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Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC vs.
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 54 | Line 55
55   #include "math/Vector3.hpp"
56   #include "primitives/Molecule.hpp"
57   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/DarkSide/neighborLists_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"
62 > #include "brains/ForceField.hpp"
63   #include "nonbonded/SwitchingFunction.hpp"
64 –
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
68 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 74 | Line 72 | namespace OpenMD {
72      forceField_(ff), simParams_(simParams),
73      ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75 <    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75 >    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78 <    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
78 >    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79      calcBoxDipole_(false), useAtomicVirial_(true) {    
80      
81      MoleculeStamp* molStamp;
# Line 131 | Line 129 | namespace OpenMD {
129      //equal to the total number of atoms minus number of atoms belong to
130      //cutoff group defined in meta-data file plus the number of cutoff
131      //groups defined in meta-data file
132 +
133      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134      
135      //every free atom (atom does not belong to rigid bodies) is an
# Line 226 | Line 225 | namespace OpenMD {
225  
226  
227    void SimInfo::calcNdf() {
228 <    int ndf_local;
228 >    int ndf_local, nfq_local;
229      MoleculeIterator i;
230      vector<StuntDouble*>::iterator j;
231 +    vector<Atom*>::iterator k;
232 +
233      Molecule* mol;
234      StuntDouble* integrableObject;
235 +    Atom* atom;
236  
237      ndf_local = 0;
238 +    nfq_local = 0;
239      
240      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
# Line 247 | Line 250 | namespace OpenMD {
250              ndf_local += 3;
251            }
252          }
250 –            
253        }
254 +      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255 +           atom = mol->nextFluctuatingCharge(k)) {
256 +        if (atom->isFluctuatingCharge()) {
257 +          nfq_local++;
258 +        }
259 +      }
260      }
261      
262 +    ndfLocal_ = ndf_local;
263 +
264      // n_constraints is local, so subtract them on each processor
265      ndf_local -= nConstraints_;
266  
267   #ifdef IS_MPI
268      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270   #else
271      ndf_ = ndf_local;
272 +    nGlobalFluctuatingCharges_ = nfq_local;
273   #endif
274  
275      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 274 | Line 286 | namespace OpenMD {
286   #endif
287      return fdf_;
288    }
289 +  
290 +  unsigned int SimInfo::getNLocalCutoffGroups(){
291 +    int nLocalCutoffAtoms = 0;
292 +    Molecule* mol;
293 +    MoleculeIterator mi;
294 +    CutoffGroup* cg;
295 +    Molecule::CutoffGroupIterator ci;
296 +    
297 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
298 +      
299 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
300 +           cg = mol->nextCutoffGroup(ci)) {
301 +        nLocalCutoffAtoms += cg->getNumAtom();
302 +        
303 +      }        
304 +    }
305 +    
306 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
307 +  }
308      
309    void SimInfo::calcNdfRaw() {
310      int ndfRaw_local;
# Line 680 | Line 711 | namespace OpenMD {
711      Atom* atom;
712      set<AtomType*> atomTypes;
713      
714 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
715 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
714 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715 >      for(atom = mol->beginAtom(ai); atom != NULL;
716 >          atom = mol->nextAtom(ai)) {
717          atomTypes.insert(atom->getAtomType());
718        }      
719      }    
720 <
720 >    
721   #ifdef IS_MPI
722  
723      // loop over the found atom types on this processor, and add their
724      // numerical idents to a vector:
725 <
725 >    
726      vector<int> foundTypes;
727      set<AtomType*>::iterator i;
728      for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
# Line 699 | Line 731 | namespace OpenMD {
731      // count_local holds the number of found types on this processor
732      int count_local = foundTypes.size();
733  
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 –
734      int nproc = MPI::COMM_WORLD.Get_size();
735 <    counts.resize(nproc);
736 <    vector<int> disps;
737 <    disps.resize(nproc);
735 >
736 >    // we need arrays to hold the counts and displacement vectors for
737 >    // all processors
738 >    vector<int> counts(nproc, 0);
739 >    vector<int> disps(nproc, 0);
740  
741 <    // now spray out the foundTypes to all the other processors:
741 >    // fill the counts array
742 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
743 >                              1, MPI::INT);
744 >  
745 >    // use the processor counts to compute the displacement array
746 >    disps[0] = 0;    
747 >    int totalCount = counts[0];
748 >    for (int iproc = 1; iproc < nproc; iproc++) {
749 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
750 >      totalCount += counts[iproc];
751 >    }
752 >
753 >    // we need a (possibly redundant) set of all found types:
754 >    vector<int> ftGlobal(totalCount);
755      
756 +    // now spray out the foundTypes to all the other processors:    
757      MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
758 <                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
758 >                               &ftGlobal[0], &counts[0], &disps[0],
759 >                               MPI::INT);
760  
761 +    vector<int>::iterator j;
762 +
763      // foundIdents is a stl set, so inserting an already found ident
764      // will have no effect.
765      set<int> foundIdents;
766 <    vector<int>::iterator j;
766 >
767      for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768        foundIdents.insert((*j));
769      
770      // now iterate over the foundIdents and get the actual atom types
771      // that correspond to these:
772      set<int>::iterator it;
773 <    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
773 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774        atomTypes.insert( forceField_->getAtomType((*it)) );
775  
776   #endif
777 <    
777 >
778      return atomTypes;        
779    }
780  
# Line 745 | Line 786 | namespace OpenMD {
786        if ( simParams_->getAccumulateBoxDipole() ) {
787          calcBoxDipole_ = true;      
788        }
789 <
789 >    
790      set<AtomType*>::iterator i;
791      set<AtomType*> atomTypes;
792      atomTypes = getSimulatedAtomTypes();    
793 <    int usesElectrostatic = 0;
794 <    int usesMetallic = 0;
795 <    int usesDirectional = 0;
793 >    bool usesElectrostatic = false;
794 >    bool usesMetallic = false;
795 >    bool usesDirectional = false;
796 >    bool usesFluctuatingCharges =  false;
797      //loop over all of the atom types
798      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799        usesElectrostatic |= (*i)->isElectrostatic();
800        usesMetallic |= (*i)->isMetal();
801        usesDirectional |= (*i)->isDirectional();
802 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
803      }
804  
805 < #ifdef IS_MPI    
806 <    int temp;
805 > #ifdef IS_MPI
806 >    bool temp;
807      temp = usesDirectional;
808 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
809 <
808 >    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
809 >                              MPI::LOR);
810 >        
811      temp = usesMetallic;
812 <    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
813 <
812 >    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
813 >                              MPI::LOR);
814 >    
815      temp = usesElectrostatic;
816 <    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816 >    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
817 >                              MPI::LOR);
818 >
819 >    temp = usesFluctuatingCharges;
820 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
821 >                              MPI::LOR);
822 > #else
823 >
824 >    usesDirectionalAtoms_ = usesDirectional;
825 >    usesMetallicAtoms_ = usesMetallic;
826 >    usesElectrostaticAtoms_ = usesElectrostatic;
827 >    usesFluctuatingCharges_ = usesFluctuatingCharges;
828 >
829   #endif
830 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
831 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
832 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
833 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
777 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
778 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
830 >    
831 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
832 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
833 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
834    }
835  
836 <  void SimInfo::setupFortran() {
837 <    int isError;
838 <    int nExclude, nOneTwo, nOneThree, nOneFour;
839 <    vector<int> fortranGlobalGroupMembership;
836 >
837 >  vector<int> SimInfo::getGlobalAtomIndices() {
838 >    SimInfo::MoleculeIterator mi;
839 >    Molecule* mol;
840 >    Molecule::AtomIterator ai;
841 >    Atom* atom;
842 >
843 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
844      
845 <    isError = 0;
845 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
846 >      
847 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
849 >      }
850 >    }
851 >    return GlobalAtomIndices;
852 >  }
853  
854 <    //globalGroupMembership_ is filled by SimCreator    
855 <    for (int i = 0; i < nGlobalAtoms_; i++) {
856 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
854 >
855 >  vector<int> SimInfo::getGlobalGroupIndices() {
856 >    SimInfo::MoleculeIterator mi;
857 >    Molecule* mol;
858 >    Molecule::CutoffGroupIterator ci;
859 >    CutoffGroup* cg;
860 >
861 >    vector<int> GlobalGroupIndices;
862 >    
863 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
864 >      
865 >      //local index of cutoff group is trivial, it only depends on the
866 >      //order of travesing
867 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
868 >           cg = mol->nextCutoffGroup(ci)) {
869 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
870 >      }        
871      }
872 +    return GlobalGroupIndices;
873 +  }
874  
875 +
876 +  void SimInfo::prepareTopology() {
877 +    int nExclude, nOneTwo, nOneThree, nOneFour;
878 +
879      //calculate mass ratio of cutoff group
794 –    vector<RealType> mfact;
880      SimInfo::MoleculeIterator mi;
881      Molecule* mol;
882      Molecule::CutoffGroupIterator ci;
# Line 800 | Line 885 | namespace OpenMD {
885      Atom* atom;
886      RealType totalMass;
887  
888 <    //to avoid memory reallocation, reserve enough space for mfact
889 <    mfact.reserve(getNCutoffGroups());
888 >    /**
889 >     * The mass factor is the relative mass of an atom to the total
890 >     * mass of the cutoff group it belongs to.  By default, all atoms
891 >     * are their own cutoff groups, and therefore have mass factors of
892 >     * 1.  We need some special handling for massless atoms, which
893 >     * will be treated as carrying the entire mass of the cutoff
894 >     * group.
895 >     */
896 >    massFactors_.clear();
897 >    massFactors_.resize(getNAtoms(), 1.0);
898      
899      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
900 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
900 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
901 >           cg = mol->nextCutoffGroup(ci)) {
902  
903          totalMass = cg->getMass();
904          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
905            // Check for massless groups - set mfact to 1 if true
906 <          if (totalMass != 0)
907 <            mfact.push_back(atom->getMass()/totalMass);
906 >          if (totalMass != 0)
907 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
908            else
909 <            mfact.push_back( 1.0 );
909 >            massFactors_[atom->getLocalIndex()] = 1.0;
910          }
911        }      
912      }
913  
914 <    //fill ident array of local atoms (it is actually ident of
821 <    //AtomType, it is so confusing !!!)
822 <    vector<int> identArray;
914 >    // Build the identArray_
915  
916 <    //to avoid memory reallocation, reserve enough space identArray
917 <    identArray.reserve(getNAtoms());
826 <    
916 >    identArray_.clear();
917 >    identArray_.reserve(getNAtoms());    
918      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
919        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
920 <        identArray.push_back(atom->getIdent());
920 >        identArray_.push_back(atom->getIdent());
921        }
922      }    
832 –
833 –    //fill molMembershipArray
834 –    //molMembershipArray is filled by SimCreator    
835 –    vector<int> molMembershipArray(nGlobalAtoms_);
836 –    for (int i = 0; i < nGlobalAtoms_; i++) {
837 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
838 –    }
923      
924 <    //setup fortran simulation
924 >    //scan topology
925  
926      nExclude = excludedInteractions_.getSize();
927      nOneTwo = oneTwoInteractions_.getSize();
# Line 849 | Line 933 | namespace OpenMD {
933      int* oneThreeList = oneThreeInteractions_.getPairList();
934      int* oneFourList = oneFourInteractions_.getPairList();
935  
936 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
853 <                   &nExclude, excludeList,
854 <                   &nOneTwo, oneTwoList,
855 <                   &nOneThree, oneThreeList,
856 <                   &nOneFour, oneFourList,
857 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
858 <                   &fortranGlobalGroupMembership[0], &isError);
859 <    
860 <    if( isError ){
861 <      
862 <      sprintf( painCave.errMsg,
863 <               "There was an error setting the simulation information in fortran.\n" );
864 <      painCave.isFatal = 1;
865 <      painCave.severity = OPENMD_ERROR;
866 <      simError();
867 <    }
868 <    
869 <    
870 <    sprintf( checkPointMsg,
871 <             "succesfully sent the simulation information to fortran.\n");
872 <    
873 <    errorCheckPoint();
874 <    
875 <    // Setup number of neighbors in neighbor list if present
876 <    if (simParams_->haveNeighborListNeighbors()) {
877 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
878 <      setNeighbors(&nlistNeighbors);
879 <    }
880 <  
881 < #ifdef IS_MPI    
882 <    //SimInfo is responsible for creating localToGlobalAtomIndex and
883 <    //localToGlobalGroupIndex
884 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
885 <    vector<int> localToGlobalCutoffGroupIndex;
886 <    mpiSimData parallelData;
887 <
888 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889 <
890 <      //local index(index in DataStorge) of atom is important
891 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893 <      }
894 <
895 <      //local index of cutoff group is trivial, it only depends on the order of travesing
896 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898 <      }        
899 <        
900 <    }
901 <
902 <    //fill up mpiSimData struct
903 <    parallelData.nMolGlobal = getNGlobalMolecules();
904 <    parallelData.nMolLocal = getNMolecules();
905 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
906 <    parallelData.nAtomsLocal = getNAtoms();
907 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
908 <    parallelData.nGroupsLocal = getNCutoffGroups();
909 <    parallelData.myNode = worldRank;
910 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
911 <
912 <    //pass mpiSimData struct and index arrays to fortran
913 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
914 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
915 <                    &localToGlobalCutoffGroupIndex[0], &isError);
916 <
917 <    if (isError) {
918 <      sprintf(painCave.errMsg,
919 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
920 <      painCave.isFatal = 1;
921 <      simError();
922 <    }
923 <
924 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
925 <    errorCheckPoint();
926 < #endif
927 <    fortranInitialized_ = true;
936 >    topologyDone_ = true;
937    }
938  
939    void SimInfo::addProperty(GenericData* genData) {
# Line 961 | Line 970 | namespace OpenMD {
970      Molecule* mol;
971      RigidBody* rb;
972      Atom* atom;
973 +    CutoffGroup* cg;
974      SimInfo::MoleculeIterator mi;
975      Molecule::RigidBodyIterator rbIter;
976 <    Molecule::AtomIterator atomIter;;
976 >    Molecule::AtomIterator atomIter;
977 >    Molecule::CutoffGroupIterator cgIter;
978  
979      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
980          
# Line 974 | Line 985 | namespace OpenMD {
985        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
986          rb->setSnapshotManager(sman_);
987        }
988 +
989 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
990 +        cg->setSnapshotManager(sman_);
991 +      }
992      }    
993      
994    }
995  
981 –  Vector3d SimInfo::getComVel(){
982 –    SimInfo::MoleculeIterator i;
983 –    Molecule* mol;
996  
985 –    Vector3d comVel(0.0);
986 –    RealType totalMass = 0.0;
987 –    
988 –
989 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
990 –      RealType mass = mol->getMass();
991 –      totalMass += mass;
992 –      comVel += mass * mol->getComVel();
993 –    }  
994 –
995 – #ifdef IS_MPI
996 –    RealType tmpMass = totalMass;
997 –    Vector3d tmpComVel(comVel);    
998 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
999 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1000 – #endif
1001 –
1002 –    comVel /= totalMass;
1003 –
1004 –    return comVel;
1005 –  }
1006 –
1007 –  Vector3d SimInfo::getCom(){
1008 –    SimInfo::MoleculeIterator i;
1009 –    Molecule* mol;
1010 –
1011 –    Vector3d com(0.0);
1012 –    RealType totalMass = 0.0;
1013 –    
1014 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1015 –      RealType mass = mol->getMass();
1016 –      totalMass += mass;
1017 –      com += mass * mol->getCom();
1018 –    }  
1019 –
1020 – #ifdef IS_MPI
1021 –    RealType tmpMass = totalMass;
1022 –    Vector3d tmpCom(com);    
1023 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1024 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1025 – #endif
1026 –
1027 –    com /= totalMass;
1028 –
1029 –    return com;
1030 –
1031 –  }        
1032 –
997    ostream& operator <<(ostream& o, SimInfo& info) {
998  
999      return o;
1000    }
1001    
1002 <  
1039 <   /*
1040 <   Returns center of mass and center of mass velocity in one function call.
1041 <   */
1042 <  
1043 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1044 <      SimInfo::MoleculeIterator i;
1045 <      Molecule* mol;
1046 <      
1047 <    
1048 <      RealType totalMass = 0.0;
1049 <    
1050 <
1051 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1052 <         RealType mass = mol->getMass();
1053 <         totalMass += mass;
1054 <         com += mass * mol->getCom();
1055 <         comVel += mass * mol->getComVel();          
1056 <      }  
1057 <      
1058 < #ifdef IS_MPI
1059 <      RealType tmpMass = totalMass;
1060 <      Vector3d tmpCom(com);  
1061 <      Vector3d tmpComVel(comVel);
1062 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1063 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1064 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1065 < #endif
1066 <      
1067 <      com /= totalMass;
1068 <      comVel /= totalMass;
1069 <   }        
1070 <  
1071 <   /*
1072 <   Return intertia tensor for entire system and angular momentum Vector.
1073 <
1074 <
1075 <       [  Ixx -Ixy  -Ixz ]
1076 <    J =| -Iyx  Iyy  -Iyz |
1077 <       [ -Izx -Iyz   Izz ]
1078 <    */
1079 <
1080 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1081 <      
1082 <
1083 <      RealType xx = 0.0;
1084 <      RealType yy = 0.0;
1085 <      RealType zz = 0.0;
1086 <      RealType xy = 0.0;
1087 <      RealType xz = 0.0;
1088 <      RealType yz = 0.0;
1089 <      Vector3d com(0.0);
1090 <      Vector3d comVel(0.0);
1091 <      
1092 <      getComAll(com, comVel);
1093 <      
1094 <      SimInfo::MoleculeIterator i;
1095 <      Molecule* mol;
1096 <      
1097 <      Vector3d thisq(0.0);
1098 <      Vector3d thisv(0.0);
1099 <
1100 <      RealType thisMass = 0.0;
1101 <    
1102 <      
1103 <      
1104 <  
1105 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1106 <        
1107 <         thisq = mol->getCom()-com;
1108 <         thisv = mol->getComVel()-comVel;
1109 <         thisMass = mol->getMass();
1110 <         // Compute moment of intertia coefficients.
1111 <         xx += thisq[0]*thisq[0]*thisMass;
1112 <         yy += thisq[1]*thisq[1]*thisMass;
1113 <         zz += thisq[2]*thisq[2]*thisMass;
1114 <        
1115 <         // compute products of intertia
1116 <         xy += thisq[0]*thisq[1]*thisMass;
1117 <         xz += thisq[0]*thisq[2]*thisMass;
1118 <         yz += thisq[1]*thisq[2]*thisMass;
1119 <            
1120 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1121 <            
1122 <      }  
1123 <      
1124 <      
1125 <      inertiaTensor(0,0) = yy + zz;
1126 <      inertiaTensor(0,1) = -xy;
1127 <      inertiaTensor(0,2) = -xz;
1128 <      inertiaTensor(1,0) = -xy;
1129 <      inertiaTensor(1,1) = xx + zz;
1130 <      inertiaTensor(1,2) = -yz;
1131 <      inertiaTensor(2,0) = -xz;
1132 <      inertiaTensor(2,1) = -yz;
1133 <      inertiaTensor(2,2) = xx + yy;
1134 <      
1135 < #ifdef IS_MPI
1136 <      Mat3x3d tmpI(inertiaTensor);
1137 <      Vector3d tmpAngMom;
1138 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1139 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1140 < #endif
1141 <              
1142 <      return;
1143 <   }
1144 <
1145 <   //Returns the angular momentum of the system
1146 <   Vector3d SimInfo::getAngularMomentum(){
1147 <      
1148 <      Vector3d com(0.0);
1149 <      Vector3d comVel(0.0);
1150 <      Vector3d angularMomentum(0.0);
1151 <      
1152 <      getComAll(com,comVel);
1153 <      
1154 <      SimInfo::MoleculeIterator i;
1155 <      Molecule* mol;
1156 <      
1157 <      Vector3d thisr(0.0);
1158 <      Vector3d thisp(0.0);
1159 <      
1160 <      RealType thisMass;
1161 <      
1162 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1163 <        thisMass = mol->getMass();
1164 <        thisr = mol->getCom()-com;
1165 <        thisp = (mol->getComVel()-comVel)*thisMass;
1166 <        
1167 <        angularMomentum += cross( thisr, thisp );
1168 <        
1169 <      }  
1170 <      
1171 < #ifdef IS_MPI
1172 <      Vector3d tmpAngMom;
1173 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1174 < #endif
1175 <      
1176 <      return angularMomentum;
1177 <   }
1178 <  
1002 >  
1003    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1004      return IOIndexToIntegrableObject.at(index);
1005    }
# Line 1183 | Line 1007 | namespace OpenMD {
1007    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1008      IOIndexToIntegrableObject= v;
1009    }
1186 –
1187 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1188 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1189 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1190 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1191 –  */
1192 –  void SimInfo::getGyrationalVolume(RealType &volume){
1193 –    Mat3x3d intTensor;
1194 –    RealType det;
1195 –    Vector3d dummyAngMom;
1196 –    RealType sysconstants;
1197 –    RealType geomCnst;
1198 –
1199 –    geomCnst = 3.0/2.0;
1200 –    /* Get the inertial tensor and angular momentum for free*/
1201 –    getInertiaTensor(intTensor,dummyAngMom);
1202 –    
1203 –    det = intTensor.determinant();
1204 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1205 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1206 –    return;
1207 –  }
1208 –
1209 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1210 –    Mat3x3d intTensor;
1211 –    Vector3d dummyAngMom;
1212 –    RealType sysconstants;
1213 –    RealType geomCnst;
1214 –
1215 –    geomCnst = 3.0/2.0;
1216 –    /* Get the inertial tensor and angular momentum for free*/
1217 –    getInertiaTensor(intTensor,dummyAngMom);
1218 –    
1219 –    detI = intTensor.determinant();
1220 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1221 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1222 –    return;
1223 –  }
1010   /*
1011     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1012        assert( v.size() == nAtoms_ + nRigidBodies_);

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