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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 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/DarkSide/neighborLists_interface.h"
58 – #include "UseTheForce/doForces_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"
65 –
66 – #ifdef IS_MPI
67 – #include "UseTheForce/mpiComponentPlan.h"
68 – #include "UseTheForce/DarkSide/simParallel_interface.h"
69 – #endif
63  
64   using namespace std;
65   namespace OpenMD {
# Line 78 | 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 132 | 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 274 | 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 681 | 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 700 | 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
704 <    // (some will be redundant with the ones found locally):
705 <    int count;
706 <    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 746 | 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 759 | 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_;
778 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
779 <    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 >        cerr << "LI = " << atom->getLocalIndex() << "GAI = " << GlobalAtomIndices[atom->getLocalIndex()] << "\n";
823 >      }
824 >    }
825 >    return GlobalAtomIndices;
826 >  }
827  
828 <    //globalGroupMembership_ is filled by SimCreator    
829 <    for (int i = 0; i < nGlobalAtoms_; i++) {
830 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
828 >
829 >  vector<int> SimInfo::getGlobalGroupIndices() {
830 >    SimInfo::MoleculeIterator mi;
831 >    Molecule* mol;
832 >    Molecule::CutoffGroupIterator ci;
833 >    CutoffGroup* cg;
834 >
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
795 –    vector<RealType> mfact;
855      SimInfo::MoleculeIterator mi;
856      Molecule* mol;
857      Molecule::CutoffGroupIterator ci;
# Line 801 | 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
822 <    //AtomType, it is so confusing !!!)
823 <    vector<int> identArray;
889 >    // Build the identArray_
890  
891 <    //to avoid memory reallocation, reserve enough space identArray
892 <    identArray.reserve(getNAtoms());
827 <    
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      }    
833 –
834 –    //fill molMembershipArray
835 –    //molMembershipArray is filled by SimCreator    
836 –    vector<int> molMembershipArray(nGlobalAtoms_);
837 –    for (int i = 0; i < nGlobalAtoms_; i++) {
838 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
839 –    }
898      
899 <    //setup fortran simulation
899 >    //scan topology
900  
901      nExclude = excludedInteractions_.getSize();
902      nOneTwo = oneTwoInteractions_.getSize();
# Line 850 | Line 908 | namespace OpenMD {
908      int* oneThreeList = oneThreeInteractions_.getPairList();
909      int* oneFourList = oneFourInteractions_.getPairList();
910  
911 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
854 <                   &nExclude, excludeList,
855 <                   &nOneTwo, oneTwoList,
856 <                   &nOneThree, oneThreeList,
857 <                   &nOneFour, oneFourList,
858 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
859 <                   &fortranGlobalGroupMembership[0], &isError);
860 <    
861 <    if( isError ){
862 <      
863 <      sprintf( painCave.errMsg,
864 <               "There was an error setting the simulation information in fortran.\n" );
865 <      painCave.isFatal = 1;
866 <      painCave.severity = OPENMD_ERROR;
867 <      simError();
868 <    }
869 <    
870 <    
871 <    sprintf( checkPointMsg,
872 <             "succesfully sent the simulation information to fortran.\n");
873 <    
874 <    errorCheckPoint();
875 <    
876 <    // Setup number of neighbors in neighbor list if present
877 <    if (simParams_->haveNeighborListNeighbors()) {
878 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
879 <      setNeighbors(&nlistNeighbors);
880 <    }
881 <  
882 < #ifdef IS_MPI    
883 <    //SimInfo is responsible for creating localToGlobalAtomIndex and
884 <    //localToGlobalGroupIndex
885 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
886 <    vector<int> localToGlobalCutoffGroupIndex;
887 <    mpiSimData parallelData;
888 <
889 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
890 <
891 <      //local index(index in DataStorge) of atom is important
892 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
894 <      }
895 <
896 <      //local index of cutoff group is trivial, it only depends on the order of travesing
897 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
898 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
899 <      }        
900 <        
901 <    }
902 <
903 <    //fill up mpiSimData struct
904 <    parallelData.nMolGlobal = getNGlobalMolecules();
905 <    parallelData.nMolLocal = getNMolecules();
906 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
907 <    parallelData.nAtomsLocal = getNAtoms();
908 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
909 <    parallelData.nGroupsLocal = getNCutoffGroups();
910 <    parallelData.myNode = worldRank;
911 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
912 <
913 <    //pass mpiSimData struct and index arrays to fortran
914 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
915 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
916 <                    &localToGlobalCutoffGroupIndex[0], &isError);
917 <
918 <    if (isError) {
919 <      sprintf(painCave.errMsg,
920 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
921 <      painCave.isFatal = 1;
922 <      simError();
923 <    }
924 <
925 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
926 <    errorCheckPoint();
927 < #endif
928 <
929 <    initFortranFF(&isError);
930 <    if (isError) {
931 <      sprintf(painCave.errMsg,
932 <              "initFortranFF errror: fortran didn't like something we gave it.\n");
933 <      painCave.isFatal = 1;
934 <      simError();
935 <    }
936 <    fortranInitialized_ = true;
911 >    topologyDone_ = true;
912    }
913  
914    void SimInfo::addProperty(GenericData* genData) {
# Line 970 | 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 982 | 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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