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Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC vs.
Revision 1764 by gezelter, Tue Jul 3 18:32:27 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 "UseTheForce/doForces_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"
65 –
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
69 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 75 | 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 132 | 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
135 –    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136 –    std::cerr << "nCA = " << nCutoffAtoms << "\n";
137 –    std::cerr << "nG = " << nGroups << "\n";
132  
133      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140 –
141 –    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
134      
135      //every free atom (atom does not belong to rigid bodies) is an
136      //integrable object therefore the total number of integrable objects
# Line 233 | 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 254 | Line 250 | namespace OpenMD {
250              ndf_local += 3;
251            }
252          }
257 –            
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 281 | 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;
311  
# Line 687 | 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 706 | Line 731 | namespace OpenMD {
731      // count_local holds the number of found types on this processor
732      int count_local = foundTypes.size();
733  
734 <    // 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);
734 >    int nproc = MPI::COMM_WORLD.Get_size();
735  
736 <    // create a vector to hold the globally found types, and resize it:
737 <    vector<int> ftGlobal;
738 <    ftGlobal.resize(count);
739 <    vector<int> counts;
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 <    int nproc = MPI::COMM_WORLD.Get_size();
742 <    counts.resize(nproc);
743 <    vector<int> disps;
744 <    disps.resize(nproc);
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 <    // now spray out the foundTypes to all the other processors:
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 752 | 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;
796 +    int usesFluctuatingCharges =  0;
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;
807      temp = usesDirectional;
808      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
809 <
809 >    
810      temp = usesMetallic;
811      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
812 <
812 >    
813      temp = usesElectrostatic;
814      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815 +
816 +    temp = usesFluctuatingCharges;
817 +    MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818 + #else
819 +
820 +    usesDirectionalAtoms_ = usesDirectional;
821 +    usesMetallicAtoms_ = usesMetallic;
822 +    usesElectrostaticAtoms_ = usesElectrostatic;
823 +    usesFluctuatingCharges_ = usesFluctuatingCharges;
824 +
825   #endif
826 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
827 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
828 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
829 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
826 >    
827 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
828 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
829 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
830    }
831  
832 <  void SimInfo::setupFortran() {
833 <    int isError;
834 <    int nExclude, nOneTwo, nOneThree, nOneFour;
835 <    vector<int> fortranGlobalGroupMembership;
832 >
833 >  vector<int> SimInfo::getGlobalAtomIndices() {
834 >    SimInfo::MoleculeIterator mi;
835 >    Molecule* mol;
836 >    Molecule::AtomIterator ai;
837 >    Atom* atom;
838 >
839 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
840      
841 <    isError = 0;
841 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
842 >      
843 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
844 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
845 >      }
846 >    }
847 >    return GlobalAtomIndices;
848 >  }
849  
850 <    //globalGroupMembership_ is filled by SimCreator    
851 <    for (int i = 0; i < nGlobalAtoms_; i++) {
852 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
850 >
851 >  vector<int> SimInfo::getGlobalGroupIndices() {
852 >    SimInfo::MoleculeIterator mi;
853 >    Molecule* mol;
854 >    Molecule::CutoffGroupIterator ci;
855 >    CutoffGroup* cg;
856 >
857 >    vector<int> GlobalGroupIndices;
858 >    
859 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
860 >      
861 >      //local index of cutoff group is trivial, it only depends on the
862 >      //order of travesing
863 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
864 >           cg = mol->nextCutoffGroup(ci)) {
865 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
866 >      }        
867      }
868 +    return GlobalGroupIndices;
869 +  }
870  
871 +
872 +  void SimInfo::prepareTopology() {
873 +    int nExclude, nOneTwo, nOneThree, nOneFour;
874 +
875      //calculate mass ratio of cutoff group
801 –    vector<RealType> mfact;
876      SimInfo::MoleculeIterator mi;
877      Molecule* mol;
878      Molecule::CutoffGroupIterator ci;
# Line 807 | Line 881 | namespace OpenMD {
881      Atom* atom;
882      RealType totalMass;
883  
884 <    //to avoid memory reallocation, reserve enough space for mfact
885 <    mfact.reserve(getNCutoffGroups());
884 >    /**
885 >     * The mass factor is the relative mass of an atom to the total
886 >     * mass of the cutoff group it belongs to.  By default, all atoms
887 >     * are their own cutoff groups, and therefore have mass factors of
888 >     * 1.  We need some special handling for massless atoms, which
889 >     * will be treated as carrying the entire mass of the cutoff
890 >     * group.
891 >     */
892 >    massFactors_.clear();
893 >    massFactors_.resize(getNAtoms(), 1.0);
894      
895      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
896 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
896 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
897 >           cg = mol->nextCutoffGroup(ci)) {
898  
899          totalMass = cg->getMass();
900          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
901            // Check for massless groups - set mfact to 1 if true
902 <          if (totalMass != 0)
903 <            mfact.push_back(atom->getMass()/totalMass);
902 >          if (totalMass != 0)
903 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
904            else
905 <            mfact.push_back( 1.0 );
905 >            massFactors_[atom->getLocalIndex()] = 1.0;
906          }
907        }      
908      }
# Line 833 | Line 916 | namespace OpenMD {
916          identArray_.push_back(atom->getIdent());
917        }
918      }    
836 –
837 –    //fill molMembershipArray
838 –    //molMembershipArray is filled by SimCreator    
839 –    vector<int> molMembershipArray(nGlobalAtoms_);
840 –    for (int i = 0; i < nGlobalAtoms_; i++) {
841 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
842 –    }
919      
920 <    //setup fortran simulation
920 >    //scan topology
921  
922      nExclude = excludedInteractions_.getSize();
923      nOneTwo = oneTwoInteractions_.getSize();
# Line 852 | Line 928 | namespace OpenMD {
928      int* oneTwoList = oneTwoInteractions_.getPairList();
929      int* oneThreeList = oneThreeInteractions_.getPairList();
930      int* oneFourList = oneFourInteractions_.getPairList();
855 –
856 –    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
857 –                   &nExclude, excludeList,
858 –                   &nOneTwo, oneTwoList,
859 –                   &nOneThree, oneThreeList,
860 –                   &nOneFour, oneFourList,
861 –                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862 –                   &fortranGlobalGroupMembership[0], &isError);
863 –    
864 –    if( isError ){
865 –      
866 –      sprintf( painCave.errMsg,
867 –               "There was an error setting the simulation information in fortran.\n" );
868 –      painCave.isFatal = 1;
869 –      painCave.severity = OPENMD_ERROR;
870 –      simError();
871 –    }
872 –    
873 –    
874 –    sprintf( checkPointMsg,
875 –             "succesfully sent the simulation information to fortran.\n");
876 –    
877 –    errorCheckPoint();
878 –    
879 –    // Setup number of neighbors in neighbor list if present
880 –    if (simParams_->haveNeighborListNeighbors()) {
881 –      int nlistNeighbors = simParams_->getNeighborListNeighbors();
882 –      setNeighbors(&nlistNeighbors);
883 –    }
884 –  
885 – #ifdef IS_MPI    
886 –    //SimInfo is responsible for creating localToGlobalAtomIndex and
887 –    //localToGlobalGroupIndex
888 –    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
889 –    vector<int> localToGlobalCutoffGroupIndex;
890 –    mpiSimData parallelData;
891 –
892 –    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
893 –
894 –      //local index(index in DataStorge) of atom is important
895 –      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896 –        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
897 –      }
898 –
899 –      //local index of cutoff group is trivial, it only depends on the order of travesing
900 –      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
901 –        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
902 –      }        
903 –        
904 –    }
931  
932 <    //fill up mpiSimData struct
907 <    parallelData.nMolGlobal = getNGlobalMolecules();
908 <    parallelData.nMolLocal = getNMolecules();
909 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
910 <    parallelData.nAtomsLocal = getNAtoms();
911 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
912 <    parallelData.nGroupsLocal = getNCutoffGroups();
913 <    parallelData.myNode = worldRank;
914 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
915 <
916 <    //pass mpiSimData struct and index arrays to fortran
917 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
918 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
919 <                    &localToGlobalCutoffGroupIndex[0], &isError);
920 <
921 <    if (isError) {
922 <      sprintf(painCave.errMsg,
923 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
924 <      painCave.isFatal = 1;
925 <      simError();
926 <    }
927 <
928 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
929 <    errorCheckPoint();
930 < #endif
931 <
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;
932 >    topologyDone_ = true;
933    }
934  
935    void SimInfo::addProperty(GenericData* genData) {
# Line 996 | Line 989 | namespace OpenMD {
989      
990    }
991  
999 –  Vector3d SimInfo::getComVel(){
1000 –    SimInfo::MoleculeIterator i;
1001 –    Molecule* mol;
992  
1003 –    Vector3d comVel(0.0);
1004 –    RealType totalMass = 0.0;
1005 –    
1006 –
1007 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1008 –      RealType mass = mol->getMass();
1009 –      totalMass += mass;
1010 –      comVel += mass * mol->getComVel();
1011 –    }  
1012 –
1013 – #ifdef IS_MPI
1014 –    RealType tmpMass = totalMass;
1015 –    Vector3d tmpComVel(comVel);    
1016 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1017 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1018 – #endif
1019 –
1020 –    comVel /= totalMass;
1021 –
1022 –    return comVel;
1023 –  }
1024 –
1025 –  Vector3d SimInfo::getCom(){
1026 –    SimInfo::MoleculeIterator i;
1027 –    Molecule* mol;
1028 –
1029 –    Vector3d com(0.0);
1030 –    RealType totalMass = 0.0;
1031 –    
1032 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1033 –      RealType mass = mol->getMass();
1034 –      totalMass += mass;
1035 –      com += mass * mol->getCom();
1036 –    }  
1037 –
1038 – #ifdef IS_MPI
1039 –    RealType tmpMass = totalMass;
1040 –    Vector3d tmpCom(com);    
1041 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1042 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1043 – #endif
1044 –
1045 –    com /= totalMass;
1046 –
1047 –    return com;
1048 –
1049 –  }        
1050 –
993    ostream& operator <<(ostream& o, SimInfo& info) {
994  
995      return o;
996    }
997    
998 <  
1057 <   /*
1058 <   Returns center of mass and center of mass velocity in one function call.
1059 <   */
1060 <  
1061 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1062 <      SimInfo::MoleculeIterator i;
1063 <      Molecule* mol;
1064 <      
1065 <    
1066 <      RealType totalMass = 0.0;
1067 <    
1068 <
1069 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1070 <         RealType mass = mol->getMass();
1071 <         totalMass += mass;
1072 <         com += mass * mol->getCom();
1073 <         comVel += mass * mol->getComVel();          
1074 <      }  
1075 <      
1076 < #ifdef IS_MPI
1077 <      RealType tmpMass = totalMass;
1078 <      Vector3d tmpCom(com);  
1079 <      Vector3d tmpComVel(comVel);
1080 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1081 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1082 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1083 < #endif
1084 <      
1085 <      com /= totalMass;
1086 <      comVel /= totalMass;
1087 <   }        
1088 <  
1089 <   /*
1090 <   Return intertia tensor for entire system and angular momentum Vector.
1091 <
1092 <
1093 <       [  Ixx -Ixy  -Ixz ]
1094 <    J =| -Iyx  Iyy  -Iyz |
1095 <       [ -Izx -Iyz   Izz ]
1096 <    */
1097 <
1098 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1099 <      
1100 <
1101 <      RealType xx = 0.0;
1102 <      RealType yy = 0.0;
1103 <      RealType zz = 0.0;
1104 <      RealType xy = 0.0;
1105 <      RealType xz = 0.0;
1106 <      RealType yz = 0.0;
1107 <      Vector3d com(0.0);
1108 <      Vector3d comVel(0.0);
1109 <      
1110 <      getComAll(com, comVel);
1111 <      
1112 <      SimInfo::MoleculeIterator i;
1113 <      Molecule* mol;
1114 <      
1115 <      Vector3d thisq(0.0);
1116 <      Vector3d thisv(0.0);
1117 <
1118 <      RealType thisMass = 0.0;
1119 <    
1120 <      
1121 <      
1122 <  
1123 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1124 <        
1125 <         thisq = mol->getCom()-com;
1126 <         thisv = mol->getComVel()-comVel;
1127 <         thisMass = mol->getMass();
1128 <         // Compute moment of intertia coefficients.
1129 <         xx += thisq[0]*thisq[0]*thisMass;
1130 <         yy += thisq[1]*thisq[1]*thisMass;
1131 <         zz += thisq[2]*thisq[2]*thisMass;
1132 <        
1133 <         // compute products of intertia
1134 <         xy += thisq[0]*thisq[1]*thisMass;
1135 <         xz += thisq[0]*thisq[2]*thisMass;
1136 <         yz += thisq[1]*thisq[2]*thisMass;
1137 <            
1138 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1139 <            
1140 <      }  
1141 <      
1142 <      
1143 <      inertiaTensor(0,0) = yy + zz;
1144 <      inertiaTensor(0,1) = -xy;
1145 <      inertiaTensor(0,2) = -xz;
1146 <      inertiaTensor(1,0) = -xy;
1147 <      inertiaTensor(1,1) = xx + zz;
1148 <      inertiaTensor(1,2) = -yz;
1149 <      inertiaTensor(2,0) = -xz;
1150 <      inertiaTensor(2,1) = -yz;
1151 <      inertiaTensor(2,2) = xx + yy;
1152 <      
1153 < #ifdef IS_MPI
1154 <      Mat3x3d tmpI(inertiaTensor);
1155 <      Vector3d tmpAngMom;
1156 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1157 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1158 < #endif
1159 <              
1160 <      return;
1161 <   }
1162 <
1163 <   //Returns the angular momentum of the system
1164 <   Vector3d SimInfo::getAngularMomentum(){
1165 <      
1166 <      Vector3d com(0.0);
1167 <      Vector3d comVel(0.0);
1168 <      Vector3d angularMomentum(0.0);
1169 <      
1170 <      getComAll(com,comVel);
1171 <      
1172 <      SimInfo::MoleculeIterator i;
1173 <      Molecule* mol;
1174 <      
1175 <      Vector3d thisr(0.0);
1176 <      Vector3d thisp(0.0);
1177 <      
1178 <      RealType thisMass;
1179 <      
1180 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1181 <        thisMass = mol->getMass();
1182 <        thisr = mol->getCom()-com;
1183 <        thisp = (mol->getComVel()-comVel)*thisMass;
1184 <        
1185 <        angularMomentum += cross( thisr, thisp );
1186 <        
1187 <      }  
1188 <      
1189 < #ifdef IS_MPI
1190 <      Vector3d tmpAngMom;
1191 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1192 < #endif
1193 <      
1194 <      return angularMomentum;
1195 <   }
1196 <  
998 >  
999    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1000      return IOIndexToIntegrableObject.at(index);
1001    }
# Line 1201 | Line 1003 | namespace OpenMD {
1003    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1004      IOIndexToIntegrableObject= v;
1005    }
1204 –
1205 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1206 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1207 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1208 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1209 –  */
1210 –  void SimInfo::getGyrationalVolume(RealType &volume){
1211 –    Mat3x3d intTensor;
1212 –    RealType det;
1213 –    Vector3d dummyAngMom;
1214 –    RealType sysconstants;
1215 –    RealType geomCnst;
1216 –
1217 –    geomCnst = 3.0/2.0;
1218 –    /* Get the inertial tensor and angular momentum for free*/
1219 –    getInertiaTensor(intTensor,dummyAngMom);
1220 –    
1221 –    det = intTensor.determinant();
1222 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1223 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1224 –    return;
1225 –  }
1226 –
1227 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1228 –    Mat3x3d intTensor;
1229 –    Vector3d dummyAngMom;
1230 –    RealType sysconstants;
1231 –    RealType geomCnst;
1232 –
1233 –    geomCnst = 3.0/2.0;
1234 –    /* Get the inertial tensor and angular momentum for free*/
1235 –    getInertiaTensor(intTensor,dummyAngMom);
1236 –    
1237 –    detI = intTensor.determinant();
1238 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1239 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1240 –    return;
1241 –  }
1006   /*
1007     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1008        assert( v.size() == nAtoms_ + nRigidBodies_);

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