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Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 59 | 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>
# Line 72 | 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 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 225 | Line 226 | namespace OpenMD {
226  
227  
228    void SimInfo::calcNdf() {
229 <    int ndf_local;
229 >    int ndf_local, nfq_local;
230      MoleculeIterator i;
231      vector<StuntDouble*>::iterator j;
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)) {
237 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
238 –           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          }
249 –            
255        }
256 +
257 +      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258 +           atom = mol->nextFluctuatingCharge(k)) {
259 +        if (atom->isFluctuatingCharge()) {
260 +          nfq_local++;
261 +        }
262 +      }
263      }
264      
265 +    ndfLocal_ = ndf_local;
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);
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;
277   #endif
278  
279      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 267 | 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 299 | 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)) {
308 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309 –           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 322 | 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 335 | 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 371 | 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;
378 <         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 389 | 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 524 | 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;
531 <         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 542 | 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 763 | 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 777 | 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;
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();
821        usesMetallic |= (*i)->isMetal();
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::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
842 >                              MPI::LOR);
843   #else
844  
845      usesDirectionalAtoms_ = usesDirectional;
846      usesMetallicAtoms_ = usesMetallic;
847      usesElectrostaticAtoms_ = usesElectrostatic;
848 +    usesFluctuatingCharges_ = usesFluctuatingCharges;
849  
850   #endif
851      
# Line 851 | Line 895 | namespace OpenMD {
895  
896  
897    void SimInfo::prepareTopology() {
854 –    int nExclude, nOneTwo, nOneThree, nOneFour;
898  
899      //calculate mass ratio of cutoff group
900      SimInfo::MoleculeIterator mi;
# Line 898 | Line 941 | namespace OpenMD {
941        }
942      }    
943      
901 –    //scan topology
902 –
903 –    nExclude = excludedInteractions_.getSize();
904 –    nOneTwo = oneTwoInteractions_.getSize();
905 –    nOneThree = oneThreeInteractions_.getSize();
906 –    nOneFour = oneFourInteractions_.getSize();
907 –
908 –    int* excludeList = excludedInteractions_.getPairList();
909 –    int* oneTwoList = oneTwoInteractions_.getPairList();
910 –    int* oneThreeList = oneThreeInteractions_.getPairList();
911 –    int* oneFourList = oneFourInteractions_.getPairList();
912 –
944      topologyDone_ = true;
945    }
946  
# Line 955 | Line 986 | namespace OpenMD {
986  
987      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
988          
989 <      for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
989 >      for (atom = mol->beginAtom(atomIter); atom != NULL;
990 >           atom = mol->nextAtom(atomIter)) {
991          atom->setSnapshotManager(sman_);
992        }
993          
994 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
994 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
995 >           rb = mol->nextRigidBody(rbIter)) {
996          rb->setSnapshotManager(sman_);
997        }
998  
999 <      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
999 >      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1000 >           cg = mol->nextCutoffGroup(cgIter)) {
1001          cg->setSnapshotManager(sman_);
1002        }
1003      }    
1004      
1005    }
1006  
973 –  Vector3d SimInfo::getComVel(){
974 –    SimInfo::MoleculeIterator i;
975 –    Molecule* mol;
1007  
977 –    Vector3d comVel(0.0);
978 –    RealType totalMass = 0.0;
979 –    
980 –
981 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
982 –      RealType mass = mol->getMass();
983 –      totalMass += mass;
984 –      comVel += mass * mol->getComVel();
985 –    }  
986 –
987 – #ifdef IS_MPI
988 –    RealType tmpMass = totalMass;
989 –    Vector3d tmpComVel(comVel);    
990 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
992 – #endif
993 –
994 –    comVel /= totalMass;
995 –
996 –    return comVel;
997 –  }
998 –
999 –  Vector3d SimInfo::getCom(){
1000 –    SimInfo::MoleculeIterator i;
1001 –    Molecule* mol;
1002 –
1003 –    Vector3d com(0.0);
1004 –    RealType totalMass = 0.0;
1005 –    
1006 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1007 –      RealType mass = mol->getMass();
1008 –      totalMass += mass;
1009 –      com += mass * mol->getCom();
1010 –    }  
1011 –
1012 – #ifdef IS_MPI
1013 –    RealType tmpMass = totalMass;
1014 –    Vector3d tmpCom(com);    
1015 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1017 – #endif
1018 –
1019 –    com /= totalMass;
1020 –
1021 –    return com;
1022 –
1023 –  }        
1024 –
1008    ostream& operator <<(ostream& o, SimInfo& info) {
1009  
1010      return o;
1011    }
1012    
1013 <  
1031 <   /*
1032 <   Returns center of mass and center of mass velocity in one function call.
1033 <   */
1034 <  
1035 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1036 <      SimInfo::MoleculeIterator i;
1037 <      Molecule* mol;
1038 <      
1039 <    
1040 <      RealType totalMass = 0.0;
1041 <    
1042 <
1043 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1044 <         RealType mass = mol->getMass();
1045 <         totalMass += mass;
1046 <         com += mass * mol->getCom();
1047 <         comVel += mass * mol->getComVel();          
1048 <      }  
1049 <      
1050 < #ifdef IS_MPI
1051 <      RealType tmpMass = totalMass;
1052 <      Vector3d tmpCom(com);  
1053 <      Vector3d tmpComVel(comVel);
1054 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1057 < #endif
1058 <      
1059 <      com /= totalMass;
1060 <      comVel /= totalMass;
1061 <   }        
1062 <  
1063 <   /*
1064 <   Return intertia tensor for entire system and angular momentum Vector.
1065 <
1066 <
1067 <       [  Ixx -Ixy  -Ixz ]
1068 <    J =| -Iyx  Iyy  -Iyz |
1069 <       [ -Izx -Iyz   Izz ]
1070 <    */
1071 <
1072 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1073 <      
1074 <
1075 <      RealType xx = 0.0;
1076 <      RealType yy = 0.0;
1077 <      RealType zz = 0.0;
1078 <      RealType xy = 0.0;
1079 <      RealType xz = 0.0;
1080 <      RealType yz = 0.0;
1081 <      Vector3d com(0.0);
1082 <      Vector3d comVel(0.0);
1083 <      
1084 <      getComAll(com, comVel);
1085 <      
1086 <      SimInfo::MoleculeIterator i;
1087 <      Molecule* mol;
1088 <      
1089 <      Vector3d thisq(0.0);
1090 <      Vector3d thisv(0.0);
1091 <
1092 <      RealType thisMass = 0.0;
1093 <    
1094 <      
1095 <      
1096 <  
1097 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1098 <        
1099 <         thisq = mol->getCom()-com;
1100 <         thisv = mol->getComVel()-comVel;
1101 <         thisMass = mol->getMass();
1102 <         // Compute moment of intertia coefficients.
1103 <         xx += thisq[0]*thisq[0]*thisMass;
1104 <         yy += thisq[1]*thisq[1]*thisMass;
1105 <         zz += thisq[2]*thisq[2]*thisMass;
1106 <        
1107 <         // compute products of intertia
1108 <         xy += thisq[0]*thisq[1]*thisMass;
1109 <         xz += thisq[0]*thisq[2]*thisMass;
1110 <         yz += thisq[1]*thisq[2]*thisMass;
1111 <            
1112 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1113 <            
1114 <      }  
1115 <      
1116 <      
1117 <      inertiaTensor(0,0) = yy + zz;
1118 <      inertiaTensor(0,1) = -xy;
1119 <      inertiaTensor(0,2) = -xz;
1120 <      inertiaTensor(1,0) = -xy;
1121 <      inertiaTensor(1,1) = xx + zz;
1122 <      inertiaTensor(1,2) = -yz;
1123 <      inertiaTensor(2,0) = -xz;
1124 <      inertiaTensor(2,1) = -yz;
1125 <      inertiaTensor(2,2) = xx + yy;
1126 <      
1127 < #ifdef IS_MPI
1128 <      Mat3x3d tmpI(inertiaTensor);
1129 <      Vector3d tmpAngMom;
1130 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1132 < #endif
1133 <              
1134 <      return;
1135 <   }
1136 <
1137 <   //Returns the angular momentum of the system
1138 <   Vector3d SimInfo::getAngularMomentum(){
1139 <      
1140 <      Vector3d com(0.0);
1141 <      Vector3d comVel(0.0);
1142 <      Vector3d angularMomentum(0.0);
1143 <      
1144 <      getComAll(com,comVel);
1145 <      
1146 <      SimInfo::MoleculeIterator i;
1147 <      Molecule* mol;
1148 <      
1149 <      Vector3d thisr(0.0);
1150 <      Vector3d thisp(0.0);
1151 <      
1152 <      RealType thisMass;
1153 <      
1154 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1155 <        thisMass = mol->getMass();
1156 <        thisr = mol->getCom()-com;
1157 <        thisp = (mol->getComVel()-comVel)*thisMass;
1158 <        
1159 <        angularMomentum += cross( thisr, thisp );
1160 <        
1161 <      }  
1162 <      
1163 < #ifdef IS_MPI
1164 <      Vector3d tmpAngMom;
1165 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1166 < #endif
1167 <      
1168 <      return angularMomentum;
1169 <   }
1170 <  
1013 >  
1014    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1015 <    return IOIndexToIntegrableObject.at(index);
1015 >    if (index >= int(IOIndexToIntegrableObject.size())) {
1016 >      sprintf(painCave.errMsg,
1017 >              "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1018 >              "\tindex exceeds number of known objects!\n");
1019 >      painCave.isFatal = 1;
1020 >      simError();
1021 >      return NULL;
1022 >    } else
1023 >      return IOIndexToIntegrableObject.at(index);
1024    }
1025    
1026    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1027      IOIndexToIntegrableObject= v;
1028    }
1029  
1179 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1180 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1181 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1182 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1183 –  */
1184 –  void SimInfo::getGyrationalVolume(RealType &volume){
1185 –    Mat3x3d intTensor;
1186 –    RealType det;
1187 –    Vector3d dummyAngMom;
1188 –    RealType sysconstants;
1189 –    RealType geomCnst;
1190 –
1191 –    geomCnst = 3.0/2.0;
1192 –    /* Get the inertial tensor and angular momentum for free*/
1193 –    getInertiaTensor(intTensor,dummyAngMom);
1194 –    
1195 –    det = intTensor.determinant();
1196 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1197 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1198 –    return;
1199 –  }
1200 –
1201 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1202 –    Mat3x3d intTensor;
1203 –    Vector3d dummyAngMom;
1204 –    RealType sysconstants;
1205 –    RealType geomCnst;
1206 –
1207 –    geomCnst = 3.0/2.0;
1208 –    /* Get the inertial tensor and angular momentum for free*/
1209 –    getInertiaTensor(intTensor,dummyAngMom);
1210 –    
1211 –    detI = intTensor.determinant();
1212 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1213 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1214 –    return;
1215 –  }
1216 – /*
1217 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1218 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1219 –      sdByGlobalIndex_ = v;
1220 –    }
1221 –
1222 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1223 –      //assert(index < nAtoms_ + nRigidBodies_);
1224 –      return sdByGlobalIndex_.at(index);
1225 –    }  
1226 – */  
1030    int SimInfo::getNGlobalConstraints() {
1031      int nGlobalConstraints;
1032   #ifdef IS_MPI
1033 <    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1034 <                  MPI_COMM_WORLD);    
1033 >    MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1034 >                              MPI::INT, MPI::SUM);
1035   #else
1036      nGlobalConstraints =  nConstraints_;
1037   #endif

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