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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 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
Revision 1547 by gezelter, Mon Apr 11 18:44:16 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 #include "UseTheForce/doForces_interface.h"
57   #include "UseTheForce/DarkSide/neighborLists_interface.h"
58 + #include "UseTheForce/doForces_interface.h"
59   #include "utils/MemoryUtils.hpp"
60   #include "utils/simError.h"
61   #include "selection/SelectionManager.hpp"
# Line 63 | Line 63
63   #include "UseTheForce/ForceField.hpp"
64   #include "nonbonded/SwitchingFunction.hpp"
65  
66
66   #ifdef IS_MPI
67   #include "UseTheForce/mpiComponentPlan.h"
68   #include "UseTheForce/DarkSide/simParallel_interface.h"
# Line 133 | Line 132 | namespace OpenMD {
132      //equal to the total number of atoms minus number of atoms belong to
133      //cutoff group defined in meta-data file plus the number of cutoff
134      //groups defined in meta-data file
135 +    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136 +    std::cerr << "nCA = " << nCutoffAtoms << "\n";
137 +    std::cerr << "nG = " << nGroups << "\n";
138 +
139      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140 +
141 +    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
142      
143      //every free atom (atom does not belong to rigid bodies) is an
144      //integrable object therefore the total number of integrable objects
# Line 657 | Line 662 | namespace OpenMD {
662    /**
663     * update
664     *
665 <   *  Performs the global checks and variable settings after the objects have been
666 <   *  created.
665 >   *  Performs the global checks and variable settings after the
666 >   *  objects have been created.
667     *
668     */
669 <  void SimInfo::update() {
665 <    
669 >  void SimInfo::update() {  
670      setupSimVariables();
667    setupCutoffs();
668    setupSwitching();
669    setupElectrostatics();
670    setupNeighborlists();
671
672 #ifdef IS_MPI
673    setupFortranParallel();
674 #endif
675    setupFortranSim();
676    fortranInitialized_ = true;
677
671      calcNdf();
672      calcNdfRaw();
673      calcNdfTrans();
674    }
675    
676 +  /**
677 +   * getSimulatedAtomTypes
678 +   *
679 +   * Returns an STL set of AtomType* that are actually present in this
680 +   * simulation.  Must query all processors to assemble this information.
681 +   *
682 +   */
683    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684      SimInfo::MoleculeIterator mi;
685      Molecule* mol;
# Line 692 | Line 692 | namespace OpenMD {
692          atomTypes.insert(atom->getAtomType());
693        }      
694      }    
695    return atomTypes;        
696  }
695  
696 <  /**
699 <   * setupCutoffs
700 <   *
701 <   * Sets the values of cutoffRadius and cutoffMethod
702 <   *
703 <   * cutoffRadius : realType
704 <   *  If the cutoffRadius was explicitly set, use that value.
705 <   *  If the cutoffRadius was not explicitly set:
706 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
707 <   *      No electrostatic atoms?  Poll the atom types present in the
708 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709 <   *      Use the maximum suggested value that was found.
710 <   *
711 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712 <   *      If cutoffMethod was explicitly set, use that choice.
713 <   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714 <   */
715 <  void SimInfo::setupCutoffs() {
716 <    
717 <    if (simParams_->haveCutoffRadius()) {
718 <      cutoffRadius_ = simParams_->getCutoffRadius();
719 <    } else {      
720 <      if (usesElectrostaticAtoms_) {
721 <        sprintf(painCave.errMsg,
722 <                "SimInfo: No value was set for the cutoffRadius.\n"
723 <                "\tOpenMD will use a default value of 12.0 angstroms"
724 <                "\tfor the cutoffRadius.\n");
725 <        painCave.isFatal = 0;
726 <        painCave.severity = OPENMD_INFO;
727 <        simError();
728 <        cutoffRadius_ = 12.0;
729 <      } else {
730 <        RealType thisCut;
731 <        set<AtomType*>::iterator i;
732 <        set<AtomType*> atomTypes;
733 <        atomTypes = getSimulatedAtomTypes();        
734 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
737 <        }
738 <        sprintf(painCave.errMsg,
739 <                "SimInfo: No value was set for the cutoffRadius.\n"
740 <                "\tOpenMD will use %lf angstroms.\n",
741 <                cutoffRadius_);
742 <        painCave.isFatal = 0;
743 <        painCave.severity = OPENMD_INFO;
744 <        simError();
745 <      }            
746 <    }
696 > #ifdef IS_MPI
697  
698 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
698 >    // loop over the found atom types on this processor, and add their
699 >    // numerical idents to a vector:
700  
701 <    map<string, CutoffMethod> stringToCutoffMethod;
702 <    stringToCutoffMethod["HARD"] = HARD;
703 <    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
704 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
754 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
755 <  
756 <    if (simParams_->haveCutoffMethod()) {
757 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
758 <      map<string, CutoffMethod>::iterator i;
759 <      i = stringToCutoffMethod.find(cutMeth);
760 <      if (i == stringToCutoffMethod.end()) {
761 <        sprintf(painCave.errMsg,
762 <                "SimInfo: Could not find chosen cutoffMethod %s\n"
763 <                "\tShould be one of: "
764 <                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765 <                cutMeth.c_str());
766 <        painCave.isFatal = 1;
767 <        painCave.severity = OPENMD_ERROR;
768 <        simError();
769 <      } else {
770 <        cutoffMethod_ = i->second;
771 <      }
772 <    } else {
773 <      sprintf(painCave.errMsg,
774 <              "SimInfo: No value was set for the cutoffMethod.\n"
775 <              "\tOpenMD will use SHIFTED_FORCE.\n");
776 <        painCave.isFatal = 0;
777 <        painCave.severity = OPENMD_INFO;
778 <        simError();
779 <        cutoffMethod_ = SHIFTED_FORCE;        
780 <    }
701 >    vector<int> foundTypes;
702 >    set<AtomType*>::iterator i;
703 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
704 >      foundTypes.push_back( (*i)->getIdent() );
705  
706 <    InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
707 <  }
784 <  
785 <  /**
786 <   * setupSwitching
787 <   *
788 <   * Sets the values of switchingRadius and
789 <   *  If the switchingRadius was explicitly set, use that value (but check it)
790 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791 <   */
792 <  void SimInfo::setupSwitching() {
793 <    
794 <    if (simParams_->haveSwitchingRadius()) {
795 <      switchingRadius_ = simParams_->getSwitchingRadius();
796 <      if (switchingRadius_ > cutoffRadius_) {        
797 <        sprintf(painCave.errMsg,
798 <                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799 <                switchingRadius_, cutoffRadius_);
800 <        painCave.isFatal = 1;
801 <        painCave.severity = OPENMD_ERROR;
802 <        simError();
803 <      }
804 <    } else {      
805 <      switchingRadius_ = 0.85 * cutoffRadius_;
806 <      sprintf(painCave.errMsg,
807 <              "SimInfo: No value was set for the switchingRadius.\n"
808 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810 <      painCave.isFatal = 0;
811 <      painCave.severity = OPENMD_WARNING;
812 <      simError();
813 <    }          
814 <  
815 <    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
706 >    // count_local holds the number of found types on this processor
707 >    int count_local = foundTypes.size();
708  
709 <    SwitchingFunctionType ft;
709 >    // count holds the total number of found types on all processors
710 >    // (some will be redundant with the ones found locally):
711 >    int count;
712 >    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
713 >
714 >    // create a vector to hold the globally found types, and resize it:
715 >    vector<int> ftGlobal;
716 >    ftGlobal.resize(count);
717 >    vector<int> counts;
718 >
719 >    int nproc = MPI::COMM_WORLD.Get_size();
720 >    counts.resize(nproc);
721 >    vector<int> disps;
722 >    disps.resize(nproc);
723 >
724 >    // now spray out the foundTypes to all the other processors:
725      
726 <    if (simParams_->haveSwitchingFunctionType()) {
727 <      string funcType = simParams_->getSwitchingFunctionType();
821 <      toUpper(funcType);
822 <      if (funcType == "CUBIC") {
823 <        ft = cubic;
824 <      } else {
825 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826 <          ft = fifth_order_poly;
827 <        } else {
828 <          // throw error        
829 <          sprintf( painCave.errMsg,
830 <                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831 <                   "\tswitchingFunctionType must be one of: "
832 <                   "\"cubic\" or \"fifth_order_polynomial\".",
833 <                   funcType.c_str() );
834 <          painCave.isFatal = 1;
835 <          painCave.severity = OPENMD_ERROR;
836 <          simError();
837 <        }          
838 <      }
839 <    }
726 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
727 >                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
728  
729 <    InteractionManager::Instance()->setSwitchingFunctionType(ft);
729 >    // foundIdents is a stl set, so inserting an already found ident
730 >    // will have no effect.
731 >    set<int> foundIdents;
732 >    vector<int>::iterator j;
733 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
734 >      foundIdents.insert((*j));
735 >    
736 >    // now iterate over the foundIdents and get the actual atom types
737 >    // that correspond to these:
738 >    set<int>::iterator it;
739 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
740 >      atomTypes.insert( forceField_->getAtomType((*it)) );
741 >
742 > #endif
743 >    
744 >    return atomTypes;        
745    }
746  
747 <  /**
748 <   * setupSkinThickness
749 <   *
750 <   *  If the skinThickness was explicitly set, use that value (but check it)
751 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
752 <   */
753 <  void SimInfo::setupSkinThickness() {    
754 <    if (simParams_->haveSkinThickness()) {
852 <      skinThickness_ = simParams_->getSkinThickness();
853 <    } else {      
854 <      skinThickness_ = 1.0;
855 <      sprintf(painCave.errMsg,
856 <              "SimInfo Warning: No value was set for the skinThickness.\n"
857 <              "\tOpenMD will use a default value of %f Angstroms\n"
858 <              "\tfor this simulation\n", skinThickness_);
859 <      painCave.isFatal = 0;
860 <      simError();
861 <    }            
862 <  }
747 >  void SimInfo::setupSimVariables() {
748 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
749 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
750 >    calcBoxDipole_ = false;
751 >    if ( simParams_->haveAccumulateBoxDipole() )
752 >      if ( simParams_->getAccumulateBoxDipole() ) {
753 >        calcBoxDipole_ = true;      
754 >      }
755  
864  void SimInfo::setupSimType() {
756      set<AtomType*>::iterator i;
757      set<AtomType*> atomTypes;
758 <    atomTypes = getSimulatedAtomTypes();
868 <
869 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
870 <
758 >    atomTypes = getSimulatedAtomTypes();    
759      int usesElectrostatic = 0;
760      int usesMetallic = 0;
761      int usesDirectional = 0;
# Line 897 | Line 785 | namespace OpenMD {
785      fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
786    }
787  
788 <  void SimInfo::setupFortranSim() {
788 >  void SimInfo::setupFortran() {
789      int isError;
790      int nExclude, nOneTwo, nOneThree, nOneFour;
791      vector<int> fortranGlobalGroupMembership;
792      
905    notifyFortranSkinThickness(&skinThickness_);
906
907    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
910
793      isError = 0;
794  
795      //globalGroupMembership_ is filled by SimCreator    
# Line 942 | Line 824 | namespace OpenMD {
824        }      
825      }
826  
827 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946 <    vector<int> identArray;
827 >    // Build the identArray_
828  
829 <    //to avoid memory reallocation, reserve enough space identArray
830 <    identArray.reserve(getNAtoms());
950 <    
829 >    identArray_.clear();
830 >    identArray_.reserve(getNAtoms());    
831      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
832        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
833 <        identArray.push_back(atom->getIdent());
833 >        identArray_.push_back(atom->getIdent());
834        }
835      }    
836  
# Line 973 | Line 853 | namespace OpenMD {
853      int* oneThreeList = oneThreeInteractions_.getPairList();
854      int* oneFourList = oneFourInteractions_.getPairList();
855  
856 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
856 >    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
857                     &nExclude, excludeList,
858                     &nOneTwo, oneTwoList,
859                     &nOneThree, oneThreeList,
# Line 1002 | Line 882 | namespace OpenMD {
882        setNeighbors(&nlistNeighbors);
883      }
884    
1005
1006  }
1007
1008
1009  void SimInfo::setupFortranParallel() {
885   #ifdef IS_MPI    
886 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
886 >    //SimInfo is responsible for creating localToGlobalAtomIndex and
887 >    //localToGlobalGroupIndex
888      vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
889      vector<int> localToGlobalCutoffGroupIndex;
1014    SimInfo::MoleculeIterator mi;
1015    Molecule::AtomIterator ai;
1016    Molecule::CutoffGroupIterator ci;
1017    Molecule* mol;
1018    Atom* atom;
1019    CutoffGroup* cg;
890      mpiSimData parallelData;
1021    int isError;
891  
892      for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
893  
# Line 1058 | Line 927 | namespace OpenMD {
927  
928      sprintf(checkPointMsg, " mpiRefresh successful.\n");
929      errorCheckPoint();
1061
930   #endif
1063  }
931  
932 <
933 <  void SimInfo::setupSwitchingFunction() {    
934 <
935 <  }
936 <
937 <  void SimInfo::setupAccumulateBoxDipole() {    
938 <
939 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073 <    if ( simParams_->haveAccumulateBoxDipole() )
1074 <      if ( simParams_->getAccumulateBoxDipole() ) {
1075 <        calcBoxDipole_ = true;
1076 <      }
1077 <
932 >    initFortranFF(&isError);
933 >    if (isError) {
934 >      sprintf(painCave.errMsg,
935 >              "initFortranFF errror: fortran didn't like something we gave it.\n");
936 >      painCave.isFatal = 1;
937 >      simError();
938 >    }
939 >    fortranInitialized_ = true;
940    }
941  
942    void SimInfo::addProperty(GenericData* genData) {
# Line 1111 | Line 973 | namespace OpenMD {
973      Molecule* mol;
974      RigidBody* rb;
975      Atom* atom;
976 +    CutoffGroup* cg;
977      SimInfo::MoleculeIterator mi;
978      Molecule::RigidBodyIterator rbIter;
979 <    Molecule::AtomIterator atomIter;;
979 >    Molecule::AtomIterator atomIter;
980 >    Molecule::CutoffGroupIterator cgIter;
981  
982      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
983          
# Line 1123 | Line 987 | namespace OpenMD {
987          
988        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
989          rb->setSnapshotManager(sman_);
990 +      }
991 +
992 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
993 +        cg->setSnapshotManager(sman_);
994        }
995      }    
996      

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