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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 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1550 by gezelter, Wed Apr 27 21:49:59 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/fCutoffPolicy.h"
58 – #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59 – #include "UseTheForce/doForces_interface.h"
60 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
61 – #include "UseTheForce/DarkSide/switcheroo_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/InteractionManager.hpp"
62 > #include "nonbonded/SwitchingFunction.hpp"
63  
69 –
70 – #ifdef IS_MPI
71 – #include "UseTheForce/mpiComponentPlan.h"
72 – #include "UseTheForce/DarkSide/simParallel_interface.h"
73 – #endif
74 –
64   using namespace std;
65   namespace OpenMD {
66    
# Line 136 | 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 656 | Line 651 | namespace OpenMD {
651      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652    }
653  
659 –  void SimInfo::update() {
654  
655 <    setupSimType();
656 <    setupCutoffRadius();
657 <    setupSwitchingRadius();
658 <    setupCutoffMethod();
659 <    setupSkinThickness();
660 <    setupSwitchingFunction();
661 <    setupAccumulateBoxDipole();
662 <
663 < #ifdef IS_MPI
670 <    setupFortranParallel();
671 < #endif
672 <    setupFortranSim();
673 <    fortranInitialized_ = true;
674 <
655 >  /**
656 >   * update
657 >   *
658 >   *  Performs the global checks and variable settings after the
659 >   *  objects have been created.
660 >   *
661 >   */
662 >  void SimInfo::update() {  
663 >    setupSimVariables();
664      calcNdf();
665      calcNdfRaw();
666      calcNdfTrans();
667    }
668    
669 +  /**
670 +   * getSimulatedAtomTypes
671 +   *
672 +   * Returns an STL set of AtomType* that are actually present in this
673 +   * simulation.  Must query all processors to assemble this information.
674 +   *
675 +   */
676    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677      SimInfo::MoleculeIterator mi;
678      Molecule* mol;
# Line 684 | Line 680 | namespace OpenMD {
680      Atom* atom;
681      set<AtomType*> atomTypes;
682      
683 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688 <      
683 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
684        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685          atomTypes.insert(atom->getAtomType());
686 <      }
687 <      
688 <    }
686 >      }      
687 >    }    
688 >
689 > #ifdef IS_MPI
690 >
691 >    // loop over the found atom types on this processor, and add their
692 >    // numerical idents to a vector:
693 >
694 >    vector<int> foundTypes;
695 >    set<AtomType*>::iterator i;
696 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697 >      foundTypes.push_back( (*i)->getIdent() );
698 >
699 >    // count_local holds the number of found types on this processor
700 >    int count_local = foundTypes.size();
701 >
702 >    // count holds the total number of found types on all processors
703 >    // (some will be redundant with the ones found locally):
704 >    int count;
705 >    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706 >
707 >    // create a vector to hold the globally found types, and resize it:
708 >    vector<int> ftGlobal;
709 >    ftGlobal.resize(count);
710 >    vector<int> counts;
711 >
712 >    int nproc = MPI::COMM_WORLD.Get_size();
713 >    counts.resize(nproc);
714 >    vector<int> disps;
715 >    disps.resize(nproc);
716 >
717 >    // now spray out the foundTypes to all the other processors:
718      
719 +    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720 +                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721 +
722 +    // foundIdents is a stl set, so inserting an already found ident
723 +    // will have no effect.
724 +    set<int> foundIdents;
725 +    vector<int>::iterator j;
726 +    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727 +      foundIdents.insert((*j));
728 +    
729 +    // now iterate over the foundIdents and get the actual atom types
730 +    // that correspond to these:
731 +    set<int>::iterator it;
732 +    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733 +      atomTypes.insert( forceField_->getAtomType((*it)) );
734 +
735 + #endif
736 +    
737      return atomTypes;        
738    }
739  
740 <  /**
741 <   * setupCutoffRadius
742 <   *
743 <   *  If the cutoffRadius was explicitly set, use that value.
744 <   *  If the cutoffRadius was not explicitly set:
745 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
746 <   *      No electrostatic atoms?  Poll the atom types present in the
705 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
706 <   *      Use the maximum suggested value that was found.
707 <   */
708 <  void SimInfo::setupCutoffRadius() {
709 <    
710 <    if (simParams_->haveCutoffRadius()) {
711 <      cutoffRadius_ = simParams_->getCutoffRadius();
712 <    } else {      
713 <      if (usesElectrostaticAtoms_) {
714 <        sprintf(painCave.errMsg,
715 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
716 <                "\tOpenMD will use a default value of 12.0 angstroms"
717 <                "\tfor the cutoffRadius.\n");
718 <        painCave.isFatal = 0;
719 <        simError();
720 <        cutoffRadius_ = 12.0;
721 <      } else {
722 <        RealType thisCut;
723 <        set<AtomType*>::iterator i;
724 <        set<AtomType*> atomTypes;
725 <        atomTypes = getSimulatedAtomTypes();        
726 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
727 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
728 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
729 <        }
730 <        sprintf(painCave.errMsg,
731 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
732 <                "\tOpenMD will use %lf angstroms.\n",
733 <                cutoffRadius_);
734 <        painCave.isFatal = 0;
735 <        simError();
736 <      }            
737 <    }
738 <
739 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
740 <  }
741 <  
742 <  /**
743 <   * setupSwitchingRadius
744 <   *
745 <   *  If the switchingRadius was explicitly set, use that value (but check it)
746 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
747 <   */
748 <  void SimInfo::setupSwitchingRadius() {
749 <    
750 <    if (simParams_->haveSwitchingRadius()) {
751 <      switchingRadius_ = simParams_->getSwitchingRadius();
752 <      if (switchingRadius_ > cutoffRadius_) {        
753 <        sprintf(painCave.errMsg,
754 <                "SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755 <                switchingRadius_, cutoffRadius_);
756 <        painCave.isFatal = 1;
757 <        simError();
758 <
740 >  void SimInfo::setupSimVariables() {
741 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
742 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743 >    calcBoxDipole_ = false;
744 >    if ( simParams_->haveAccumulateBoxDipole() )
745 >      if ( simParams_->getAccumulateBoxDipole() ) {
746 >        calcBoxDipole_ = true;      
747        }
760 –    } else {      
761 –      switchingRadius_ = 0.85 * cutoffRadius_;
762 –      sprintf(painCave.errMsg,
763 –              "SimInfo Warning: No value was set for the switchingRadius.\n"
764 –              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
765 –              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
766 –      painCave.isFatal = 0;
767 –      simError();
768 –    }            
769 –    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
770 –  }
748  
772 –  /**
773 –   * setupSkinThickness
774 –   *
775 –   *  If the skinThickness was explicitly set, use that value (but check it)
776 –   *  If the skinThickness was not explicitly set: use 1.0 angstroms
777 –   */
778 –  void SimInfo::setupSkinThickness() {    
779 –    if (simParams_->haveSkinThickness()) {
780 –      skinThickness_ = simParams_->getSkinThickness();
781 –    } else {      
782 –      skinThickness_ = 1.0;
783 –      sprintf(painCave.errMsg,
784 –              "SimInfo Warning: No value was set for the skinThickness.\n"
785 –              "\tOpenMD will use a default value of %f Angstroms\n"
786 –              "\tfor this simulation\n", skinThickness_);
787 –      painCave.isFatal = 0;
788 –      simError();
789 –    }            
790 –  }
791 –
792 –  void SimInfo::setupSimType() {
749      set<AtomType*>::iterator i;
750      set<AtomType*> atomTypes;
751 <    atomTypes = getSimulatedAtomTypes();
796 <
797 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
798 <
751 >    atomTypes = getSimulatedAtomTypes();    
752      int usesElectrostatic = 0;
753      int usesMetallic = 0;
754      int usesDirectional = 0;
# Line 825 | Line 778 | namespace OpenMD {
778      fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
779    }
780  
781 <  void SimInfo::setupFortranSim() {
781 >
782 >  vector<int> SimInfo::getGlobalAtomIndices() {
783 >    SimInfo::MoleculeIterator mi;
784 >    Molecule* mol;
785 >    Molecule::AtomIterator ai;
786 >    Atom* atom;
787 >
788 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
789 >    
790 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
791 >      
792 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
793 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
794 >      }
795 >    }
796 >    return GlobalAtomIndices;
797 >  }
798 >
799 >
800 >  vector<int> SimInfo::getGlobalGroupIndices() {
801 >    SimInfo::MoleculeIterator mi;
802 >    Molecule* mol;
803 >    Molecule::CutoffGroupIterator ci;
804 >    CutoffGroup* cg;
805 >
806 >    vector<int> GlobalGroupIndices;
807 >    
808 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
809 >      
810 >      //local index of cutoff group is trivial, it only depends on the
811 >      //order of travesing
812 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
813 >           cg = mol->nextCutoffGroup(ci)) {
814 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
815 >      }        
816 >    }
817 >    return GlobalGroupIndices;
818 >  }
819 >
820 >
821 >  void SimInfo::setupFortran() {
822      int isError;
823      int nExclude, nOneTwo, nOneThree, nOneFour;
824      vector<int> fortranGlobalGroupMembership;
825      
833 –    notifyFortranSkinThickness(&skinThickness_);
834 –
835 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
838 –
826      isError = 0;
827  
828      //globalGroupMembership_ is filled by SimCreator    
# Line 870 | Line 857 | namespace OpenMD {
857        }      
858      }
859  
860 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874 <    vector<int> identArray;
860 >    // Build the identArray_
861  
862 <    //to avoid memory reallocation, reserve enough space identArray
863 <    identArray.reserve(getNAtoms());
878 <    
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  
# Line 901 | Line 886 | namespace OpenMD {
886      int* oneThreeList = oneThreeInteractions_.getPairList();
887      int* oneFourList = oneFourInteractions_.getPairList();
888  
889 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
890 <                   &nExclude, excludeList,
891 <                   &nOneTwo, oneTwoList,
892 <                   &nOneThree, oneThreeList,
893 <                   &nOneFour, oneFourList,
894 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
895 <                   &fortranGlobalGroupMembership[0], &isError);
889 >    //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
890 >    //               &nExclude, excludeList,
891 >    //               &nOneTwo, oneTwoList,
892 >    //               &nOneThree, oneThreeList,
893 >    //               &nOneFour, oneFourList,
894 >    //               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
895 >    //               &fortranGlobalGroupMembership[0], &isError);
896      
897 <    if( isError ){
898 <      
899 <      sprintf( painCave.errMsg,
900 <               "There was an error setting the simulation information in fortran.\n" );
901 <      painCave.isFatal = 1;
902 <      painCave.severity = OPENMD_ERROR;
903 <      simError();
904 <    }
897 >    // if( isError ){
898 >    //  
899 >    //  sprintf( painCave.errMsg,
900 >    //         "There was an error setting the simulation information in fortran.\n" );
901 >    //  painCave.isFatal = 1;
902 >    //  painCave.severity = OPENMD_ERROR;
903 >    //  simError();
904 >    //}
905      
906      
907 <    sprintf( checkPointMsg,
908 <             "succesfully sent the simulation information to fortran.\n");
907 >    // sprintf( checkPointMsg,
908 >    //          "succesfully sent the simulation information to fortran.\n");
909      
910 <    errorCheckPoint();
910 >    // errorCheckPoint();
911      
912      // Setup number of neighbors in neighbor list if present
913 <    if (simParams_->haveNeighborListNeighbors()) {
914 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
915 <      setNeighbors(&nlistNeighbors);
916 <    }
913 >    //if (simParams_->haveNeighborListNeighbors()) {
914 >    //  int nlistNeighbors = simParams_->getNeighborListNeighbors();
915 >    //  setNeighbors(&nlistNeighbors);
916 >    //}
917    
933 –
934 –  }
935 –
936 –
937 –  void SimInfo::setupFortranParallel() {
918   #ifdef IS_MPI    
919 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
940 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941 <    vector<int> localToGlobalCutoffGroupIndex;
942 <    SimInfo::MoleculeIterator mi;
943 <    Molecule::AtomIterator ai;
944 <    Molecule::CutoffGroupIterator ci;
945 <    Molecule* mol;
946 <    Atom* atom;
947 <    CutoffGroup* cg;
948 <    mpiSimData parallelData;
949 <    int isError;
919 >    // mpiSimData parallelData;
920  
921 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
922 <
923 <      //local index(index in DataStorge) of atom is important
924 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
925 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
926 <      }
921 >    //fill up mpiSimData struct
922 >    // parallelData.nMolGlobal = getNGlobalMolecules();
923 >    // parallelData.nMolLocal = getNMolecules();
924 >    // parallelData.nAtomsGlobal = getNGlobalAtoms();
925 >    // parallelData.nAtomsLocal = getNAtoms();
926 >    // parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
927 >    // parallelData.nGroupsLocal = getNCutoffGroups();
928 >    // parallelData.myNode = worldRank;
929 >    // MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
930  
958 –      //local index of cutoff group is trivial, it only depends on the order of travesing
959 –      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
960 –        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
961 –      }        
962 –        
963 –    }
964 –
965 –    //fill up mpiSimData struct
966 –    parallelData.nMolGlobal = getNGlobalMolecules();
967 –    parallelData.nMolLocal = getNMolecules();
968 –    parallelData.nAtomsGlobal = getNGlobalAtoms();
969 –    parallelData.nAtomsLocal = getNAtoms();
970 –    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
971 –    parallelData.nGroupsLocal = getNCutoffGroups();
972 –    parallelData.myNode = worldRank;
973 –    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
974 –
931      //pass mpiSimData struct and index arrays to fortran
932 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
933 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
934 <                    &localToGlobalCutoffGroupIndex[0], &isError);
932 >    //setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
933 >    //                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
934 >    //                &localToGlobalCutoffGroupIndex[0], &isError);
935  
936 <    if (isError) {
937 <      sprintf(painCave.errMsg,
938 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
939 <      painCave.isFatal = 1;
940 <      simError();
941 <    }
936 >    // if (isError) {
937 >    //   sprintf(painCave.errMsg,
938 >    //           "mpiRefresh errror: fortran didn't like something we gave it.\n");
939 >    //   painCave.isFatal = 1;
940 >    //   simError();
941 >    // }
942  
943 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
944 <    errorCheckPoint();
989 <
943 >    // sprintf(checkPointMsg, " mpiRefresh successful.\n");
944 >    // errorCheckPoint();
945   #endif
991 –  }
946  
947 <
948 <  void SimInfo::setupSwitchingFunction() {    
949 <    int ft = CUBIC;
950 <    
951 <    if (simParams_->haveSwitchingFunctionType()) {
952 <      string funcType = simParams_->getSwitchingFunctionType();
953 <      toUpper(funcType);
954 <      if (funcType == "CUBIC") {
1001 <        ft = CUBIC;
1002 <      } else {
1003 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1004 <          ft = FIFTH_ORDER_POLY;
1005 <        } else {
1006 <          // throw error        
1007 <          sprintf( painCave.errMsg,
1008 <                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1009 <          painCave.isFatal = 1;
1010 <          simError();
1011 <        }          
1012 <      }
1013 <    }
1014 <
1015 <    // send switching function notification to switcheroo
1016 <    setFunctionType(&ft);
1017 <
1018 <  }
1019 <
1020 <  void SimInfo::setupAccumulateBoxDipole() {    
1021 <
1022 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1023 <    if ( simParams_->haveAccumulateBoxDipole() )
1024 <      if ( simParams_->getAccumulateBoxDipole() ) {
1025 <        calcBoxDipole_ = true;
1026 <      }
1027 <
947 >    // initFortranFF(&isError);
948 >    // if (isError) {
949 >    //   sprintf(painCave.errMsg,
950 >    //           "initFortranFF errror: fortran didn't like something we gave it.\n");
951 >    //   painCave.isFatal = 1;
952 >    //   simError();
953 >    // }
954 >    // fortranInitialized_ = true;
955    }
956  
957    void SimInfo::addProperty(GenericData* genData) {
# Line 1061 | Line 988 | namespace OpenMD {
988      Molecule* mol;
989      RigidBody* rb;
990      Atom* atom;
991 +    CutoffGroup* cg;
992      SimInfo::MoleculeIterator mi;
993      Molecule::RigidBodyIterator rbIter;
994 <    Molecule::AtomIterator atomIter;;
994 >    Molecule::AtomIterator atomIter;
995 >    Molecule::CutoffGroupIterator cgIter;
996  
997      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
998          
# Line 1074 | Line 1003 | namespace OpenMD {
1003        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1004          rb->setSnapshotManager(sman_);
1005        }
1006 +
1007 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1008 +        cg->setSnapshotManager(sman_);
1009 +      }
1010      }    
1011      
1012    }

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