAtoms_ = usesMetallic;
800 +    usesElectrostaticAtoms_ = usesElectrostatic;
801 +
802   #endif
803 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
804 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
805 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
806 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
803 >    
804 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
805 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
806 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
807    }
808  
809 <  void SimInfo::setupFortranSim() {
810 <    int isError;
811 <    int nExclude, nOneTwo, nOneThree, nOneFour;
812 <    vector<int> fortranGlobalGroupMembership;
809 >
810 >  vector<int> SimInfo::getGlobalAtomIndices() {
811 >    SimInfo::MoleculeIterator mi;
812 >    Molecule* mol;
813 >    Molecule::AtomIterator ai;
814 >    Atom* atom;
815 >
816 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
817      
818 <    notifyFortranSkinThickness(&skinThickness_);
818 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
819 >      
820 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
821 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
822 >        cerr << "LI = " << atom->getLocalIndex() << "GAI = " << GlobalAtomIndices[atom->getLocalIndex()] << "\n";
823 >      }
824 >    }
825 >    return GlobalAtomIndices;
826 >  }
827  
835 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
828  
829 <    isError = 0;
829 >  vector<int> SimInfo::getGlobalGroupIndices() {
830 >    SimInfo::MoleculeIterator mi;
831 >    Molecule* mol;
832 >    Molecule::CutoffGroupIterator ci;
833 >    CutoffGroup* cg;
834  
835 <    //globalGroupMembership_ is filled by SimCreator    
836 <    for (int i = 0; i < nGlobalAtoms_; i++) {
837 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
835 >    vector<int> GlobalGroupIndices;
836 >    
837 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
838 >      
839 >      //local index of cutoff group is trivial, it only depends on the
840 >      //order of travesing
841 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
842 >           cg = mol->nextCutoffGroup(ci)) {
843 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
844 >        cerr << "LI, GGI = " << GlobalGroupIndices.size() << " " << cg->getGlobalIndex() << "\n";
845 >      }        
846      }
847 +    return GlobalGroupIndices;
848 +  }
849  
850 +
851 +  void SimInfo::prepareTopology() {
852 +    int nExclude, nOneTwo, nOneThree, nOneFour;
853 +
854      //calculate mass ratio of cutoff group
847 –    vector<RealType> mfact;
855      SimInfo::MoleculeIterator mi;
856      Molecule* mol;
857      Molecule::CutoffGroupIterator ci;
# Line 853 | Line 860 | namespace OpenMD {
860      Atom* atom;
861      RealType totalMass;
862  
863 <    //to avoid memory reallocation, reserve enough space for mfact
864 <    mfact.reserve(getNCutoffGroups());
863 >    /**
864 >     * The mass factor is the relative mass of an atom to the total
865 >     * mass of the cutoff group it belongs to.  By default, all atoms
866 >     * are their own cutoff groups, and therefore have mass factors of
867 >     * 1.  We need some special handling for massless atoms, which
868 >     * will be treated as carrying the entire mass of the cutoff
869 >     * group.
870 >     */
871 >    massFactors_.clear();
872 >    massFactors_.resize(getNAtoms(), 1.0);
873      
874      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
875 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
875 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
876 >           cg = mol->nextCutoffGroup(ci)) {
877  
878          totalMass = cg->getMass();
879          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
880            // Check for massless groups - set mfact to 1 if true
881 <          if (totalMass != 0)
882 <            mfact.push_back(atom->getMass()/totalMass);
881 >          if (totalMass != 0)
882 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
883            else
884 <            mfact.push_back( 1.0 );
884 >            massFactors_[atom->getLocalIndex()] = 1.0;
885          }
886        }      
887      }
888  
889 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874 <    vector<int> identArray;
889 >    // Build the identArray_
890  
891 <    //to avoid memory reallocation, reserve enough space identArray
892 <    identArray.reserve(getNAtoms());
878 <    
891 >    identArray_.clear();
892 >    identArray_.reserve(getNAtoms());    
893      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
894        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895 <        identArray.push_back(atom->getIdent());
895 >        identArray_.push_back(atom->getIdent());
896        }
897      }    
884 –
885 –    //fill molMembershipArray
886 –    //molMembershipArray is filled by SimCreator    
887 –    vector<int> molMembershipArray(nGlobalAtoms_);
888 –    for (int i = 0; i < nGlobalAtoms_; i++) {
889 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
890 –    }
898      
899 <    //setup fortran simulation
899 >    //scan topology
900  
901      nExclude = excludedInteractions_.getSize();
902      nOneTwo = oneTwoInteractions_.getSize();
# Line 901 | Line 908 | namespace OpenMD {
908      int* oneThreeList = oneThreeInteractions_.getPairList();
909      int* oneFourList = oneFourInteractions_.getPairList();
910  
911 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
905 <                   &nExclude, excludeList,
906 <                   &nOneTwo, oneTwoList,
907 <                   &nOneThree, oneThreeList,
908 <                   &nOneFour, oneFourList,
909 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
910 <                   &fortranGlobalGroupMembership[0], &isError);
911 <    
912 <    if( isError ){
913 <      
914 <      sprintf( painCave.errMsg,
915 <               "There was an error setting the simulation information in fortran.\n" );
916 <      painCave.isFatal = 1;
917 <      painCave.severity = OPENMD_ERROR;
918 <      simError();
919 <    }
920 <    
921 <    
922 <    sprintf( checkPointMsg,
923 <             "succesfully sent the simulation information to fortran.\n");
924 <    
925 <    errorCheckPoint();
926 <    
927 <    // Setup number of neighbors in neighbor list if present
928 <    if (simParams_->haveNeighborListNeighbors()) {
929 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
930 <      setNeighbors(&nlistNeighbors);
931 <    }
932 <  
933 <
934 <  }
935 <
936 <
937 <  void SimInfo::setupFortranParallel() {
938 < #ifdef IS_MPI    
939 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
940 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941 <    vector<int> localToGlobalCutoffGroupIndex;
942 <    SimInfo::MoleculeIterator mi;
943 <    Molecule::AtomIterator ai;
944 <    Molecule::CutoffGroupIterator ci;
945 <    Molecule* mol;
946 <    Atom* atom;
947 <    CutoffGroup* cg;
948 <    mpiSimData parallelData;
949 <    int isError;
950 <
951 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
952 <
953 <      //local index(index in DataStorge) of atom is important
954 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
955 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
956 <      }
957 <
958 <      //local index of cutoff group is trivial, it only depends on the order of travesing
959 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
960 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
961 <      }        
962 <        
963 <    }
964 <
965 <    //fill up mpiSimData struct
966 <    parallelData.nMolGlobal = getNGlobalMolecules();
967 <    parallelData.nMolLocal = getNMolecules();
968 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
969 <    parallelData.nAtomsLocal = getNAtoms();
970 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
971 <    parallelData.nGroupsLocal = getNCutoffGroups();
972 <    parallelData.myNode = worldRank;
973 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
974 <
975 <    //pass mpiSimData struct and index arrays to fortran
976 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
977 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
978 <                    &localToGlobalCutoffGroupIndex[0], &isError);
979 <
980 <    if (isError) {
981 <      sprintf(painCave.errMsg,
982 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
983 <      painCave.isFatal = 1;
984 <      simError();
985 <    }
986 <
987 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
988 <    errorCheckPoint();
989 <
990 < #endif
991 <  }
992 <
993 <
994 <  void SimInfo::setupSwitchingFunction() {    
995 <    int ft = CUBIC;
996 <    
997 <    if (simParams_->haveSwitchingFunctionType()) {
998 <      string funcType = simParams_->getSwitchingFunctionType();
999 <      toUpper(funcType);
1000 <      if (funcType == "CUBIC") {
1001 <        ft = CUBIC;
1002 <      } else {
1003 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1004 <          ft = FIFTH_ORDER_POLY;
1005 <        } else {
1006 <          // throw error        
1007 <          sprintf( painCave.errMsg,
1008 <                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1009 <          painCave.isFatal = 1;
1010 <          simError();
1011 <        }          
1012 <      }
1013 <    }
1014 <
1015 <    // send switching function notification to switcheroo
1016 <    setFunctionType(&ft);
1017 <
911 >    topologyDone_ = true;
912    }
913  
1020 –  void SimInfo::setupAccumulateBoxDipole() {    
1021 –
1022 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1023 –    if ( simParams_->haveAccumulateBoxDipole() )
1024 –      if ( simParams_->getAccumulateBoxDipole() ) {
1025 –        calcBoxDipole_ = true;
1026 –      }
1027 –
1028 –  }
1029 –
914    void SimInfo::addProperty(GenericData* genData) {
915      properties_.addProperty(genData);  
916    }
# Line 1061 | Line 945 | namespace OpenMD {
945      Molecule* mol;
946      RigidBody* rb;
947      Atom* atom;
948 +    CutoffGroup* cg;
949      SimInfo::MoleculeIterator mi;
950      Molecule::RigidBodyIterator rbIter;
951 <    Molecule::AtomIterator atomIter;;
951 >    Molecule::AtomIterator atomIter;
952 >    Molecule::CutoffGroupIterator cgIter;
953  
954      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
955          
# Line 1073 | Line 959 | namespace OpenMD {
959          
960        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
961          rb->setSnapshotManager(sman_);
962 +      }
963 +
964 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
965 +        cg->setSnapshotManager(sman_);
966        }
967      }    
968      

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