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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 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC vs.
Revision 1586 by gezelter, Tue Jun 21 06:34:35 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"
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
135 –    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136 –    std::cerr << "nCA = " << nCutoffAtoms << "\n";
137 –    std::cerr << "nG = " << nGroups << "\n";
128  
129      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140 –
141 –    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
130      
131      //every free atom (atom does not belong to rigid bodies) is an
132      //integrable object therefore the total number of integrable objects
# Line 281 | 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;
294  
# Line 752 | Line 759 | namespace OpenMD {
759        if ( simParams_->getAccumulateBoxDipole() ) {
760          calcBoxDipole_ = true;      
761        }
762 <
762 >    
763      set<AtomType*>::iterator i;
764      set<AtomType*> atomTypes;
765      atomTypes = getSimulatedAtomTypes();    
# Line 765 | Line 772 | namespace OpenMD {
772        usesMetallic |= (*i)->isMetal();
773        usesDirectional |= (*i)->isDirectional();
774      }
775 <
775 >    
776   #ifdef IS_MPI    
777      int temp;
778      temp = usesDirectional;
779      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
780 <
780 >    
781      temp = usesMetallic;
782      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
783 <
783 >    
784      temp = usesElectrostatic;
785      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786 + #else
787 +
788 +    usesDirectionalAtoms_ = usesDirectional;
789 +    usesMetallicAtoms_ = usesMetallic;
790 +    usesElectrostaticAtoms_ = usesElectrostatic;
791 +
792   #endif
793 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
794 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
795 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
796 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
793 >    
794 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
795 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
796 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
797    }
798  
788 –  void SimInfo::setupFortran() {
789 –    int isError;
790 –    int nExclude, nOneTwo, nOneThree, nOneFour;
791 –    vector<int> fortranGlobalGroupMembership;
792 –    
793 –    isError = 0;
799  
800 <    //globalGroupMembership_ is filled by SimCreator    
801 <    for (int i = 0; i < nGlobalAtoms_; i++) {
802 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
800 >  vector<int> SimInfo::getGlobalAtomIndices() {
801 >    SimInfo::MoleculeIterator mi;
802 >    Molecule* mol;
803 >    Molecule::AtomIterator ai;
804 >    Atom* atom;
805 >
806 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
807 >    
808 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
809 >      
810 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
811 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
812 >      }
813      }
814 +    return GlobalAtomIndices;
815 +  }
816  
817 +
818 +  vector<int> SimInfo::getGlobalGroupIndices() {
819 +    SimInfo::MoleculeIterator mi;
820 +    Molecule* mol;
821 +    Molecule::CutoffGroupIterator ci;
822 +    CutoffGroup* cg;
823 +
824 +    vector<int> GlobalGroupIndices;
825 +    
826 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
827 +      
828 +      //local index of cutoff group is trivial, it only depends on the
829 +      //order of travesing
830 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
831 +           cg = mol->nextCutoffGroup(ci)) {
832 +        GlobalGroupIndices.push_back(cg->getGlobalIndex());
833 +      }        
834 +    }
835 +    return GlobalGroupIndices;
836 +  }
837 +
838 +
839 +  void SimInfo::prepareTopology() {
840 +    int nExclude, nOneTwo, nOneThree, nOneFour;
841 +
842      //calculate mass ratio of cutoff group
801 –    vector<RealType> mfact;
843      SimInfo::MoleculeIterator mi;
844      Molecule* mol;
845      Molecule::CutoffGroupIterator ci;
# Line 807 | Line 848 | namespace OpenMD {
848      Atom* atom;
849      RealType totalMass;
850  
851 <    //to avoid memory reallocation, reserve enough space for mfact
852 <    mfact.reserve(getNCutoffGroups());
851 >    /**
852 >     * The mass factor is the relative mass of an atom to the total
853 >     * mass of the cutoff group it belongs to.  By default, all atoms
854 >     * are their own cutoff groups, and therefore have mass factors of
855 >     * 1.  We need some special handling for massless atoms, which
856 >     * will be treated as carrying the entire mass of the cutoff
857 >     * group.
858 >     */
859 >    massFactors_.clear();
860 >    massFactors_.resize(getNAtoms(), 1.0);
861      
862 +    cerr << "mfs in si = " << massFactors_.size() << "\n";
863      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
864 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
864 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865 >           cg = mol->nextCutoffGroup(ci)) {
866  
867          totalMass = cg->getMass();
868          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
869            // Check for massless groups - set mfact to 1 if true
870 <          if (totalMass != 0)
871 <            mfact.push_back(atom->getMass()/totalMass);
870 >          if (totalMass != 0)
871 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
872            else
873 <            mfact.push_back( 1.0 );
873 >            massFactors_[atom->getLocalIndex()] = 1.0;
874          }
875        }      
876      }
877  
878 <    //fill ident array of local atoms (it is actually ident of
828 <    //AtomType, it is so confusing !!!)
829 <    vector<int> identArray;
878 >    // Build the identArray_
879  
880 <    //to avoid memory reallocation, reserve enough space identArray
881 <    identArray.reserve(getNAtoms());
833 <    
880 >    identArray_.clear();
881 >    identArray_.reserve(getNAtoms());    
882      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
883        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
884 <        identArray.push_back(atom->getIdent());
884 >        identArray_.push_back(atom->getIdent());
885        }
886      }    
839 –
840 –    //fill molMembershipArray
841 –    //molMembershipArray is filled by SimCreator    
842 –    vector<int> molMembershipArray(nGlobalAtoms_);
843 –    for (int i = 0; i < nGlobalAtoms_; i++) {
844 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
845 –    }
887      
888 <    //setup fortran simulation
888 >    //scan topology
889  
890      nExclude = excludedInteractions_.getSize();
891      nOneTwo = oneTwoInteractions_.getSize();
# Line 856 | Line 897 | namespace OpenMD {
897      int* oneThreeList = oneThreeInteractions_.getPairList();
898      int* oneFourList = oneFourInteractions_.getPairList();
899  
900 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860 <                   &nExclude, excludeList,
861 <                   &nOneTwo, oneTwoList,
862 <                   &nOneThree, oneThreeList,
863 <                   &nOneFour, oneFourList,
864 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
865 <                   &fortranGlobalGroupMembership[0], &isError);
866 <    
867 <    if( isError ){
868 <      
869 <      sprintf( painCave.errMsg,
870 <               "There was an error setting the simulation information in fortran.\n" );
871 <      painCave.isFatal = 1;
872 <      painCave.severity = OPENMD_ERROR;
873 <      simError();
874 <    }
875 <    
876 <    
877 <    sprintf( checkPointMsg,
878 <             "succesfully sent the simulation information to fortran.\n");
879 <    
880 <    errorCheckPoint();
881 <    
882 <    // Setup number of neighbors in neighbor list if present
883 <    if (simParams_->haveNeighborListNeighbors()) {
884 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
885 <      setNeighbors(&nlistNeighbors);
886 <    }
887 <  
888 < #ifdef IS_MPI    
889 <    //SimInfo is responsible for creating localToGlobalAtomIndex and
890 <    //localToGlobalGroupIndex
891 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
892 <    vector<int> localToGlobalCutoffGroupIndex;
893 <    mpiSimData parallelData;
894 <
895 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
896 <
897 <      //local index(index in DataStorge) of atom is important
898 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
899 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
900 <      }
901 <
902 <      //local index of cutoff group is trivial, it only depends on the order of travesing
903 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
904 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
905 <      }        
906 <        
907 <    }
908 <
909 <    //fill up mpiSimData struct
910 <    parallelData.nMolGlobal = getNGlobalMolecules();
911 <    parallelData.nMolLocal = getNMolecules();
912 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
913 <    parallelData.nAtomsLocal = getNAtoms();
914 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
915 <    parallelData.nGroupsLocal = getNCutoffGroups();
916 <    parallelData.myNode = worldRank;
917 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
918 <
919 <    //pass mpiSimData struct and index arrays to fortran
920 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
921 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
922 <                    &localToGlobalCutoffGroupIndex[0], &isError);
923 <
924 <    if (isError) {
925 <      sprintf(painCave.errMsg,
926 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
927 <      painCave.isFatal = 1;
928 <      simError();
929 <    }
930 <
931 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
932 <    errorCheckPoint();
933 < #endif
934 <
935 <    initFortranFF(&isError);
936 <    if (isError) {
937 <      sprintf(painCave.errMsg,
938 <              "initFortranFF errror: fortran didn't like something we gave it.\n");
939 <      painCave.isFatal = 1;
940 <      simError();
941 <    }
942 <    fortranInitialized_ = true;
900 >    topologyDone_ = true;
901    }
902  
903    void SimInfo::addProperty(GenericData* genData) {

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