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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 1587 by gezelter, Fri Jul 8 20:25:32 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"
62 > #include "nonbonded/SwitchingFunction.hpp"
63  
69 –
70 – #ifdef IS_MPI
71 – #include "UseTheForce/mpiComponentPlan.h"
72 – #include "UseTheForce/DarkSide/simParallel_interface.h"
73 – #endif
74 –
64   using namespace std;
65   namespace OpenMD {
66    
# 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() {
660 –
661 –    setupSimType();
662 –    setupCutoffRadius();
663 –    setupSwitchingRadius();
664 –    setupCutoffMethod();
665 –    setupSkinThickness();
666 –    setupSwitchingFunction();
667 –    setupAccumulateBoxDipole();
668  
669 < #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)) {
688 <      
697 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
698        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
699          atomTypes.insert(atom->getAtomType());
700 <      }
701 <      
702 <    }
700 >      }      
701 >    }    
702 >
703 > #ifdef IS_MPI
704 >
705 >    // loop over the found atom types on this processor, and add their
706 >    // numerical idents to a vector:
707 >
708 >    vector<int> foundTypes;
709 >    set<AtomType*>::iterator i;
710 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
711 >      foundTypes.push_back( (*i)->getIdent() );
712 >
713 >    // count_local holds the number of found types on this processor
714 >    int count_local = foundTypes.size();
715 >
716 >    // count holds the total number of found types on all processors
717 >    // (some will be redundant with the ones found locally):
718 >    int count;
719 >    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
720 >
721 >    // create a vector to hold the globally found types, and resize it:
722 >    vector<int> ftGlobal;
723 >    ftGlobal.resize(count);
724 >    vector<int> counts;
725 >
726 >    int nproc = MPI::COMM_WORLD.Get_size();
727 >    counts.resize(nproc);
728 >    vector<int> disps;
729 >    disps.resize(nproc);
730 >
731 >    // now spray out the foundTypes to all the other processors:
732      
733 +    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
734 +                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
735 +
736 +    // foundIdents is a stl set, so inserting an already found ident
737 +    // will have no effect.
738 +    set<int> foundIdents;
739 +    vector<int>::iterator j;
740 +    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
741 +      foundIdents.insert((*j));
742 +    
743 +    // now iterate over the foundIdents and get the actual atom types
744 +    // that correspond to these:
745 +    set<int>::iterator it;
746 +    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
747 +      atomTypes.insert( forceField_->getAtomType((*it)) );
748 +
749 + #endif
750 +    
751      return atomTypes;        
752    }
753  
754 <  /**
755 <   * setupCutoffRadius
756 <   *
757 <   *  If the cutoffRadius was explicitly set, use that value.
758 <   *  If the cutoffRadius was not explicitly set:
759 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
760 <   *      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() {
709 <    
710 <    if (simParams_->haveCutoffRadius()) {
711 <      cutoffRadius_ = simParams_->getCutoffRadius();
712 <    } else {      
713 <      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 <    }
738 <
739 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
740 <  }
741 <  
742 <  /**
743 <   * setupSwitchingRadius
744 <   *
745 <   *  If the switchingRadius was explicitly set, use that value (but check it)
746 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
747 <   */
748 <  void SimInfo::setupSwitchingRadius() {
749 <    
750 <    if (simParams_->haveSwitchingRadius()) {
751 <      switchingRadius_ = simParams_->getSwitchingRadius();
752 <      if (switchingRadius_ > cutoffRadius_) {        
753 <        sprintf(painCave.errMsg,
754 <                "SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755 <                switchingRadius_, cutoffRadius_);
756 <        painCave.isFatal = 1;
757 <        simError();
758 <
754 >  void SimInfo::setupSimVariables() {
755 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
756 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
757 >    calcBoxDipole_ = false;
758 >    if ( simParams_->haveAccumulateBoxDipole() )
759 >      if ( simParams_->getAccumulateBoxDipole() ) {
760 >        calcBoxDipole_ = true;      
761        }
762 <    } 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 <  }
771 <
772 <  /**
773 <   * setupSkinThickness
774 <   *
775 <   *  If the skinThickness was explicitly set, use that value (but check it)
776 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
777 <   */
778 <  void SimInfo::setupSkinThickness() {    
779 <    if (simParams_->haveSkinThickness()) {
780 <      skinThickness_ = simParams_->getSkinThickness();
781 <    } else {      
782 <      skinThickness_ = 1.0;
783 <      sprintf(painCave.errMsg,
784 <              "SimInfo Warning: No value was set for the skinThickness.\n"
785 <              "\tOpenMD will use a default value of %f Angstroms\n"
786 <              "\tfor this simulation\n", skinThickness_);
787 <      painCave.isFatal = 0;
788 <      simError();
789 <    }            
790 <  }
791 <
792 <  void SimInfo::setupSimType() {
762 >    
763      set<AtomType*>::iterator i;
764      set<AtomType*> atomTypes;
765 <    atomTypes = getSimulatedAtomTypes();
796 <
797 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
798 <
765 >    atomTypes = getSimulatedAtomTypes();    
766      int usesElectrostatic = 0;
767      int usesMetallic = 0;
768      int usesDirectional = 0;
# Line 805 | Line 772 | namespace OpenMD {
772        usesMetallic |= (*i)->isMetal();
773        usesDirectional |= (*i)->isDirectional();
774      }
775 <
775 >    
776   #ifdef IS_MPI    
777      int temp;
778      temp = usesDirectional;
779      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
780 <
780 >    
781      temp = usesMetallic;
782      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
783 <
783 >    
784      temp = usesElectrostatic;
785      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786 + #else
787 +
788 +    usesDirectionalAtoms_ = usesDirectional;
789 +    usesMetallicAtoms_ = usesMetallic;
790 +    usesElectrostaticAtoms_ = usesElectrostatic;
791 +
792   #endif
793 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
794 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
795 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
796 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
793 >    
794 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
795 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
796 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
797    }
798  
799 <  void SimInfo::setupFortranSim() {
800 <    int isError;
801 <    int nExclude, nOneTwo, nOneThree, nOneFour;
802 <    vector<int> fortranGlobalGroupMembership;
799 >
800 >  vector<int> SimInfo::getGlobalAtomIndices() {
801 >    SimInfo::MoleculeIterator mi;
802 >    Molecule* mol;
803 >    Molecule::AtomIterator ai;
804 >    Atom* atom;
805 >
806 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
807      
808 <    notifyFortranSkinThickness(&skinThickness_);
808 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
809 >      
810 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
811 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
812 >      }
813 >    }
814 >    return GlobalAtomIndices;
815 >  }
816  
835 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
817  
818 <    isError = 0;
818 >  vector<int> SimInfo::getGlobalGroupIndices() {
819 >    SimInfo::MoleculeIterator mi;
820 >    Molecule* mol;
821 >    Molecule::CutoffGroupIterator ci;
822 >    CutoffGroup* cg;
823  
824 <    //globalGroupMembership_ is filled by SimCreator    
825 <    for (int i = 0; i < nGlobalAtoms_; i++) {
826 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
824 >    vector<int> GlobalGroupIndices;
825 >    
826 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
827 >      
828 >      //local index of cutoff group is trivial, it only depends on the
829 >      //order of travesing
830 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
831 >           cg = mol->nextCutoffGroup(ci)) {
832 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
833 >      }        
834      }
835 +    return GlobalGroupIndices;
836 +  }
837  
838 +
839 +  void SimInfo::prepareTopology() {
840 +    int nExclude, nOneTwo, nOneThree, nOneFour;
841 +
842      //calculate mass ratio of cutoff group
847 –    vector<RealType> mfact;
843      SimInfo::MoleculeIterator mi;
844      Molecule* mol;
845      Molecule::CutoffGroupIterator ci;
# Line 853 | Line 848 | namespace OpenMD {
848      Atom* atom;
849      RealType totalMass;
850  
851 <    //to avoid memory reallocation, reserve enough space for mfact
852 <    mfact.reserve(getNCutoffGroups());
851 >    /**
852 >     * The mass factor is the relative mass of an atom to the total
853 >     * mass of the cutoff group it belongs to.  By default, all atoms
854 >     * are their own cutoff groups, and therefore have mass factors of
855 >     * 1.  We need some special handling for massless atoms, which
856 >     * will be treated as carrying the entire mass of the cutoff
857 >     * group.
858 >     */
859 >    massFactors_.clear();
860 >    massFactors_.resize(getNAtoms(), 1.0);
861      
862      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
863 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
863 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
864 >           cg = mol->nextCutoffGroup(ci)) {
865  
866          totalMass = cg->getMass();
867          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
868            // Check for massless groups - set mfact to 1 if true
869 <          if (totalMass != 0)
870 <            mfact.push_back(atom->getMass()/totalMass);
869 >          if (totalMass != 0)
870 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
871            else
872 <            mfact.push_back( 1.0 );
872 >            massFactors_[atom->getLocalIndex()] = 1.0;
873          }
874        }      
875      }
876  
877 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874 <    vector<int> identArray;
877 >    // Build the identArray_
878  
879 <    //to avoid memory reallocation, reserve enough space identArray
880 <    identArray.reserve(getNAtoms());
878 <    
879 >    identArray_.clear();
880 >    identArray_.reserve(getNAtoms());    
881      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
882        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883 <        identArray.push_back(atom->getIdent());
883 >        identArray_.push_back(atom->getIdent());
884        }
885      }    
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 –    }
886      
887 <    //setup fortran simulation
887 >    //scan topology
888  
889      nExclude = excludedInteractions_.getSize();
890      nOneTwo = oneTwoInteractions_.getSize();
# Line 901 | Line 896 | namespace OpenMD {
896      int* oneThreeList = oneThreeInteractions_.getPairList();
897      int* oneFourList = oneFourInteractions_.getPairList();
898  
899 <    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 <
899 >    topologyDone_ = true;
900    }
901  
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 –
1018 –  }
1019 –
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 –
902    void SimInfo::addProperty(GenericData* genData) {
903      properties_.addProperty(genData);  
904    }
# Line 1061 | Line 933 | namespace OpenMD {
933      Molecule* mol;
934      RigidBody* rb;
935      Atom* atom;
936 +    CutoffGroup* cg;
937      SimInfo::MoleculeIterator mi;
938      Molecule::RigidBodyIterator rbIter;
939 <    Molecule::AtomIterator atomIter;;
939 >    Molecule::AtomIterator atomIter;
940 >    Molecule::CutoffGroupIterator cgIter;
941  
942      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
943          
# Line 1073 | Line 947 | namespace OpenMD {
947          
948        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
949          rb->setSnapshotManager(sman_);
950 +      }
951 +
952 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
953 +        cg->setSnapshotManager(sman_);
954        }
955      }    
956      

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