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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC vs.
Revision 1849 by gezelter, Wed Feb 20 13:52:51 2013 UTC

# Line 88 | Line 88 | namespace OpenMD {
88      
89      vector<Component*> components = simParams->getComponents();
90      
91 <    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91 >    for (vector<Component*>::iterator i = components.begin();
92 >         i !=components.end(); ++i) {
93        molStamp = (*i)->getMoleculeStamp();
94        nMolWithSameStamp = (*i)->getNMol();
95        
# Line 231 | Line 232 | namespace OpenMD {
232      vector<Atom*>::iterator k;
233  
234      Molecule* mol;
235 <    StuntDouble* integrableObject;
235 >    StuntDouble* sd;
236      Atom* atom;
237  
238      ndf_local = 0;
239      nfq_local = 0;
240      
241      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242 –           integrableObject = mol->nextIntegrableObject(j)) {
242  
243 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
244 +           sd = mol->nextIntegrableObject(j)) {
245 +
246          ndf_local += 3;
247  
248 <        if (integrableObject->isDirectional()) {
249 <          if (integrableObject->isLinear()) {
248 >        if (sd->isDirectional()) {
249 >          if (sd->isLinear()) {
250              ndf_local += 2;
251            } else {
252              ndf_local += 3;
253            }
254          }
255        }
256 +
257        for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258             atom = mol->nextFluctuatingCharge(k)) {
259          if (atom->isFluctuatingCharge()) {
# Line 260 | Line 263 | namespace OpenMD {
263      }
264      
265      ndfLocal_ = ndf_local;
263 –    cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
266  
267      // n_constraints is local, so subtract them on each processor
268      ndf_local -= nConstraints_;
269  
270   #ifdef IS_MPI
271 <    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272 <    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271 >    MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
272 >    MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
273 >                              MPI::INT, MPI::SUM);
274   #else
275      ndf_ = ndf_local;
276      nGlobalFluctuatingCharges_ = nfq_local;
# Line 281 | Line 284 | namespace OpenMD {
284  
285    int SimInfo::getFdf() {
286   #ifdef IS_MPI
287 <    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
287 >    MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
288   #else
289      fdf_ = fdf_local;
290   #endif
# Line 313 | Line 316 | namespace OpenMD {
316      MoleculeIterator i;
317      vector<StuntDouble*>::iterator j;
318      Molecule* mol;
319 <    StuntDouble* integrableObject;
319 >    StuntDouble* sd;
320  
321      // Raw degrees of freedom that we have to set
322      ndfRaw_local = 0;
323      
324      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
322 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
323 –           integrableObject = mol->nextIntegrableObject(j)) {
325  
326 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
327 +           sd = mol->nextIntegrableObject(j)) {
328 +
329          ndfRaw_local += 3;
330  
331 <        if (integrableObject->isDirectional()) {
332 <          if (integrableObject->isLinear()) {
331 >        if (sd->isDirectional()) {
332 >          if (sd->isLinear()) {
333              ndfRaw_local += 2;
334            } else {
335              ndfRaw_local += 3;
# Line 336 | Line 340 | namespace OpenMD {
340      }
341      
342   #ifdef IS_MPI
343 <    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343 >    MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
344   #else
345      ndfRaw_ = ndfRaw_local;
346   #endif
# Line 349 | Line 353 | namespace OpenMD {
353  
354  
355   #ifdef IS_MPI
356 <    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356 >    MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
357 >                              MPI::INT, MPI::SUM);
358   #else
359      ndfTrans_ = ndfTrans_local;
360   #endif
# Line 385 | Line 390 | namespace OpenMD {
390      Molecule::RigidBodyIterator rbIter;
391      RigidBody* rb;
392      Molecule::IntegrableObjectIterator ii;
393 <    StuntDouble* integrableObject;
393 >    StuntDouble* sd;
394      
395 <    for (integrableObject = mol->beginIntegrableObject(ii);
396 <         integrableObject != NULL;
392 <         integrableObject = mol->nextIntegrableObject(ii)) {
395 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
396 >         sd = mol->nextIntegrableObject(ii)) {
397        
398 <      if (integrableObject->isRigidBody()) {
399 <        rb = static_cast<RigidBody*>(integrableObject);
398 >      if (sd->isRigidBody()) {
399 >        rb = static_cast<RigidBody*>(sd);
400          vector<Atom*> atoms = rb->getAtoms();
401          set<int> rigidAtoms;
402          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 403 | Line 407 | namespace OpenMD {
407          }      
408        } else {
409          set<int> oneAtomSet;
410 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
411 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
410 >        oneAtomSet.insert(sd->getGlobalIndex());
411 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
412        }
413      }  
414            
# Line 538 | Line 542 | namespace OpenMD {
542      Molecule::RigidBodyIterator rbIter;
543      RigidBody* rb;
544      Molecule::IntegrableObjectIterator ii;
545 <    StuntDouble* integrableObject;
545 >    StuntDouble* sd;
546      
547 <    for (integrableObject = mol->beginIntegrableObject(ii);
548 <         integrableObject != NULL;
545 <         integrableObject = mol->nextIntegrableObject(ii)) {
547 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
548 >         sd = mol->nextIntegrableObject(ii)) {
549        
550 <      if (integrableObject->isRigidBody()) {
551 <        rb = static_cast<RigidBody*>(integrableObject);
550 >      if (sd->isRigidBody()) {
551 >        rb = static_cast<RigidBody*>(sd);
552          vector<Atom*> atoms = rb->getAtoms();
553          set<int> rigidAtoms;
554          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 556 | Line 559 | namespace OpenMD {
559          }      
560        } else {
561          set<int> oneAtomSet;
562 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
563 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
562 >        oneAtomSet.insert(sd->getGlobalIndex());
563 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
564        }
565      }  
566  
# Line 777 | Line 780 | namespace OpenMD {
780   #endif
781  
782      return atomTypes;        
783 +  }
784 +
785 +
786 +  int getGlobalCountOfType(AtomType* atype) {
787 +    /*
788 +    set<AtomType*> atypes = getSimulatedAtomTypes();
789 +    map<AtomType*, int> counts_;
790 +
791 +    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
792 +      for(atom = mol->beginAtom(ai); atom != NULL;
793 +          atom = mol->nextAtom(ai)) {
794 +        atom->getAtomType();
795 +      }      
796 +    }    
797 +    */
798 +    return 0;
799    }
800  
801    void SimInfo::setupSimVariables() {
802      useAtomicVirial_ = simParams_->getUseAtomicVirial();
803 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
803 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole
804 >    // parameter is true
805      calcBoxDipole_ = false;
806      if ( simParams_->haveAccumulateBoxDipole() )
807        if ( simParams_->getAccumulateBoxDipole() ) {
# Line 791 | Line 811 | namespace OpenMD {
811      set<AtomType*>::iterator i;
812      set<AtomType*> atomTypes;
813      atomTypes = getSimulatedAtomTypes();    
814 <    int usesElectrostatic = 0;
815 <    int usesMetallic = 0;
816 <    int usesDirectional = 0;
817 <    int usesFluctuatingCharges =  0;
814 >    bool usesElectrostatic = false;
815 >    bool usesMetallic = false;
816 >    bool usesDirectional = false;
817 >    bool usesFluctuatingCharges =  false;
818      //loop over all of the atom types
819      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
820        usesElectrostatic |= (*i)->isElectrostatic();
# Line 802 | Line 822 | namespace OpenMD {
822        usesDirectional |= (*i)->isDirectional();
823        usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
824      }
825 <    
826 < #ifdef IS_MPI    
827 <    int temp;
825 >
826 > #ifdef IS_MPI
827 >    bool temp;
828      temp = usesDirectional;
829 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
830 <    
829 >    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
830 >                              MPI::LOR);
831 >        
832      temp = usesMetallic;
833 <    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
833 >    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
834 >                              MPI::LOR);
835      
836      temp = usesElectrostatic;
837 <    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837 >    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
838 >                              MPI::LOR);
839  
840      temp = usesFluctuatingCharges;
841 <    MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
842 >                              MPI::LOR);
843   #else
844  
845      usesDirectionalAtoms_ = usesDirectional;
# Line 871 | Line 895 | namespace OpenMD {
895  
896  
897    void SimInfo::prepareTopology() {
874 –    int nExclude, nOneTwo, nOneThree, nOneFour;
898  
899      //calculate mass ratio of cutoff group
900      SimInfo::MoleculeIterator mi;
# Line 920 | Line 943 | namespace OpenMD {
943      
944      //scan topology
945  
923 –    nExclude = excludedInteractions_.getSize();
924 –    nOneTwo = oneTwoInteractions_.getSize();
925 –    nOneThree = oneThreeInteractions_.getSize();
926 –    nOneFour = oneFourInteractions_.getSize();
927 –
946      int* excludeList = excludedInteractions_.getPairList();
947      int* oneTwoList = oneTwoInteractions_.getPairList();
948      int* oneThreeList = oneThreeInteractions_.getPairList();
# Line 975 | Line 993 | namespace OpenMD {
993  
994      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
995          
996 <      for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
996 >      for (atom = mol->beginAtom(atomIter); atom != NULL;
997 >           atom = mol->nextAtom(atomIter)) {
998          atom->setSnapshotManager(sman_);
999        }
1000          
1001 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1001 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1002 >           rb = mol->nextRigidBody(rbIter)) {
1003          rb->setSnapshotManager(sman_);
1004        }
1005  
1006 <      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1006 >      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1007 >           cg = mol->nextCutoffGroup(cgIter)) {
1008          cg->setSnapshotManager(sman_);
1009        }
1010      }    
1011      
1012    }
1013  
993 –  Vector3d SimInfo::getComVel(){
994 –    SimInfo::MoleculeIterator i;
995 –    Molecule* mol;
1014  
997 –    Vector3d comVel(0.0);
998 –    RealType totalMass = 0.0;
999 –    
1000 –
1001 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1002 –      RealType mass = mol->getMass();
1003 –      totalMass += mass;
1004 –      comVel += mass * mol->getComVel();
1005 –    }  
1006 –
1007 – #ifdef IS_MPI
1008 –    RealType tmpMass = totalMass;
1009 –    Vector3d tmpComVel(comVel);    
1010 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1011 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1012 – #endif
1013 –
1014 –    comVel /= totalMass;
1015 –
1016 –    return comVel;
1017 –  }
1018 –
1019 –  Vector3d SimInfo::getCom(){
1020 –    SimInfo::MoleculeIterator i;
1021 –    Molecule* mol;
1022 –
1023 –    Vector3d com(0.0);
1024 –    RealType totalMass = 0.0;
1025 –    
1026 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1027 –      RealType mass = mol->getMass();
1028 –      totalMass += mass;
1029 –      com += mass * mol->getCom();
1030 –    }  
1031 –
1032 – #ifdef IS_MPI
1033 –    RealType tmpMass = totalMass;
1034 –    Vector3d tmpCom(com);    
1035 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1036 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1037 – #endif
1038 –
1039 –    com /= totalMass;
1040 –
1041 –    return com;
1042 –
1043 –  }        
1044 –
1015    ostream& operator <<(ostream& o, SimInfo& info) {
1016  
1017      return o;
1018    }
1049 –  
1050 –  
1051 –   /*
1052 –   Returns center of mass and center of mass velocity in one function call.
1053 –   */
1054 –  
1055 –   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1056 –      SimInfo::MoleculeIterator i;
1057 –      Molecule* mol;
1058 –      
1059 –    
1060 –      RealType totalMass = 0.0;
1061 –    
1062 –
1063 –      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1064 –         RealType mass = mol->getMass();
1065 –         totalMass += mass;
1066 –         com += mass * mol->getCom();
1067 –         comVel += mass * mol->getComVel();          
1068 –      }  
1069 –      
1070 – #ifdef IS_MPI
1071 –      RealType tmpMass = totalMass;
1072 –      Vector3d tmpCom(com);  
1073 –      Vector3d tmpComVel(comVel);
1074 –      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1075 –      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1076 –      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1077 – #endif
1078 –      
1079 –      com /= totalMass;
1080 –      comVel /= totalMass;
1081 –   }        
1019    
1020 <   /*
1084 <   Return intertia tensor for entire system and angular momentum Vector.
1085 <
1086 <
1087 <       [  Ixx -Ixy  -Ixz ]
1088 <    J =| -Iyx  Iyy  -Iyz |
1089 <       [ -Izx -Iyz   Izz ]
1090 <    */
1091 <
1092 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1093 <      
1094 <
1095 <      RealType xx = 0.0;
1096 <      RealType yy = 0.0;
1097 <      RealType zz = 0.0;
1098 <      RealType xy = 0.0;
1099 <      RealType xz = 0.0;
1100 <      RealType yz = 0.0;
1101 <      Vector3d com(0.0);
1102 <      Vector3d comVel(0.0);
1103 <      
1104 <      getComAll(com, comVel);
1105 <      
1106 <      SimInfo::MoleculeIterator i;
1107 <      Molecule* mol;
1108 <      
1109 <      Vector3d thisq(0.0);
1110 <      Vector3d thisv(0.0);
1111 <
1112 <      RealType thisMass = 0.0;
1113 <    
1114 <      
1115 <      
1116 <  
1117 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1118 <        
1119 <         thisq = mol->getCom()-com;
1120 <         thisv = mol->getComVel()-comVel;
1121 <         thisMass = mol->getMass();
1122 <         // Compute moment of intertia coefficients.
1123 <         xx += thisq[0]*thisq[0]*thisMass;
1124 <         yy += thisq[1]*thisq[1]*thisMass;
1125 <         zz += thisq[2]*thisq[2]*thisMass;
1126 <        
1127 <         // compute products of intertia
1128 <         xy += thisq[0]*thisq[1]*thisMass;
1129 <         xz += thisq[0]*thisq[2]*thisMass;
1130 <         yz += thisq[1]*thisq[2]*thisMass;
1131 <            
1132 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1133 <            
1134 <      }  
1135 <      
1136 <      
1137 <      inertiaTensor(0,0) = yy + zz;
1138 <      inertiaTensor(0,1) = -xy;
1139 <      inertiaTensor(0,2) = -xz;
1140 <      inertiaTensor(1,0) = -xy;
1141 <      inertiaTensor(1,1) = xx + zz;
1142 <      inertiaTensor(1,2) = -yz;
1143 <      inertiaTensor(2,0) = -xz;
1144 <      inertiaTensor(2,1) = -yz;
1145 <      inertiaTensor(2,2) = xx + yy;
1146 <      
1147 < #ifdef IS_MPI
1148 <      Mat3x3d tmpI(inertiaTensor);
1149 <      Vector3d tmpAngMom;
1150 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1152 < #endif
1153 <              
1154 <      return;
1155 <   }
1156 <
1157 <   //Returns the angular momentum of the system
1158 <   Vector3d SimInfo::getAngularMomentum(){
1159 <      
1160 <      Vector3d com(0.0);
1161 <      Vector3d comVel(0.0);
1162 <      Vector3d angularMomentum(0.0);
1163 <      
1164 <      getComAll(com,comVel);
1165 <      
1166 <      SimInfo::MoleculeIterator i;
1167 <      Molecule* mol;
1168 <      
1169 <      Vector3d thisr(0.0);
1170 <      Vector3d thisp(0.0);
1171 <      
1172 <      RealType thisMass;
1173 <      
1174 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1175 <        thisMass = mol->getMass();
1176 <        thisr = mol->getCom()-com;
1177 <        thisp = (mol->getComVel()-comVel)*thisMass;
1178 <        
1179 <        angularMomentum += cross( thisr, thisp );
1180 <        
1181 <      }  
1182 <      
1183 < #ifdef IS_MPI
1184 <      Vector3d tmpAngMom;
1185 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1186 < #endif
1187 <      
1188 <      return angularMomentum;
1189 <   }
1190 <  
1020 >  
1021    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1022 <    return IOIndexToIntegrableObject.at(index);
1022 >    if (index >= int(IOIndexToIntegrableObject.size())) {
1023 >      sprintf(painCave.errMsg,
1024 >              "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1025 >              "\tindex exceeds number of known objects!\n");
1026 >      painCave.isFatal = 1;
1027 >      simError();
1028 >      return NULL;
1029 >    } else
1030 >      return IOIndexToIntegrableObject.at(index);
1031    }
1032    
1033    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1034      IOIndexToIntegrableObject= v;
1035    }
1036  
1199 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1200 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1201 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1202 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1203 –  */
1204 –  void SimInfo::getGyrationalVolume(RealType &volume){
1205 –    Mat3x3d intTensor;
1206 –    RealType det;
1207 –    Vector3d dummyAngMom;
1208 –    RealType sysconstants;
1209 –    RealType geomCnst;
1210 –
1211 –    geomCnst = 3.0/2.0;
1212 –    /* Get the inertial tensor and angular momentum for free*/
1213 –    getInertiaTensor(intTensor,dummyAngMom);
1214 –    
1215 –    det = intTensor.determinant();
1216 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1218 –    return;
1219 –  }
1220 –
1221 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1222 –    Mat3x3d intTensor;
1223 –    Vector3d dummyAngMom;
1224 –    RealType sysconstants;
1225 –    RealType geomCnst;
1226 –
1227 –    geomCnst = 3.0/2.0;
1228 –    /* Get the inertial tensor and angular momentum for free*/
1229 –    getInertiaTensor(intTensor,dummyAngMom);
1230 –    
1231 –    detI = intTensor.determinant();
1232 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1234 –    return;
1235 –  }
1236 – /*
1237 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1238 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1239 –      sdByGlobalIndex_ = v;
1240 –    }
1241 –
1242 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1243 –      //assert(index < nAtoms_ + nRigidBodies_);
1244 –      return sdByGlobalIndex_.at(index);
1245 –    }  
1246 – */  
1037    int SimInfo::getNGlobalConstraints() {
1038      int nGlobalConstraints;
1039   #ifdef IS_MPI
1040 <    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1041 <                  MPI_COMM_WORLD);    
1040 >    MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1041 >                              MPI::INT, MPI::SUM);
1042   #else
1043      nGlobalConstraints =  nConstraints_;
1044   #endif

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