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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 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC vs.
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/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"
# Line 63 | Line 61
61   #include "UseTheForce/ForceField.hpp"
62   #include "nonbonded/SwitchingFunction.hpp"
63  
66 – #ifdef IS_MPI
67 – #include "UseTheForce/mpiComponentPlan.h"
68 – #include "UseTheForce/DarkSide/simParallel_interface.h"
69 – #endif
70 –
64   using namespace std;
65   namespace OpenMD {
66    
# 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 +    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129 +    std::cerr << "nCA = " << nCutoffAtoms << "\n";
130 +    std::cerr << "nG = " << nGroups << "\n";
131 +
132      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133 +
134 +    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135      
136      //every free atom (atom does not belong to rigid bodies) is an
137      //integrable object therefore the total number of integrable objects
# Line 771 | Line 770 | namespace OpenMD {
770      temp = usesElectrostatic;
771      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772   #endif
774 –    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
775 –    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
776 –    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
777 –    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
778 –    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
779 –    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
773    }
774  
782 –  void SimInfo::setupFortran() {
783 –    int isError;
784 –    int nExclude, nOneTwo, nOneThree, nOneFour;
785 –    vector<int> fortranGlobalGroupMembership;
786 –    
787 –    isError = 0;
775  
776 <    //globalGroupMembership_ is filled by SimCreator    
777 <    for (int i = 0; i < nGlobalAtoms_; i++) {
778 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
776 >  vector<int> SimInfo::getGlobalAtomIndices() {
777 >    SimInfo::MoleculeIterator mi;
778 >    Molecule* mol;
779 >    Molecule::AtomIterator ai;
780 >    Atom* atom;
781 >
782 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
783 >    
784 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
785 >      
786 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
787 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
788 >      }
789 >    }
790 >    return GlobalAtomIndices;
791 >  }
792 >
793 >
794 >  vector<int> SimInfo::getGlobalGroupIndices() {
795 >    SimInfo::MoleculeIterator mi;
796 >    Molecule* mol;
797 >    Molecule::CutoffGroupIterator ci;
798 >    CutoffGroup* cg;
799 >
800 >    vector<int> GlobalGroupIndices;
801 >    
802 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
803 >      
804 >      //local index of cutoff group is trivial, it only depends on the
805 >      //order of travesing
806 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
807 >           cg = mol->nextCutoffGroup(ci)) {
808 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
809 >      }        
810      }
811 +    return GlobalGroupIndices;
812 +  }
813  
814 +
815 +  void SimInfo::prepareTopology() {
816 +    int nExclude, nOneTwo, nOneThree, nOneFour;
817 +
818      //calculate mass ratio of cutoff group
795 –    vector<RealType> mfact;
819      SimInfo::MoleculeIterator mi;
820      Molecule* mol;
821      Molecule::CutoffGroupIterator ci;
# Line 801 | Line 824 | namespace OpenMD {
824      Atom* atom;
825      RealType totalMass;
826  
827 <    //to avoid memory reallocation, reserve enough space for mfact
828 <    mfact.reserve(getNCutoffGroups());
827 >    //to avoid memory reallocation, reserve enough space for massFactors_
828 >    massFactors_.clear();
829 >    massFactors_.reserve(getNCutoffGroups());
830      
831      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
832 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
832 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
833 >           cg = mol->nextCutoffGroup(ci)) {
834  
835          totalMass = cg->getMass();
836          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
837            // Check for massless groups - set mfact to 1 if true
838            if (totalMass != 0)
839 <            mfact.push_back(atom->getMass()/totalMass);
839 >            massFactors_.push_back(atom->getMass()/totalMass);
840            else
841 <            mfact.push_back( 1.0 );
841 >            massFactors_.push_back( 1.0 );
842          }
843        }      
844      }
845  
846 <    //fill ident array of local atoms (it is actually ident of
822 <    //AtomType, it is so confusing !!!)
823 <    vector<int> identArray;
846 >    // Build the identArray_
847  
848 <    //to avoid memory reallocation, reserve enough space identArray
849 <    identArray.reserve(getNAtoms());
827 <    
848 >    identArray_.clear();
849 >    identArray_.reserve(getNAtoms());    
850      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
851        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
852 <        identArray.push_back(atom->getIdent());
852 >        identArray_.push_back(atom->getIdent());
853        }
854      }    
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 –    }
855      
856 <    //setup fortran simulation
856 >    //scan topology
857  
858      nExclude = excludedInteractions_.getSize();
859      nOneTwo = oneTwoInteractions_.getSize();
# Line 850 | Line 865 | namespace OpenMD {
865      int* oneThreeList = oneThreeInteractions_.getPairList();
866      int* oneFourList = oneFourInteractions_.getPairList();
867  
868 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
869 <                   &nExclude, excludeList,
870 <                   &nOneTwo, oneTwoList,
871 <                   &nOneThree, oneThreeList,
872 <                   &nOneFour, oneFourList,
873 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874 <                   &fortranGlobalGroupMembership[0], &isError);
868 >    //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
869 >    //               &nExclude, excludeList,
870 >    //               &nOneTwo, oneTwoList,
871 >    //               &nOneThree, oneThreeList,
872 >    //               &nOneFour, oneFourList,
873 >    //               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874 >    //               &fortranGlobalGroupMembership[0], &isError);
875      
876 <    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;
876 >    topologyDone_ = true;
877    }
878  
879    void SimInfo::addProperty(GenericData* genData) {
# Line 970 | Line 910 | namespace OpenMD {
910      Molecule* mol;
911      RigidBody* rb;
912      Atom* atom;
913 +    CutoffGroup* cg;
914      SimInfo::MoleculeIterator mi;
915      Molecule::RigidBodyIterator rbIter;
916 <    Molecule::AtomIterator atomIter;;
916 >    Molecule::AtomIterator atomIter;
917 >    Molecule::CutoffGroupIterator cgIter;
918  
919      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920          
# Line 983 | Line 925 | namespace OpenMD {
925        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
926          rb->setSnapshotManager(sman_);
927        }
928 +
929 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
930 +        cg->setSnapshotManager(sman_);
931 +      }
932      }    
933      
934    }

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