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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1535 by gezelter, Fri Dec 31 18:31:56 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/DarkSide/neighborLists_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/SwitchingFunction.hpp"
64 –
65 – #ifdef IS_MPI
66 – #include "UseTheForce/mpiComponentPlan.h"
67 – #include "UseTheForce/DarkSide/simParallel_interface.h"
68 – #endif
63  
64   using namespace std;
65   namespace OpenMD {
# Line 77 | 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 131 | 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 273 | 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 680 | 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      }    
703 <
703 >    
704   #ifdef IS_MPI
705  
706      // loop over the found atom types on this processor, and add their
707      // numerical idents to a vector:
708 <
708 >    
709      vector<int> foundTypes;
710      set<AtomType*>::iterator i;
711      for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
# Line 699 | Line 714 | namespace OpenMD {
714      // count_local holds the number of found types on this processor
715      int count_local = foundTypes.size();
716  
717 <    // count holds the total number of found types on all processors
703 <    // (some will be redundant with the ones found locally):
704 <    int count;
705 <    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
717 >    int nproc = MPI::COMM_WORLD.Get_size();
718  
719 <    // create a vector to hold the globally found types, and resize it:
720 <    vector<int> ftGlobal;
721 <    ftGlobal.resize(count);
722 <    vector<int> counts;
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 <    int nproc = MPI::COMM_WORLD.Get_size();
725 <    counts.resize(nproc);
726 <    vector<int> disps;
727 <    disps.resize(nproc);
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 <    // now spray out the foundTypes to all the other processors:
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], 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 <    vector<int>::iterator j;
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)
756 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
757        atomTypes.insert( forceField_->getAtomType((*it)) );
758  
759   #endif
760 <    
760 >
761      return atomTypes;        
762    }
763  
# Line 745 | Line 769 | namespace OpenMD {
769        if ( simParams_->getAccumulateBoxDipole() ) {
770          calcBoxDipole_ = true;      
771        }
772 <
772 >    
773      set<AtomType*>::iterator i;
774      set<AtomType*> atomTypes;
775      atomTypes = getSimulatedAtomTypes();    
# Line 758 | 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_;
777 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
778 <    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::setupFortran() {
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 <    isError = 0;
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  
827 <    //globalGroupMembership_ is filled by SimCreator    
828 <    for (int i = 0; i < nGlobalAtoms_; i++) {
829 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
827 >
828 >  vector<int> SimInfo::getGlobalGroupIndices() {
829 >    SimInfo::MoleculeIterator mi;
830 >    Molecule* mol;
831 >    Molecule::CutoffGroupIterator ci;
832 >    CutoffGroup* cg;
833 >
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
794 –    vector<RealType> mfact;
853      SimInfo::MoleculeIterator mi;
854      Molecule* mol;
855      Molecule::CutoffGroupIterator ci;
# Line 800 | 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
821 <    //AtomType, it is so confusing !!!)
822 <    vector<int> identArray;
887 >    // Build the identArray_
888  
889 <    //to avoid memory reallocation, reserve enough space identArray
890 <    identArray.reserve(getNAtoms());
826 <    
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      }    
832 –
833 –    //fill molMembershipArray
834 –    //molMembershipArray is filled by SimCreator    
835 –    vector<int> molMembershipArray(nGlobalAtoms_);
836 –    for (int i = 0; i < nGlobalAtoms_; i++) {
837 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
838 –    }
896      
897 <    //setup fortran simulation
897 >    //scan topology
898  
899      nExclude = excludedInteractions_.getSize();
900      nOneTwo = oneTwoInteractions_.getSize();
# Line 849 | Line 906 | namespace OpenMD {
906      int* oneThreeList = oneThreeInteractions_.getPairList();
907      int* oneFourList = oneFourInteractions_.getPairList();
908  
909 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
853 <                   &nExclude, excludeList,
854 <                   &nOneTwo, oneTwoList,
855 <                   &nOneThree, oneThreeList,
856 <                   &nOneFour, oneFourList,
857 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
858 <                   &fortranGlobalGroupMembership[0], &isError);
859 <    
860 <    if( isError ){
861 <      
862 <      sprintf( painCave.errMsg,
863 <               "There was an error setting the simulation information in fortran.\n" );
864 <      painCave.isFatal = 1;
865 <      painCave.severity = OPENMD_ERROR;
866 <      simError();
867 <    }
868 <    
869 <    
870 <    sprintf( checkPointMsg,
871 <             "succesfully sent the simulation information to fortran.\n");
872 <    
873 <    errorCheckPoint();
874 <    
875 <    // Setup number of neighbors in neighbor list if present
876 <    if (simParams_->haveNeighborListNeighbors()) {
877 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
878 <      setNeighbors(&nlistNeighbors);
879 <    }
880 <  
881 < #ifdef IS_MPI    
882 <    //SimInfo is responsible for creating localToGlobalAtomIndex and
883 <    //localToGlobalGroupIndex
884 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
885 <    vector<int> localToGlobalCutoffGroupIndex;
886 <    mpiSimData parallelData;
887 <
888 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889 <
890 <      //local index(index in DataStorge) of atom is important
891 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893 <      }
894 <
895 <      //local index of cutoff group is trivial, it only depends on the order of travesing
896 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898 <      }        
899 <        
900 <    }
901 <
902 <    //fill up mpiSimData struct
903 <    parallelData.nMolGlobal = getNGlobalMolecules();
904 <    parallelData.nMolLocal = getNMolecules();
905 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
906 <    parallelData.nAtomsLocal = getNAtoms();
907 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
908 <    parallelData.nGroupsLocal = getNCutoffGroups();
909 <    parallelData.myNode = worldRank;
910 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
911 <
912 <    //pass mpiSimData struct and index arrays to fortran
913 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
914 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
915 <                    &localToGlobalCutoffGroupIndex[0], &isError);
916 <
917 <    if (isError) {
918 <      sprintf(painCave.errMsg,
919 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
920 <      painCave.isFatal = 1;
921 <      simError();
922 <    }
923 <
924 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
925 <    errorCheckPoint();
926 < #endif
927 <    fortranInitialized_ = true;
909 >    topologyDone_ = true;
910    }
911  
912    void SimInfo::addProperty(GenericData* genData) {
# Line 961 | 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 973 | 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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