ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/SimInfo.cpp
(Generate patch)

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/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 <
62 > #include "nonbonded/SwitchingFunction.hpp"
63   #ifdef IS_MPI
64 < #include "UseTheForce/mpiComponentPlan.h"
65 < #include "UseTheForce/DarkSide/simParallel_interface.h"
73 < #endif
64 > #include <mpi.h>
65 > #endif
66  
67   using namespace std;
68   namespace OpenMD {
# Line 82 | Line 74 | namespace OpenMD {
74      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
76      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
77 <    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
77 >    nConstraints_(0), sman_(NULL), topologyDone_(false),
78      calcBoxDipole_(false), useAtomicVirial_(true) {    
79      
80      MoleculeStamp* molStamp;
# Line 136 | Line 128 | namespace OpenMD {
128      //equal to the total number of atoms minus number of atoms belong to
129      //cutoff group defined in meta-data file plus the number of cutoff
130      //groups defined in meta-data file
131 +
132      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133      
134      //every free atom (atom does not belong to rigid bodies) is an
# Line 279 | Line 272 | namespace OpenMD {
272   #endif
273      return fdf_;
274    }
275 +  
276 +  unsigned int SimInfo::getNLocalCutoffGroups(){
277 +    int nLocalCutoffAtoms = 0;
278 +    Molecule* mol;
279 +    MoleculeIterator mi;
280 +    CutoffGroup* cg;
281 +    Molecule::CutoffGroupIterator ci;
282      
283 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
284 +      
285 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
286 +           cg = mol->nextCutoffGroup(ci)) {
287 +        nLocalCutoffAtoms += cg->getNumAtom();
288 +        
289 +      }        
290 +    }
291 +    
292 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
293 +  }
294 +    
295    void SimInfo::calcNdfRaw() {
296      int ndfRaw_local;
297  
# Line 655 | Line 667 | namespace OpenMD {
667      moleculeStamps_.push_back(molStamp);
668      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
669    }
658 –
659 –  void SimInfo::update() {
660 –
661 –    setupSimType();
662 –    setupCutoffRadius();
663 –    setupSwitchingRadius();
664 –    setupCutoffMethod();
665 –    setupSkinThickness();
666 –    setupSwitchingFunction();
667 –    setupAccumulateBoxDipole();
670  
669 – #ifdef IS_MPI
670 –    setupFortranParallel();
671 – #endif
672 –    setupFortranSim();
673 –    fortranInitialized_ = true;
671  
672 +  /**
673 +   * update
674 +   *
675 +   *  Performs the global checks and variable settings after the
676 +   *  objects have been created.
677 +   *
678 +   */
679 +  void SimInfo::update() {  
680 +    setupSimVariables();
681      calcNdf();
682      calcNdfRaw();
683      calcNdfTrans();
684    }
685    
686 +  /**
687 +   * getSimulatedAtomTypes
688 +   *
689 +   * Returns an STL set of AtomType* that are actually present in this
690 +   * simulation.  Must query all processors to assemble this information.
691 +   *
692 +   */
693    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
694      SimInfo::MoleculeIterator mi;
695      Molecule* mol;
# Line 685 | Line 698 | namespace OpenMD {
698      set<AtomType*> atomTypes;
699      
700      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
701 <      
702 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
701 >      for(atom = mol->beginAtom(ai); atom != NULL;
702 >          atom = mol->nextAtom(ai)) {
703          atomTypes.insert(atom->getAtomType());
704 <      }
705 <      
693 <    }
704 >      }      
705 >    }    
706      
707 <    return atomTypes;        
696 <  }
707 > #ifdef IS_MPI
708  
709 <  /**
710 <   * 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() {
709 >    // loop over the found atom types on this processor, and add their
710 >    // numerical idents to a vector:
711      
712 <    if (simParams_->haveCutoffRadius()) {
713 <      cutoffRadius_ = simParams_->getCutoffRadius();
714 <    } else {      
715 <      if (usesElectrostaticAtoms_) {
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 <    }
712 >    vector<int> foundTypes;
713 >    set<AtomType*>::iterator i;
714 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
715 >      foundTypes.push_back( (*i)->getIdent() );
716  
717 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
718 <  }
717 >    // count_local holds the number of found types on this processor
718 >    int count_local = foundTypes.size();
719 >
720 >    int nproc = MPI::COMM_WORLD.Get_size();
721 >
722 >    // we need arrays to hold the counts and displacement vectors for
723 >    // all processors
724 >    vector<int> counts(nproc, 0);
725 >    vector<int> disps(nproc, 0);
726 >
727 >    // fill the counts array
728 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
729 >                              1, MPI::INT);
730    
731 <  /**
732 <   * setupSwitchingRadius
733 <   *
734 <   *  If the switchingRadius was explicitly set, use that value (but check it)
735 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
736 <   */
737 <  void SimInfo::setupSwitchingRadius() {
731 >    // use the processor counts to compute the displacement array
732 >    disps[0] = 0;    
733 >    int totalCount = counts[0];
734 >    for (int iproc = 1; iproc < nproc; iproc++) {
735 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
736 >      totalCount += counts[iproc];
737 >    }
738 >
739 >    // we need a (possibly redundant) set of all found types:
740 >    vector<int> ftGlobal(totalCount);
741      
742 <    if (simParams_->haveSwitchingRadius()) {
743 <      switchingRadius_ = simParams_->getSwitchingRadius();
744 <      if (switchingRadius_ > cutoffRadius_) {        
745 <        sprintf(painCave.errMsg,
754 <                "SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755 <                switchingRadius_, cutoffRadius_);
756 <        painCave.isFatal = 1;
757 <        simError();
742 >    // now spray out the foundTypes to all the other processors:    
743 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
744 >                               &ftGlobal[0], &counts[0], &disps[0],
745 >                               MPI::INT);
746  
747 <      }
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 <  }
747 >    vector<int>::iterator j;
748  
749 <  /**
750 <   * setupSkinThickness
751 <   *
752 <   *  If the skinThickness was explicitly set, use that value (but check it)
753 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
754 <   */
755 <  void SimInfo::setupSkinThickness() {    
756 <    if (simParams_->haveSkinThickness()) {
757 <      skinThickness_ = simParams_->getSkinThickness();
758 <    } else {      
759 <      skinThickness_ = 1.0;
760 <      sprintf(painCave.errMsg,
761 <              "SimInfo Warning: No value was set for the skinThickness.\n"
762 <              "\tOpenMD will use a default value of %f Angstroms\n"
763 <              "\tfor this simulation\n", skinThickness_);
764 <      painCave.isFatal = 0;
788 <      simError();
789 <    }            
749 >    // foundIdents is a stl set, so inserting an already found ident
750 >    // will have no effect.
751 >    set<int> foundIdents;
752 >
753 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
754 >      foundIdents.insert((*j));
755 >    
756 >    // now iterate over the foundIdents and get the actual atom types
757 >    // that correspond to these:
758 >    set<int>::iterator it;
759 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
760 >      atomTypes.insert( forceField_->getAtomType((*it)) );
761 >
762 > #endif
763 >
764 >    return atomTypes;        
765    }
766  
767 <  void SimInfo::setupSimType() {
767 >  void SimInfo::setupSimVariables() {
768 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
769 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
770 >    calcBoxDipole_ = false;
771 >    if ( simParams_->haveAccumulateBoxDipole() )
772 >      if ( simParams_->getAccumulateBoxDipole() ) {
773 >        calcBoxDipole_ = true;      
774 >      }
775 >    
776      set<AtomType*>::iterator i;
777      set<AtomType*> atomTypes;
778 <    atomTypes = getSimulatedAtomTypes();
796 <
797 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
798 <
778 >    atomTypes = getSimulatedAtomTypes();    
779      int usesElectrostatic = 0;
780      int usesMetallic = 0;
781      int usesDirectional = 0;
# Line 805 | Line 785 | namespace OpenMD {
785        usesMetallic |= (*i)->isMetal();
786        usesDirectional |= (*i)->isDirectional();
787      }
788 <
788 >    
789   #ifdef IS_MPI    
790      int temp;
791      temp = usesDirectional;
792      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
793 <
793 >    
794      temp = usesMetallic;
795      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
796 <
796 >    
797      temp = usesElectrostatic;
798      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799 + #else
800 +
801 +    usesDirectionalAtoms_ = usesDirectional;
802 +    usesMetallicAtoms_ = usesMetallic;
803 +    usesElectrostaticAtoms_ = usesElectrostatic;
804 +
805   #endif
806 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
807 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
808 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
809 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
806 >    
807 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
808 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
809 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
810    }
811  
812 <  void SimInfo::setupFortranSim() {
813 <    int isError;
814 <    int nExclude, nOneTwo, nOneThree, nOneFour;
815 <    vector<int> fortranGlobalGroupMembership;
812 >
813 >  vector<int> SimInfo::getGlobalAtomIndices() {
814 >    SimInfo::MoleculeIterator mi;
815 >    Molecule* mol;
816 >    Molecule::AtomIterator ai;
817 >    Atom* atom;
818 >
819 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
820      
821 <    notifyFortranSkinThickness(&skinThickness_);
821 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
822 >      
823 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
824 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
825 >      }
826 >    }
827 >    return GlobalAtomIndices;
828 >  }
829  
835 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
830  
831 <    isError = 0;
831 >  vector<int> SimInfo::getGlobalGroupIndices() {
832 >    SimInfo::MoleculeIterator mi;
833 >    Molecule* mol;
834 >    Molecule::CutoffGroupIterator ci;
835 >    CutoffGroup* cg;
836  
837 <    //globalGroupMembership_ is filled by SimCreator    
838 <    for (int i = 0; i < nGlobalAtoms_; i++) {
839 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
837 >    vector<int> GlobalGroupIndices;
838 >    
839 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840 >      
841 >      //local index of cutoff group is trivial, it only depends on the
842 >      //order of travesing
843 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
844 >           cg = mol->nextCutoffGroup(ci)) {
845 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
846 >      }        
847      }
848 +    return GlobalGroupIndices;
849 +  }
850  
851 +
852 +  void SimInfo::prepareTopology() {
853 +    int nExclude, nOneTwo, nOneThree, nOneFour;
854 +
855      //calculate mass ratio of cutoff group
847 –    vector<RealType> mfact;
856      SimInfo::MoleculeIterator mi;
857      Molecule* mol;
858      Molecule::CutoffGroupIterator ci;
# Line 853 | Line 861 | namespace OpenMD {
861      Atom* atom;
862      RealType totalMass;
863  
864 <    //to avoid memory reallocation, reserve enough space for mfact
865 <    mfact.reserve(getNCutoffGroups());
864 >    /**
865 >     * The mass factor is the relative mass of an atom to the total
866 >     * mass of the cutoff group it belongs to.  By default, all atoms
867 >     * are their own cutoff groups, and therefore have mass factors of
868 >     * 1.  We need some special handling for massless atoms, which
869 >     * will be treated as carrying the entire mass of the cutoff
870 >     * group.
871 >     */
872 >    massFactors_.clear();
873 >    massFactors_.resize(getNAtoms(), 1.0);
874      
875      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
876 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
876 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
877 >           cg = mol->nextCutoffGroup(ci)) {
878  
879          totalMass = cg->getMass();
880          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
881            // Check for massless groups - set mfact to 1 if true
882 <          if (totalMass != 0)
883 <            mfact.push_back(atom->getMass()/totalMass);
882 >          if (totalMass != 0)
883 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
884            else
885 <            mfact.push_back( 1.0 );
885 >            massFactors_[atom->getLocalIndex()] = 1.0;
886          }
887        }      
888      }
889  
890 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874 <    vector<int> identArray;
890 >    // Build the identArray_
891  
892 <    //to avoid memory reallocation, reserve enough space identArray
893 <    identArray.reserve(getNAtoms());
878 <    
892 >    identArray_.clear();
893 >    identArray_.reserve(getNAtoms());    
894      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
895        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896 <        identArray.push_back(atom->getIdent());
896 >        identArray_.push_back(atom->getIdent());
897        }
898      }    
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 –    }
899      
900 <    //setup fortran simulation
900 >    //scan topology
901  
902      nExclude = excludedInteractions_.getSize();
903      nOneTwo = oneTwoInteractions_.getSize();
# Line 901 | Line 909 | namespace OpenMD {
909      int* oneThreeList = oneThreeInteractions_.getPairList();
910      int* oneFourList = oneFourInteractions_.getPairList();
911  
912 <    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 <
912 >    topologyDone_ = true;
913    }
914  
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 –
915    void SimInfo::addProperty(GenericData* genData) {
916      properties_.addProperty(genData);  
917    }
# Line 1061 | Line 946 | namespace OpenMD {
946      Molecule* mol;
947      RigidBody* rb;
948      Atom* atom;
949 +    CutoffGroup* cg;
950      SimInfo::MoleculeIterator mi;
951      Molecule::RigidBodyIterator rbIter;
952 <    Molecule::AtomIterator atomIter;;
952 >    Molecule::AtomIterator atomIter;
953 >    Molecule::CutoffGroupIterator cgIter;
954  
955      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956          
# Line 1073 | Line 960 | namespace OpenMD {
960          
961        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
962          rb->setSnapshotManager(sman_);
963 +      }
964 +
965 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
966 +        cg->setSnapshotManager(sman_);
967        }
968      }    
969      

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines