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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 1535 by gezelter, Fri Dec 31 18:31:56 2010 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"
57   #include "UseTheForce/DarkSide/neighborLists_interface.h"
61 – #include "UseTheForce/DarkSide/switcheroo_interface.h"
58   #include "utils/MemoryUtils.hpp"
59   #include "utils/simError.h"
60   #include "selection/SelectionManager.hpp"
61   #include "io/ForceFieldOptions.hpp"
62   #include "UseTheForce/ForceField.hpp"
63 < #include "nonbonded/InteractionManager.hpp"
68 <
63 > #include "nonbonded/SwitchingFunction.hpp"
64  
65   #ifdef IS_MPI
66   #include "UseTheForce/mpiComponentPlan.h"
# 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 <      
693 <    }
694 <    
695 <    return atomTypes;        
696 <  }
686 >      }      
687 >    }    
688  
689 <  /**
699 <   * setupCutoffRadius
700 <   *
701 <   *  If the cutoffRadius was explicitly set, use that value.
702 <   *  If the cutoffRadius was not explicitly set:
703 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
704 <   *      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 <    }
689 > #ifdef IS_MPI
690  
691 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
692 <  }
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();
691 >    // loop over the found atom types on this processor, and add their
692 >    // numerical idents to a vector:
693  
694 <      }
695 <    } else {      
696 <      switchingRadius_ = 0.85 * cutoffRadius_;
697 <      sprintf(painCave.errMsg,
698 <              "SimInfo Warning: No value was set for the switchingRadius.\n"
699 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
700 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
701 <      painCave.isFatal = 0;
702 <      simError();
703 <    }            
704 <    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
705 <  }
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 <  /**
713 <   * setupSkinThickness
714 <   *
715 <   *  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 <  }
712 >    int nproc = MPI::COMM_WORLD.Get_size();
713 >    counts.resize(nproc);
714 >    vector<int> disps;
715 >    disps.resize(nproc);
716  
717 <  void SimInfo::setupSimType() {
718 <    set<AtomType*>::iterator i;
719 <    set<AtomType*> atomTypes;
720 <    atomTypes = getSimulatedAtomTypes();
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 +  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 +      }
748  
749 +    set<AtomType*>::iterator i;
750 +    set<AtomType*> atomTypes;
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 >  void SimInfo::setupFortran() {
782      int isError;
783      int nExclude, nOneTwo, nOneThree, nOneFour;
784      vector<int> fortranGlobalGroupMembership;
785      
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 –
786      isError = 0;
787  
788      //globalGroupMembership_ is filled by SimCreator    
# Line 870 | Line 817 | namespace OpenMD {
817        }      
818      }
819  
820 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
820 >    //fill ident array of local atoms (it is actually ident of
821 >    //AtomType, it is so confusing !!!)
822      vector<int> identArray;
823  
824      //to avoid memory reallocation, reserve enough space identArray
# Line 930 | Line 878 | namespace OpenMD {
878        setNeighbors(&nlistNeighbors);
879      }
880    
933 –
934 –  }
935 –
936 –
937 –  void SimInfo::setupFortranParallel() {
881   #ifdef IS_MPI    
882 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
882 >    //SimInfo is responsible for creating localToGlobalAtomIndex and
883 >    //localToGlobalGroupIndex
884      vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
885      vector<int> localToGlobalCutoffGroupIndex;
942 –    SimInfo::MoleculeIterator mi;
943 –    Molecule::AtomIterator ai;
944 –    Molecule::CutoffGroupIterator ci;
945 –    Molecule* mol;
946 –    Atom* atom;
947 –    CutoffGroup* cg;
886      mpiSimData parallelData;
949 –    int isError;
887  
888      for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889  
# Line 986 | Line 923 | namespace OpenMD {
923  
924      sprintf(checkPointMsg, " mpiRefresh successful.\n");
925      errorCheckPoint();
989 –
926   #endif
927 <  }
992 <
993 <
994 <  void SimInfo::setupSwitchingFunction() {    
995 <    int ft = CUBIC;
996 <    
997 <    if (simParams_->haveSwitchingFunctionType()) {
998 <      string funcType = simParams_->getSwitchingFunctionType();
999 <      toUpper(funcType);
1000 <      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 <
927 >    fortranInitialized_ = true;
928    }
929  
930    void SimInfo::addProperty(GenericData* genData) {

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