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Revision 1627 by gezelter, Tue Sep 13 22:05:04 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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   */
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>
# Line 71 | 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 87 | 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 224 | 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)) {
236 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
237 –           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          }
248 –            
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 266 | 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 298 | 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)) {
307 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
308 –           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 321 | 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 334 | 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 370 | 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;
377 <         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 388 | 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 523 | Line 542 | namespace OpenMD {
542      Molecule::RigidBodyIterator rbIter;
543      RigidBody* rb;
544      Molecule::IntegrableObjectIterator ii;
545 <    StuntDouble* integrableObject;
546 <    
547 <    for (integrableObject = mol->beginIntegrableObject(ii);
548 <         integrableObject != NULL;
530 <         integrableObject = mol->nextIntegrableObject(ii)) {
545 >    StuntDouble* sd;
546 >    
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 541 | 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 762 | 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 776 | 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 850 | Line 895 | namespace OpenMD {
895  
896  
897    void SimInfo::prepareTopology() {
853 –    int nExclude, nOneTwo, nOneThree, nOneFour;
898  
899      //calculate mass ratio of cutoff group
900      SimInfo::MoleculeIterator mi;
# Line 897 | Line 941 | namespace OpenMD {
941        }
942      }    
943      
900 –    //scan topology
901 –
902 –    nExclude = excludedInteractions_.getSize();
903 –    nOneTwo = oneTwoInteractions_.getSize();
904 –    nOneThree = oneThreeInteractions_.getSize();
905 –    nOneFour = oneFourInteractions_.getSize();
906 –
907 –    int* excludeList = excludedInteractions_.getPairList();
908 –    int* oneTwoList = oneTwoInteractions_.getPairList();
909 –    int* oneThreeList = oneThreeInteractions_.getPairList();
910 –    int* oneFourList = oneFourInteractions_.getPairList();
911 –
944      topologyDone_ = true;
945    }
946  
# Line 954 | 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    }
971 –
972 –  Vector3d SimInfo::getComVel(){
973 –    SimInfo::MoleculeIterator i;
974 –    Molecule* mol;
975 –
976 –    Vector3d comVel(0.0);
977 –    RealType totalMass = 0.0;
978 –    
979 –
980 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
981 –      RealType mass = mol->getMass();
982 –      totalMass += mass;
983 –      comVel += mass * mol->getComVel();
984 –    }  
985 –
986 – #ifdef IS_MPI
987 –    RealType tmpMass = totalMass;
988 –    Vector3d tmpComVel(comVel);    
989 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
990 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991 – #endif
992 –
993 –    comVel /= totalMass;
994 –
995 –    return comVel;
996 –  }
997 –
998 –  Vector3d SimInfo::getCom(){
999 –    SimInfo::MoleculeIterator i;
1000 –    Molecule* mol;
1001 –
1002 –    Vector3d com(0.0);
1003 –    RealType totalMass = 0.0;
1004 –    
1005 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1006 –      RealType mass = mol->getMass();
1007 –      totalMass += mass;
1008 –      com += mass * mol->getCom();
1009 –    }  
1010 –
1011 – #ifdef IS_MPI
1012 –    RealType tmpMass = totalMass;
1013 –    Vector3d tmpCom(com);    
1014 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1015 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016 – #endif
1006  
1018 –    com /= totalMass;
1007  
1020 –    return com;
1021 –
1022 –  }        
1023 –
1008    ostream& operator <<(ostream& o, SimInfo& info) {
1009  
1010      return o;
1011    }
1012    
1013 <  
1030 <   /*
1031 <   Returns center of mass and center of mass velocity in one function call.
1032 <   */
1033 <  
1034 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1035 <      SimInfo::MoleculeIterator i;
1036 <      Molecule* mol;
1037 <      
1038 <    
1039 <      RealType totalMass = 0.0;
1040 <    
1041 <
1042 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1043 <         RealType mass = mol->getMass();
1044 <         totalMass += mass;
1045 <         com += mass * mol->getCom();
1046 <         comVel += mass * mol->getComVel();          
1047 <      }  
1048 <      
1049 < #ifdef IS_MPI
1050 <      RealType tmpMass = totalMass;
1051 <      Vector3d tmpCom(com);  
1052 <      Vector3d tmpComVel(comVel);
1053 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1054 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056 < #endif
1057 <      
1058 <      com /= totalMass;
1059 <      comVel /= totalMass;
1060 <   }        
1061 <  
1062 <   /*
1063 <   Return intertia tensor for entire system and angular momentum Vector.
1064 <
1065 <
1066 <       [  Ixx -Ixy  -Ixz ]
1067 <    J =| -Iyx  Iyy  -Iyz |
1068 <       [ -Izx -Iyz   Izz ]
1069 <    */
1070 <
1071 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1072 <      
1073 <
1074 <      RealType xx = 0.0;
1075 <      RealType yy = 0.0;
1076 <      RealType zz = 0.0;
1077 <      RealType xy = 0.0;
1078 <      RealType xz = 0.0;
1079 <      RealType yz = 0.0;
1080 <      Vector3d com(0.0);
1081 <      Vector3d comVel(0.0);
1082 <      
1083 <      getComAll(com, comVel);
1084 <      
1085 <      SimInfo::MoleculeIterator i;
1086 <      Molecule* mol;
1087 <      
1088 <      Vector3d thisq(0.0);
1089 <      Vector3d thisv(0.0);
1090 <
1091 <      RealType thisMass = 0.0;
1092 <    
1093 <      
1094 <      
1095 <  
1096 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1097 <        
1098 <         thisq = mol->getCom()-com;
1099 <         thisv = mol->getComVel()-comVel;
1100 <         thisMass = mol->getMass();
1101 <         // Compute moment of intertia coefficients.
1102 <         xx += thisq[0]*thisq[0]*thisMass;
1103 <         yy += thisq[1]*thisq[1]*thisMass;
1104 <         zz += thisq[2]*thisq[2]*thisMass;
1105 <        
1106 <         // compute products of intertia
1107 <         xy += thisq[0]*thisq[1]*thisMass;
1108 <         xz += thisq[0]*thisq[2]*thisMass;
1109 <         yz += thisq[1]*thisq[2]*thisMass;
1110 <            
1111 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1112 <            
1113 <      }  
1114 <      
1115 <      
1116 <      inertiaTensor(0,0) = yy + zz;
1117 <      inertiaTensor(0,1) = -xy;
1118 <      inertiaTensor(0,2) = -xz;
1119 <      inertiaTensor(1,0) = -xy;
1120 <      inertiaTensor(1,1) = xx + zz;
1121 <      inertiaTensor(1,2) = -yz;
1122 <      inertiaTensor(2,0) = -xz;
1123 <      inertiaTensor(2,1) = -yz;
1124 <      inertiaTensor(2,2) = xx + yy;
1125 <      
1126 < #ifdef IS_MPI
1127 <      Mat3x3d tmpI(inertiaTensor);
1128 <      Vector3d tmpAngMom;
1129 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1130 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131 < #endif
1132 <              
1133 <      return;
1134 <   }
1135 <
1136 <   //Returns the angular momentum of the system
1137 <   Vector3d SimInfo::getAngularMomentum(){
1138 <      
1139 <      Vector3d com(0.0);
1140 <      Vector3d comVel(0.0);
1141 <      Vector3d angularMomentum(0.0);
1142 <      
1143 <      getComAll(com,comVel);
1144 <      
1145 <      SimInfo::MoleculeIterator i;
1146 <      Molecule* mol;
1147 <      
1148 <      Vector3d thisr(0.0);
1149 <      Vector3d thisp(0.0);
1150 <      
1151 <      RealType thisMass;
1152 <      
1153 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1154 <        thisMass = mol->getMass();
1155 <        thisr = mol->getCom()-com;
1156 <        thisp = (mol->getComVel()-comVel)*thisMass;
1157 <        
1158 <        angularMomentum += cross( thisr, thisp );
1159 <        
1160 <      }  
1161 <      
1162 < #ifdef IS_MPI
1163 <      Vector3d tmpAngMom;
1164 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1165 < #endif
1166 <      
1167 <      return angularMomentum;
1168 <   }
1169 <  
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  
1178 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1179 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1180 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1181 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1182 –  */
1183 –  void SimInfo::getGyrationalVolume(RealType &volume){
1184 –    Mat3x3d intTensor;
1185 –    RealType det;
1186 –    Vector3d dummyAngMom;
1187 –    RealType sysconstants;
1188 –    RealType geomCnst;
1189 –
1190 –    geomCnst = 3.0/2.0;
1191 –    /* Get the inertial tensor and angular momentum for free*/
1192 –    getInertiaTensor(intTensor,dummyAngMom);
1193 –    
1194 –    det = intTensor.determinant();
1195 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1196 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1197 –    return;
1198 –  }
1199 –
1200 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1201 –    Mat3x3d intTensor;
1202 –    Vector3d dummyAngMom;
1203 –    RealType sysconstants;
1204 –    RealType geomCnst;
1205 –
1206 –    geomCnst = 3.0/2.0;
1207 –    /* Get the inertial tensor and angular momentum for free*/
1208 –    getInertiaTensor(intTensor,dummyAngMom);
1209 –    
1210 –    detI = intTensor.determinant();
1211 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1212 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1213 –    return;
1214 –  }
1215 – /*
1216 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1217 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1218 –      sdByGlobalIndex_ = v;
1219 –    }
1220 –
1221 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1222 –      //assert(index < nAtoms_ + nRigidBodies_);
1223 –      return sdByGlobalIndex_.at(index);
1224 –    }  
1225 – */  
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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