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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 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC vs.
Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/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 279 | 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 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 684 | Line 694 | namespace OpenMD {
694      Atom* atom;
695      set<AtomType*> atomTypes;
696      
697 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
698 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
697 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698 >      for(atom = mol->beginAtom(ai); atom != NULL;
699 >          atom = mol->nextAtom(ai)) {
700          atomTypes.insert(atom->getAtomType());
701        }      
702      }    
692 –    return atomTypes;        
693 –  }
694 –
695 –  /**
696 –   * setupCutoffRadius
697 –   *
698 –   *  If the cutoffRadius was explicitly set, use that value.
699 –   *  If the cutoffRadius was not explicitly set:
700 –   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
701 –   *      No electrostatic atoms?  Poll the atom types present in the
702 –   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
703 –   *      Use the maximum suggested value that was found.
704 –   */
705 –  void SimInfo::setupCutoffRadius() {
703      
704 <    if (simParams_->haveCutoffRadius()) {
708 <      cutoffRadius_ = simParams_->getCutoffRadius();
709 <    } else {      
710 <      if (usesElectrostaticAtoms_) {
711 <        sprintf(painCave.errMsg,
712 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
713 <                "\tOpenMD will use a default value of 12.0 angstroms"
714 <                "\tfor the cutoffRadius.\n");
715 <        painCave.isFatal = 0;
716 <        simError();
717 <        cutoffRadius_ = 12.0;
718 <      } else {
719 <        RealType thisCut;
720 <        set<AtomType*>::iterator i;
721 <        set<AtomType*> atomTypes;
722 <        atomTypes = getSimulatedAtomTypes();        
723 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
724 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
725 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
726 <        }
727 <        sprintf(painCave.errMsg,
728 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
729 <                "\tOpenMD will use %lf angstroms.\n",
730 <                cutoffRadius_);
731 <        painCave.isFatal = 0;
732 <        simError();
733 <      }            
734 <    }
704 > #ifdef IS_MPI
705  
706 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
707 <  }
738 <  
739 <  /**
740 <   * setupSwitchingRadius
741 <   *
742 <   *  If the switchingRadius was explicitly set, use that value (but check it)
743 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
744 <   */
745 <  void SimInfo::setupSwitchingRadius() {
706 >    // loop over the found atom types on this processor, and add their
707 >    // numerical idents to a vector:
708      
709 <    if (simParams_->haveSwitchingRadius()) {
710 <      switchingRadius_ = simParams_->getSwitchingRadius();
711 <      if (switchingRadius_ > cutoffRadius_) {        
712 <        sprintf(painCave.errMsg,
751 <                "SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
752 <                switchingRadius_, cutoffRadius_);
753 <        painCave.isFatal = 1;
754 <        simError();
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 <      }
715 <    } else {      
758 <      switchingRadius_ = 0.85 * cutoffRadius_;
759 <      sprintf(painCave.errMsg,
760 <              "SimInfo Warning: No value was set for the switchingRadius.\n"
761 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
762 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
763 <      painCave.isFatal = 0;
764 <      simError();
765 <    }            
766 <    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
767 <  }
714 >    // count_local holds the number of found types on this processor
715 >    int count_local = foundTypes.size();
716  
717 <  /**
718 <   * setupSkinThickness
719 <   *
720 <   *  If the skinThickness was explicitly set, use that value (but check it)
721 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
722 <   */
723 <  void SimInfo::setupSkinThickness() {    
724 <    if (simParams_->haveSkinThickness()) {
725 <      skinThickness_ = simParams_->getSkinThickness();
726 <    } else {      
727 <      skinThickness_ = 1.0;
728 <      sprintf(painCave.errMsg,
729 <              "SimInfo Warning: No value was set for the skinThickness.\n"
730 <              "\tOpenMD will use a default value of %f Angstroms\n"
731 <              "\tfor this simulation\n", skinThickness_);
732 <      painCave.isFatal = 0;
733 <      simError();
734 <    }            
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 >    // 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 >    // 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 >    vector<int>::iterator j;
745 >
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();
793 <
794 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
795 <
775 >    atomTypes = getSimulatedAtomTypes();    
776      int usesElectrostatic = 0;
777      int usesMetallic = 0;
778      int usesDirectional = 0;
# Line 802 | 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_;
821 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
822 <    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 >      }
823 >    }
824 >    return GlobalAtomIndices;
825 >  }
826  
832 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
833 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
834 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
827  
828 <    isError = 0;
828 >  vector<int> SimInfo::getGlobalGroupIndices() {
829 >    SimInfo::MoleculeIterator mi;
830 >    Molecule* mol;
831 >    Molecule::CutoffGroupIterator ci;
832 >    CutoffGroup* cg;
833  
834 <    //globalGroupMembership_ is filled by SimCreator    
835 <    for (int i = 0; i < nGlobalAtoms_; i++) {
836 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
834 >    vector<int> GlobalGroupIndices;
835 >    
836 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
837 >      
838 >      //local index of cutoff group is trivial, it only depends on the
839 >      //order of travesing
840 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
841 >           cg = mol->nextCutoffGroup(ci)) {
842 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
843 >      }        
844      }
845 +    return GlobalGroupIndices;
846 +  }
847  
848 +
849 +  void SimInfo::prepareTopology() {
850 +    int nExclude, nOneTwo, nOneThree, nOneFour;
851 +
852      //calculate mass ratio of cutoff group
844 –    vector<RealType> mfact;
853      SimInfo::MoleculeIterator mi;
854      Molecule* mol;
855      Molecule::CutoffGroupIterator ci;
# Line 850 | Line 858 | namespace OpenMD {
858      Atom* atom;
859      RealType totalMass;
860  
861 <    //to avoid memory reallocation, reserve enough space for mfact
862 <    mfact.reserve(getNCutoffGroups());
861 >    /**
862 >     * The mass factor is the relative mass of an atom to the total
863 >     * mass of the cutoff group it belongs to.  By default, all atoms
864 >     * are their own cutoff groups, and therefore have mass factors of
865 >     * 1.  We need some special handling for massless atoms, which
866 >     * will be treated as carrying the entire mass of the cutoff
867 >     * group.
868 >     */
869 >    massFactors_.clear();
870 >    massFactors_.resize(getNAtoms(), 1.0);
871      
872      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
873 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
873 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
874 >           cg = mol->nextCutoffGroup(ci)) {
875  
876          totalMass = cg->getMass();
877          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
878            // Check for massless groups - set mfact to 1 if true
879 <          if (totalMass != 0)
880 <            mfact.push_back(atom->getMass()/totalMass);
879 >          if (totalMass != 0)
880 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
881            else
882 <            mfact.push_back( 1.0 );
882 >            massFactors_[atom->getLocalIndex()] = 1.0;
883          }
884        }      
885      }
886  
887 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
871 <    vector<int> identArray;
887 >    // Build the identArray_
888  
889 <    //to avoid memory reallocation, reserve enough space identArray
890 <    identArray.reserve(getNAtoms());
875 <    
889 >    identArray_.clear();
890 >    identArray_.reserve(getNAtoms());    
891      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
892        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893 <        identArray.push_back(atom->getIdent());
893 >        identArray_.push_back(atom->getIdent());
894        }
895      }    
881 –
882 –    //fill molMembershipArray
883 –    //molMembershipArray is filled by SimCreator    
884 –    vector<int> molMembershipArray(nGlobalAtoms_);
885 –    for (int i = 0; i < nGlobalAtoms_; i++) {
886 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
887 –    }
896      
897 <    //setup fortran simulation
897 >    //scan topology
898  
899      nExclude = excludedInteractions_.getSize();
900      nOneTwo = oneTwoInteractions_.getSize();
# Line 898 | Line 906 | namespace OpenMD {
906      int* oneThreeList = oneThreeInteractions_.getPairList();
907      int* oneFourList = oneFourInteractions_.getPairList();
908  
909 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
902 <                   &nExclude, excludeList,
903 <                   &nOneTwo, oneTwoList,
904 <                   &nOneThree, oneThreeList,
905 <                   &nOneFour, oneFourList,
906 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
907 <                   &fortranGlobalGroupMembership[0], &isError);
908 <    
909 <    if( isError ){
910 <      
911 <      sprintf( painCave.errMsg,
912 <               "There was an error setting the simulation information in fortran.\n" );
913 <      painCave.isFatal = 1;
914 <      painCave.severity = OPENMD_ERROR;
915 <      simError();
916 <    }
917 <    
918 <    
919 <    sprintf( checkPointMsg,
920 <             "succesfully sent the simulation information to fortran.\n");
921 <    
922 <    errorCheckPoint();
923 <    
924 <    // Setup number of neighbors in neighbor list if present
925 <    if (simParams_->haveNeighborListNeighbors()) {
926 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
927 <      setNeighbors(&nlistNeighbors);
928 <    }
929 <  
930 <
931 <  }
932 <
933 <
934 <  void SimInfo::setupFortranParallel() {
935 < #ifdef IS_MPI    
936 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
937 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
938 <    vector<int> localToGlobalCutoffGroupIndex;
939 <    SimInfo::MoleculeIterator mi;
940 <    Molecule::AtomIterator ai;
941 <    Molecule::CutoffGroupIterator ci;
942 <    Molecule* mol;
943 <    Atom* atom;
944 <    CutoffGroup* cg;
945 <    mpiSimData parallelData;
946 <    int isError;
947 <
948 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
949 <
950 <      //local index(index in DataStorge) of atom is important
951 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
952 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
953 <      }
954 <
955 <      //local index of cutoff group is trivial, it only depends on the order of travesing
956 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
957 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
958 <      }        
959 <        
960 <    }
961 <
962 <    //fill up mpiSimData struct
963 <    parallelData.nMolGlobal = getNGlobalMolecules();
964 <    parallelData.nMolLocal = getNMolecules();
965 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
966 <    parallelData.nAtomsLocal = getNAtoms();
967 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
968 <    parallelData.nGroupsLocal = getNCutoffGroups();
969 <    parallelData.myNode = worldRank;
970 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
971 <
972 <    //pass mpiSimData struct and index arrays to fortran
973 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
974 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
975 <                    &localToGlobalCutoffGroupIndex[0], &isError);
976 <
977 <    if (isError) {
978 <      sprintf(painCave.errMsg,
979 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
980 <      painCave.isFatal = 1;
981 <      simError();
982 <    }
983 <
984 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
985 <    errorCheckPoint();
986 <
987 < #endif
988 <  }
989 <
990 <
991 <  void SimInfo::setupSwitchingFunction() {    
992 <    int ft = CUBIC;
993 <    
994 <    if (simParams_->haveSwitchingFunctionType()) {
995 <      string funcType = simParams_->getSwitchingFunctionType();
996 <      toUpper(funcType);
997 <      if (funcType == "CUBIC") {
998 <        ft = CUBIC;
999 <      } else {
1000 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1001 <          ft = FIFTH_ORDER_POLY;
1002 <        } else {
1003 <          // throw error        
1004 <          sprintf( painCave.errMsg,
1005 <                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n"
1006 <                   "\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".",
1007 <                   funcType.c_str() );
1008 <          painCave.isFatal = 1;
1009 <          simError();
1010 <        }          
1011 <      }
1012 <    }
1013 <
1014 <    // send switching function notification to switcheroo
1015 <    setFunctionType(&ft);
1016 <
909 >    topologyDone_ = true;
910    }
911  
1019 –  void SimInfo::setupAccumulateBoxDipole() {    
1020 –
1021 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1022 –    if ( simParams_->haveAccumulateBoxDipole() )
1023 –      if ( simParams_->getAccumulateBoxDipole() ) {
1024 –        calcBoxDipole_ = true;
1025 –      }
1026 –
1027 –  }
1028 –
912    void SimInfo::addProperty(GenericData* genData) {
913      properties_.addProperty(genData);  
914    }
# Line 1060 | Line 943 | namespace OpenMD {
943      Molecule* mol;
944      RigidBody* rb;
945      Atom* atom;
946 +    CutoffGroup* cg;
947      SimInfo::MoleculeIterator mi;
948      Molecule::RigidBodyIterator rbIter;
949 <    Molecule::AtomIterator atomIter;;
949 >    Molecule::AtomIterator atomIter;
950 >    Molecule::CutoffGroupIterator cgIter;
951  
952      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
953          
# Line 1072 | Line 957 | namespace OpenMD {
957          
958        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
959          rb->setSnapshotManager(sman_);
960 +      }
961 +
962 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
963 +        cg->setSnapshotManager(sman_);
964        }
965      }    
966      

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