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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 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC vs.
Revision 1581 by gezelter, Mon Jun 13 22:13:12 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"
# Line 62 | Line 61
61   #include "UseTheForce/ForceField.hpp"
62   #include "nonbonded/SwitchingFunction.hpp"
63  
65 – #ifdef IS_MPI
66 – #include "UseTheForce/mpiComponentPlan.h"
67 – #include "UseTheForce/DarkSide/simParallel_interface.h"
68 – #endif
69 –
64   using namespace std;
65   namespace OpenMD {
66    
# 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 770 | Line 784 | namespace OpenMD {
784      temp = usesElectrostatic;
785      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786   #endif
773 –    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
774 –    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
775 –    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
776 –    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
777 –    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
778 –    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
787    }
788  
781 –  void SimInfo::setupFortran() {
782 –    int isError;
783 –    int nExclude, nOneTwo, nOneThree, nOneFour;
784 –    vector<int> fortranGlobalGroupMembership;
785 –    
786 –    isError = 0;
789  
790 <    //globalGroupMembership_ is filled by SimCreator    
791 <    for (int i = 0; i < nGlobalAtoms_; i++) {
792 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
790 >  vector<int> SimInfo::getGlobalAtomIndices() {
791 >    SimInfo::MoleculeIterator mi;
792 >    Molecule* mol;
793 >    Molecule::AtomIterator ai;
794 >    Atom* atom;
795 >
796 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
797 >    
798 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
799 >      
800 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
801 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
802 >      }
803      }
804 +    return GlobalAtomIndices;
805 +  }
806  
807 +
808 +  vector<int> SimInfo::getGlobalGroupIndices() {
809 +    SimInfo::MoleculeIterator mi;
810 +    Molecule* mol;
811 +    Molecule::CutoffGroupIterator ci;
812 +    CutoffGroup* cg;
813 +
814 +    vector<int> GlobalGroupIndices;
815 +    
816 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
817 +      
818 +      //local index of cutoff group is trivial, it only depends on the
819 +      //order of travesing
820 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
821 +           cg = mol->nextCutoffGroup(ci)) {
822 +        GlobalGroupIndices.push_back(cg->getGlobalIndex());
823 +      }        
824 +    }
825 +    return GlobalGroupIndices;
826 +  }
827 +
828 +
829 +  void SimInfo::prepareTopology() {
830 +    int nExclude, nOneTwo, nOneThree, nOneFour;
831 +
832      //calculate mass ratio of cutoff group
794 –    vector<RealType> mfact;
833      SimInfo::MoleculeIterator mi;
834      Molecule* mol;
835      Molecule::CutoffGroupIterator ci;
# Line 800 | Line 838 | namespace OpenMD {
838      Atom* atom;
839      RealType totalMass;
840  
841 <    //to avoid memory reallocation, reserve enough space for mfact
842 <    mfact.reserve(getNCutoffGroups());
841 >    /**
842 >     * The mass factor is the relative mass of an atom to the total
843 >     * mass of the cutoff group it belongs to.  By default, all atoms
844 >     * are their own cutoff groups, and therefore have mass factors of
845 >     * 1.  We need some special handling for massless atoms, which
846 >     * will be treated as carrying the entire mass of the cutoff
847 >     * group.
848 >     */
849 >    massFactors_.clear();
850 >    massFactors_.resize(getNAtoms(), 1.0);
851      
852      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
853 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
853 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
854 >           cg = mol->nextCutoffGroup(ci)) {
855  
856          totalMass = cg->getMass();
857          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
858            // Check for massless groups - set mfact to 1 if true
859 <          if (totalMass != 0)
860 <            mfact.push_back(atom->getMass()/totalMass);
859 >          if (totalMass != 0)
860 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
861            else
862 <            mfact.push_back( 1.0 );
862 >            massFactors_[atom->getLocalIndex()] = 1.0;
863          }
864        }      
865      }
866  
867 <    //fill ident array of local atoms (it is actually ident of
821 <    //AtomType, it is so confusing !!!)
822 <    vector<int> identArray;
867 >    // Build the identArray_
868  
869 <    //to avoid memory reallocation, reserve enough space identArray
870 <    identArray.reserve(getNAtoms());
826 <    
869 >    identArray_.clear();
870 >    identArray_.reserve(getNAtoms());    
871      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
872        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
873 <        identArray.push_back(atom->getIdent());
873 >        identArray_.push_back(atom->getIdent());
874        }
875      }    
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 –    }
876      
877 <    //setup fortran simulation
877 >    //scan topology
878  
879      nExclude = excludedInteractions_.getSize();
880      nOneTwo = oneTwoInteractions_.getSize();
# Line 849 | Line 886 | namespace OpenMD {
886      int* oneThreeList = oneThreeInteractions_.getPairList();
887      int* oneFourList = oneFourInteractions_.getPairList();
888  
889 <    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;
889 >    topologyDone_ = true;
890    }
891  
892    void SimInfo::addProperty(GenericData* genData) {
# Line 961 | Line 923 | namespace OpenMD {
923      Molecule* mol;
924      RigidBody* rb;
925      Atom* atom;
926 +    CutoffGroup* cg;
927      SimInfo::MoleculeIterator mi;
928      Molecule::RigidBodyIterator rbIter;
929 <    Molecule::AtomIterator atomIter;;
929 >    Molecule::AtomIterator atomIter;
930 >    Molecule::CutoffGroupIterator cgIter;
931  
932      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
933          
# Line 974 | Line 938 | namespace OpenMD {
938        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
939          rb->setSnapshotManager(sman_);
940        }
941 +
942 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
943 +        cg->setSnapshotManager(sman_);
944 +      }
945      }    
946      
947    }

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