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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 1577 by gezelter, Wed Jun 8 20:26:56 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 275 | Line 269 | namespace OpenMD {
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() {
293      int ndfRaw_local;
# Line 771 | Line 784 | namespace OpenMD {
784      temp = usesElectrostatic;
785      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786   #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_;
787    }
788  
782 –  void SimInfo::setupFortran() {
783 –    int isError;
784 –    int nExclude, nOneTwo, nOneThree, nOneFour;
785 –    vector<int> fortranGlobalGroupMembership;
786 –    
787 –    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
795 –    vector<RealType> mfact;
833      SimInfo::MoleculeIterator mi;
834      Molecule* mol;
835      Molecule::CutoffGroupIterator ci;
# Line 801 | 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 >    //to avoid memory reallocation, reserve enough space for massFactors_
842 >    massFactors_.clear();
843 >    massFactors_.reserve(getNCutoffGroups());
844      
845      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
846 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
846 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
847 >           cg = mol->nextCutoffGroup(ci)) {
848  
849          totalMass = cg->getMass();
850          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
851            // Check for massless groups - set mfact to 1 if true
852            if (totalMass != 0)
853 <            mfact.push_back(atom->getMass()/totalMass);
853 >            massFactors_.push_back(atom->getMass()/totalMass);
854            else
855 <            mfact.push_back( 1.0 );
855 >            massFactors_.push_back( 1.0 );
856          }
857        }      
858      }
859  
860 <    //fill ident array of local atoms (it is actually ident of
822 <    //AtomType, it is so confusing !!!)
823 <    vector<int> identArray;
860 >    // Build the identArray_
861  
862 <    //to avoid memory reallocation, reserve enough space identArray
863 <    identArray.reserve(getNAtoms());
827 <    
862 >    identArray_.clear();
863 >    identArray_.reserve(getNAtoms());    
864      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
865        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
866 <        identArray.push_back(atom->getIdent());
866 >        identArray_.push_back(atom->getIdent());
867        }
868      }    
869 <
870 <    //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 <    }
840 <    
841 <    //setup fortran simulation
869 >    
870 >    //scan topology
871  
872      nExclude = excludedInteractions_.getSize();
873      nOneTwo = oneTwoInteractions_.getSize();
# Line 850 | Line 879 | namespace OpenMD {
879      int* oneThreeList = oneThreeInteractions_.getPairList();
880      int* oneFourList = oneFourInteractions_.getPairList();
881  
882 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
883 <                   &nExclude, excludeList,
884 <                   &nOneTwo, oneTwoList,
885 <                   &nOneThree, oneThreeList,
886 <                   &nOneFour, oneFourList,
887 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
888 <                   &fortranGlobalGroupMembership[0], &isError);
882 >    //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
883 >    //               &nExclude, excludeList,
884 >    //               &nOneTwo, oneTwoList,
885 >    //               &nOneThree, oneThreeList,
886 >    //               &nOneFour, oneFourList,
887 >    //               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
888 >    //               &fortranGlobalGroupMembership[0], &isError);
889      
890 <    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;
890 >    topologyDone_ = true;
891    }
892  
893    void SimInfo::addProperty(GenericData* genData) {
# Line 970 | Line 924 | namespace OpenMD {
924      Molecule* mol;
925      RigidBody* rb;
926      Atom* atom;
927 +    CutoffGroup* cg;
928      SimInfo::MoleculeIterator mi;
929      Molecule::RigidBodyIterator rbIter;
930 <    Molecule::AtomIterator atomIter;;
930 >    Molecule::AtomIterator atomIter;
931 >    Molecule::CutoffGroupIterator cgIter;
932  
933      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
934          
# Line 983 | Line 939 | namespace OpenMD {
939        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
940          rb->setSnapshotManager(sman_);
941        }
942 +
943 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
944 +        cg->setSnapshotManager(sman_);
945 +      }
946      }    
947      
948    }

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