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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1586 by gezelter, Tue Jun 21 06:34:35 2011 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 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 58 | Line 59
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 + #ifdef IS_MPI
65 + #include <mpi.h>
66 + #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 68 | 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), topologyDone_(false),
78 >    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79      calcBoxDipole_(false), useAtomicVirial_(true) {    
80      
81      MoleculeStamp* molStamp;
# Line 221 | 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;
234 >    StuntDouble* sd;
235 >    Atom* atom;
236  
237      ndf_local = 0;
238 +    nfq_local = 0;
239      
240      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
233 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
234 –           integrableObject = mol->nextIntegrableObject(j)) {
241  
242 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
243 +           sd = mol->nextIntegrableObject(j)) {
244 +
245          ndf_local += 3;
246  
247 <        if (integrableObject->isDirectional()) {
248 <          if (integrableObject->isLinear()) {
247 >        if (sd->isDirectional()) {
248 >          if (sd->isLinear()) {
249              ndf_local += 2;
250            } else {
251              ndf_local += 3;
252            }
253          }
245 –            
254        }
255 +
256 +      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
257 +           atom = mol->nextFluctuatingCharge(k)) {
258 +        if (atom->isFluctuatingCharge()) {
259 +          nfq_local++;
260 +        }
261 +      }
262      }
263      
264 +    ndfLocal_ = ndf_local;
265 +
266      // n_constraints is local, so subtract them on each processor
267      ndf_local -= nConstraints_;
268  
269   #ifdef IS_MPI
270      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
272   #else
273      ndf_ = ndf_local;
274 +    nGlobalFluctuatingCharges_ = nfq_local;
275   #endif
276  
277      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 295 | Line 314 | namespace OpenMD {
314      MoleculeIterator i;
315      vector<StuntDouble*>::iterator j;
316      Molecule* mol;
317 <    StuntDouble* integrableObject;
317 >    StuntDouble* sd;
318  
319      // Raw degrees of freedom that we have to set
320      ndfRaw_local = 0;
321      
322      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
304 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
305 –           integrableObject = mol->nextIntegrableObject(j)) {
323  
324 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
325 +           sd = mol->nextIntegrableObject(j)) {
326 +
327          ndfRaw_local += 3;
328  
329 <        if (integrableObject->isDirectional()) {
330 <          if (integrableObject->isLinear()) {
329 >        if (sd->isDirectional()) {
330 >          if (sd->isLinear()) {
331              ndfRaw_local += 2;
332            } else {
333              ndfRaw_local += 3;
# Line 367 | Line 387 | namespace OpenMD {
387      Molecule::RigidBodyIterator rbIter;
388      RigidBody* rb;
389      Molecule::IntegrableObjectIterator ii;
390 <    StuntDouble* integrableObject;
390 >    StuntDouble* sd;
391      
392 <    for (integrableObject = mol->beginIntegrableObject(ii);
393 <         integrableObject != NULL;
374 <         integrableObject = mol->nextIntegrableObject(ii)) {
392 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
393 >         sd = mol->nextIntegrableObject(ii)) {
394        
395 <      if (integrableObject->isRigidBody()) {
396 <        rb = static_cast<RigidBody*>(integrableObject);
395 >      if (sd->isRigidBody()) {
396 >        rb = static_cast<RigidBody*>(sd);
397          vector<Atom*> atoms = rb->getAtoms();
398          set<int> rigidAtoms;
399          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 385 | Line 404 | namespace OpenMD {
404          }      
405        } else {
406          set<int> oneAtomSet;
407 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
408 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
407 >        oneAtomSet.insert(sd->getGlobalIndex());
408 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
409        }
410      }  
411            
# Line 520 | Line 539 | namespace OpenMD {
539      Molecule::RigidBodyIterator rbIter;
540      RigidBody* rb;
541      Molecule::IntegrableObjectIterator ii;
542 <    StuntDouble* integrableObject;
542 >    StuntDouble* sd;
543      
544 <    for (integrableObject = mol->beginIntegrableObject(ii);
545 <         integrableObject != NULL;
527 <         integrableObject = mol->nextIntegrableObject(ii)) {
544 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
545 >         sd = mol->nextIntegrableObject(ii)) {
546        
547 <      if (integrableObject->isRigidBody()) {
548 <        rb = static_cast<RigidBody*>(integrableObject);
547 >      if (sd->isRigidBody()) {
548 >        rb = static_cast<RigidBody*>(sd);
549          vector<Atom*> atoms = rb->getAtoms();
550          set<int> rigidAtoms;
551          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 538 | Line 556 | namespace OpenMD {
556          }      
557        } else {
558          set<int> oneAtomSet;
559 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
560 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
559 >        oneAtomSet.insert(sd->getGlobalIndex());
560 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
561        }
562      }  
563  
# Line 694 | Line 712 | namespace OpenMD {
712      Atom* atom;
713      set<AtomType*> atomTypes;
714      
715 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
716 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
715 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716 >      for(atom = mol->beginAtom(ai); atom != NULL;
717 >          atom = mol->nextAtom(ai)) {
718          atomTypes.insert(atom->getAtomType());
719        }      
720      }    
721 <
721 >    
722   #ifdef IS_MPI
723  
724      // loop over the found atom types on this processor, and add their
725      // numerical idents to a vector:
726 <
726 >    
727      vector<int> foundTypes;
728      set<AtomType*>::iterator i;
729      for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
# Line 713 | Line 732 | namespace OpenMD {
732      // count_local holds the number of found types on this processor
733      int count_local = foundTypes.size();
734  
716 –    // count holds the total number of found types on all processors
717 –    // (some will be redundant with the ones found locally):
718 –    int count;
719 –    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
720 –
721 –    // create a vector to hold the globally found types, and resize it:
722 –    vector<int> ftGlobal;
723 –    ftGlobal.resize(count);
724 –    vector<int> counts;
725 –
735      int nproc = MPI::COMM_WORLD.Get_size();
736 <    counts.resize(nproc);
737 <    vector<int> disps;
738 <    disps.resize(nproc);
736 >
737 >    // we need arrays to hold the counts and displacement vectors for
738 >    // all processors
739 >    vector<int> counts(nproc, 0);
740 >    vector<int> disps(nproc, 0);
741  
742 <    // now spray out the foundTypes to all the other processors:
742 >    // fill the counts array
743 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744 >                              1, MPI::INT);
745 >  
746 >    // use the processor counts to compute the displacement array
747 >    disps[0] = 0;    
748 >    int totalCount = counts[0];
749 >    for (int iproc = 1; iproc < nproc; iproc++) {
750 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
751 >      totalCount += counts[iproc];
752 >    }
753 >
754 >    // we need a (possibly redundant) set of all found types:
755 >    vector<int> ftGlobal(totalCount);
756      
757 +    // now spray out the foundTypes to all the other processors:    
758      MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759 <                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
759 >                               &ftGlobal[0], &counts[0], &disps[0],
760 >                               MPI::INT);
761  
762 +    vector<int>::iterator j;
763 +
764      // foundIdents is a stl set, so inserting an already found ident
765      // will have no effect.
766      set<int> foundIdents;
767 <    vector<int>::iterator j;
767 >
768      for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769        foundIdents.insert((*j));
770      
771      // now iterate over the foundIdents and get the actual atom types
772      // that correspond to these:
773      set<int>::iterator it;
774 <    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775        atomTypes.insert( forceField_->getAtomType((*it)) );
776  
777   #endif
778 <    
778 >
779      return atomTypes;        
780    }
781  
# Line 763 | Line 791 | namespace OpenMD {
791      set<AtomType*>::iterator i;
792      set<AtomType*> atomTypes;
793      atomTypes = getSimulatedAtomTypes();    
794 <    int usesElectrostatic = 0;
795 <    int usesMetallic = 0;
796 <    int usesDirectional = 0;
794 >    bool usesElectrostatic = false;
795 >    bool usesMetallic = false;
796 >    bool usesDirectional = false;
797 >    bool usesFluctuatingCharges =  false;
798      //loop over all of the atom types
799      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800        usesElectrostatic |= (*i)->isElectrostatic();
801        usesMetallic |= (*i)->isMetal();
802        usesDirectional |= (*i)->isDirectional();
803 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804      }
805 <    
806 < #ifdef IS_MPI    
807 <    int temp;
805 >
806 > #ifdef IS_MPI
807 >    bool temp;
808      temp = usesDirectional;
809 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
810 <    
809 >    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
810 >                              MPI::LOR);
811 >        
812      temp = usesMetallic;
813 <    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
813 >    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
814 >                              MPI::LOR);
815      
816      temp = usesElectrostatic;
817 <    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817 >    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
818 >                              MPI::LOR);
819 >
820 >    temp = usesFluctuatingCharges;
821 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
822 >                              MPI::LOR);
823   #else
824  
825      usesDirectionalAtoms_ = usesDirectional;
826      usesMetallicAtoms_ = usesMetallic;
827      usesElectrostaticAtoms_ = usesElectrostatic;
828 +    usesFluctuatingCharges_ = usesFluctuatingCharges;
829  
830   #endif
831      
# Line 859 | Line 897 | namespace OpenMD {
897      massFactors_.clear();
898      massFactors_.resize(getNAtoms(), 1.0);
899      
862 –    cerr << "mfs in si = " << massFactors_.size() << "\n";
900      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
901        for (cg = mol->beginCutoffGroup(ci); cg != NULL;
902             cg = mol->nextCutoffGroup(ci)) {
# Line 956 | Line 993 | namespace OpenMD {
993      }    
994      
995    }
959 –
960 –  Vector3d SimInfo::getComVel(){
961 –    SimInfo::MoleculeIterator i;
962 –    Molecule* mol;
963 –
964 –    Vector3d comVel(0.0);
965 –    RealType totalMass = 0.0;
966 –    
967 –
968 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
969 –      RealType mass = mol->getMass();
970 –      totalMass += mass;
971 –      comVel += mass * mol->getComVel();
972 –    }  
973 –
974 – #ifdef IS_MPI
975 –    RealType tmpMass = totalMass;
976 –    Vector3d tmpComVel(comVel);    
977 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
978 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
979 – #endif
980 –
981 –    comVel /= totalMass;
982 –
983 –    return comVel;
984 –  }
985 –
986 –  Vector3d SimInfo::getCom(){
987 –    SimInfo::MoleculeIterator i;
988 –    Molecule* mol;
989 –
990 –    Vector3d com(0.0);
991 –    RealType totalMass = 0.0;
992 –    
993 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
994 –      RealType mass = mol->getMass();
995 –      totalMass += mass;
996 –      com += mass * mol->getCom();
997 –    }  
996  
999 – #ifdef IS_MPI
1000 –    RealType tmpMass = totalMass;
1001 –    Vector3d tmpCom(com);    
1002 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1003 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1004 – #endif
997  
1006 –    com /= totalMass;
1007 –
1008 –    return com;
1009 –
1010 –  }        
1011 –
998    ostream& operator <<(ostream& o, SimInfo& info) {
999  
1000      return o;
1001    }
1002    
1003 <  
1018 <   /*
1019 <   Returns center of mass and center of mass velocity in one function call.
1020 <   */
1021 <  
1022 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1023 <      SimInfo::MoleculeIterator i;
1024 <      Molecule* mol;
1025 <      
1026 <    
1027 <      RealType totalMass = 0.0;
1028 <    
1029 <
1030 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1031 <         RealType mass = mol->getMass();
1032 <         totalMass += mass;
1033 <         com += mass * mol->getCom();
1034 <         comVel += mass * mol->getComVel();          
1035 <      }  
1036 <      
1037 < #ifdef IS_MPI
1038 <      RealType tmpMass = totalMass;
1039 <      Vector3d tmpCom(com);  
1040 <      Vector3d tmpComVel(comVel);
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 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1044 < #endif
1045 <      
1046 <      com /= totalMass;
1047 <      comVel /= totalMass;
1048 <   }        
1049 <  
1050 <   /*
1051 <   Return intertia tensor for entire system and angular momentum Vector.
1052 <
1053 <
1054 <       [  Ixx -Ixy  -Ixz ]
1055 <    J =| -Iyx  Iyy  -Iyz |
1056 <       [ -Izx -Iyz   Izz ]
1057 <    */
1058 <
1059 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1060 <      
1061 <
1062 <      RealType xx = 0.0;
1063 <      RealType yy = 0.0;
1064 <      RealType zz = 0.0;
1065 <      RealType xy = 0.0;
1066 <      RealType xz = 0.0;
1067 <      RealType yz = 0.0;
1068 <      Vector3d com(0.0);
1069 <      Vector3d comVel(0.0);
1070 <      
1071 <      getComAll(com, comVel);
1072 <      
1073 <      SimInfo::MoleculeIterator i;
1074 <      Molecule* mol;
1075 <      
1076 <      Vector3d thisq(0.0);
1077 <      Vector3d thisv(0.0);
1078 <
1079 <      RealType thisMass = 0.0;
1080 <    
1081 <      
1082 <      
1083 <  
1084 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1085 <        
1086 <         thisq = mol->getCom()-com;
1087 <         thisv = mol->getComVel()-comVel;
1088 <         thisMass = mol->getMass();
1089 <         // Compute moment of intertia coefficients.
1090 <         xx += thisq[0]*thisq[0]*thisMass;
1091 <         yy += thisq[1]*thisq[1]*thisMass;
1092 <         zz += thisq[2]*thisq[2]*thisMass;
1093 <        
1094 <         // compute products of intertia
1095 <         xy += thisq[0]*thisq[1]*thisMass;
1096 <         xz += thisq[0]*thisq[2]*thisMass;
1097 <         yz += thisq[1]*thisq[2]*thisMass;
1098 <            
1099 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1100 <            
1101 <      }  
1102 <      
1103 <      
1104 <      inertiaTensor(0,0) = yy + zz;
1105 <      inertiaTensor(0,1) = -xy;
1106 <      inertiaTensor(0,2) = -xz;
1107 <      inertiaTensor(1,0) = -xy;
1108 <      inertiaTensor(1,1) = xx + zz;
1109 <      inertiaTensor(1,2) = -yz;
1110 <      inertiaTensor(2,0) = -xz;
1111 <      inertiaTensor(2,1) = -yz;
1112 <      inertiaTensor(2,2) = xx + yy;
1113 <      
1114 < #ifdef IS_MPI
1115 <      Mat3x3d tmpI(inertiaTensor);
1116 <      Vector3d tmpAngMom;
1117 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1118 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1119 < #endif
1120 <              
1121 <      return;
1122 <   }
1123 <
1124 <   //Returns the angular momentum of the system
1125 <   Vector3d SimInfo::getAngularMomentum(){
1126 <      
1127 <      Vector3d com(0.0);
1128 <      Vector3d comVel(0.0);
1129 <      Vector3d angularMomentum(0.0);
1130 <      
1131 <      getComAll(com,comVel);
1132 <      
1133 <      SimInfo::MoleculeIterator i;
1134 <      Molecule* mol;
1135 <      
1136 <      Vector3d thisr(0.0);
1137 <      Vector3d thisp(0.0);
1138 <      
1139 <      RealType thisMass;
1140 <      
1141 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1142 <        thisMass = mol->getMass();
1143 <        thisr = mol->getCom()-com;
1144 <        thisp = (mol->getComVel()-comVel)*thisMass;
1145 <        
1146 <        angularMomentum += cross( thisr, thisp );
1147 <        
1148 <      }  
1149 <      
1150 < #ifdef IS_MPI
1151 <      Vector3d tmpAngMom;
1152 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1153 < #endif
1154 <      
1155 <      return angularMomentum;
1156 <   }
1157 <  
1003 >  
1004    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005      return IOIndexToIntegrableObject.at(index);
1006    }
# Line 1162 | Line 1008 | namespace OpenMD {
1008    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009      IOIndexToIntegrableObject= v;
1010    }
1165 –
1166 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1167 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1168 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1169 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1170 –  */
1171 –  void SimInfo::getGyrationalVolume(RealType &volume){
1172 –    Mat3x3d intTensor;
1173 –    RealType det;
1174 –    Vector3d dummyAngMom;
1175 –    RealType sysconstants;
1176 –    RealType geomCnst;
1177 –
1178 –    geomCnst = 3.0/2.0;
1179 –    /* Get the inertial tensor and angular momentum for free*/
1180 –    getInertiaTensor(intTensor,dummyAngMom);
1181 –    
1182 –    det = intTensor.determinant();
1183 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1184 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1185 –    return;
1186 –  }
1187 –
1188 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1189 –    Mat3x3d intTensor;
1190 –    Vector3d dummyAngMom;
1191 –    RealType sysconstants;
1192 –    RealType geomCnst;
1193 –
1194 –    geomCnst = 3.0/2.0;
1195 –    /* Get the inertial tensor and angular momentum for free*/
1196 –    getInertiaTensor(intTensor,dummyAngMom);
1197 –    
1198 –    detI = intTensor.determinant();
1199 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1200 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1201 –    return;
1202 –  }
1011   /*
1012     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013        assert( v.size() == nAtoms_ + nRigidBodies_);

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