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Revision 1597 by gezelter, Tue Jul 26 15:49:24 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>
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 84 | 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 221 | 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)) {
242 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
243 <           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          }
245 –            
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 263 | 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 295 | 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)) {
325 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
326 <           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 318 | 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 331 | 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 367 | 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;
374 <         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 385 | 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 520 | 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;
527 <         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 538 | 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 759 | 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 773 | 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 819 | Line 867 | namespace OpenMD {
867        
868        for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
869          GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
822 –        cerr << "LI = " << atom->getLocalIndex() << "GAI = " << GlobalAtomIndices[atom->getLocalIndex()] << "\n";
870        }
871      }
872      return GlobalAtomIndices;
# Line 841 | Line 888 | namespace OpenMD {
888        for (cg = mol->beginCutoffGroup(ci); cg != NULL;
889             cg = mol->nextCutoffGroup(ci)) {
890          GlobalGroupIndices.push_back(cg->getGlobalIndex());
844 –        cerr << "LI, GGI = " << GlobalGroupIndices.size() << " " << cg->getGlobalIndex() << "\n";
891        }        
892      }
893      return GlobalGroupIndices;
# Line 849 | Line 895 | namespace OpenMD {
895  
896  
897    void SimInfo::prepareTopology() {
852 –    int nExclude, nOneTwo, nOneThree, nOneFour;
898  
899      //calculate mass ratio of cutoff group
900      SimInfo::MoleculeIterator mi;
# Line 896 | Line 941 | namespace OpenMD {
941        }
942      }    
943      
899 –    //scan topology
900 –
901 –    nExclude = excludedInteractions_.getSize();
902 –    nOneTwo = oneTwoInteractions_.getSize();
903 –    nOneThree = oneThreeInteractions_.getSize();
904 –    nOneFour = oneFourInteractions_.getSize();
905 –
906 –    int* excludeList = excludedInteractions_.getPairList();
907 –    int* oneTwoList = oneTwoInteractions_.getPairList();
908 –    int* oneThreeList = oneThreeInteractions_.getPairList();
909 –    int* oneFourList = oneFourInteractions_.getPairList();
910 –
944      topologyDone_ = true;
945    }
946  
# Line 953 | 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  
971 –  Vector3d SimInfo::getComVel(){
972 –    SimInfo::MoleculeIterator i;
973 –    Molecule* mol;
1007  
975 –    Vector3d comVel(0.0);
976 –    RealType totalMass = 0.0;
977 –    
978 –
979 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
980 –      RealType mass = mol->getMass();
981 –      totalMass += mass;
982 –      comVel += mass * mol->getComVel();
983 –    }  
984 –
985 – #ifdef IS_MPI
986 –    RealType tmpMass = totalMass;
987 –    Vector3d tmpComVel(comVel);    
988 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
989 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
990 – #endif
991 –
992 –    comVel /= totalMass;
993 –
994 –    return comVel;
995 –  }
996 –
997 –  Vector3d SimInfo::getCom(){
998 –    SimInfo::MoleculeIterator i;
999 –    Molecule* mol;
1000 –
1001 –    Vector3d com(0.0);
1002 –    RealType totalMass = 0.0;
1003 –    
1004 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1005 –      RealType mass = mol->getMass();
1006 –      totalMass += mass;
1007 –      com += mass * mol->getCom();
1008 –    }  
1009 –
1010 – #ifdef IS_MPI
1011 –    RealType tmpMass = totalMass;
1012 –    Vector3d tmpCom(com);    
1013 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1014 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1015 – #endif
1016 –
1017 –    com /= totalMass;
1018 –
1019 –    return com;
1020 –
1021 –  }        
1022 –
1008    ostream& operator <<(ostream& o, SimInfo& info) {
1009  
1010      return o;
1011    }
1012    
1013 <  
1029 <   /*
1030 <   Returns center of mass and center of mass velocity in one function call.
1031 <   */
1032 <  
1033 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1034 <      SimInfo::MoleculeIterator i;
1035 <      Molecule* mol;
1036 <      
1037 <    
1038 <      RealType totalMass = 0.0;
1039 <    
1040 <
1041 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1042 <         RealType mass = mol->getMass();
1043 <         totalMass += mass;
1044 <         com += mass * mol->getCom();
1045 <         comVel += mass * mol->getComVel();          
1046 <      }  
1047 <      
1048 < #ifdef IS_MPI
1049 <      RealType tmpMass = totalMass;
1050 <      Vector3d tmpCom(com);  
1051 <      Vector3d tmpComVel(comVel);
1052 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1053 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1054 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055 < #endif
1056 <      
1057 <      com /= totalMass;
1058 <      comVel /= totalMass;
1059 <   }        
1060 <  
1061 <   /*
1062 <   Return intertia tensor for entire system and angular momentum Vector.
1063 <
1064 <
1065 <       [  Ixx -Ixy  -Ixz ]
1066 <    J =| -Iyx  Iyy  -Iyz |
1067 <       [ -Izx -Iyz   Izz ]
1068 <    */
1069 <
1070 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1071 <      
1072 <
1073 <      RealType xx = 0.0;
1074 <      RealType yy = 0.0;
1075 <      RealType zz = 0.0;
1076 <      RealType xy = 0.0;
1077 <      RealType xz = 0.0;
1078 <      RealType yz = 0.0;
1079 <      Vector3d com(0.0);
1080 <      Vector3d comVel(0.0);
1081 <      
1082 <      getComAll(com, comVel);
1083 <      
1084 <      SimInfo::MoleculeIterator i;
1085 <      Molecule* mol;
1086 <      
1087 <      Vector3d thisq(0.0);
1088 <      Vector3d thisv(0.0);
1089 <
1090 <      RealType thisMass = 0.0;
1091 <    
1092 <      
1093 <      
1094 <  
1095 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1096 <        
1097 <         thisq = mol->getCom()-com;
1098 <         thisv = mol->getComVel()-comVel;
1099 <         thisMass = mol->getMass();
1100 <         // Compute moment of intertia coefficients.
1101 <         xx += thisq[0]*thisq[0]*thisMass;
1102 <         yy += thisq[1]*thisq[1]*thisMass;
1103 <         zz += thisq[2]*thisq[2]*thisMass;
1104 <        
1105 <         // compute products of intertia
1106 <         xy += thisq[0]*thisq[1]*thisMass;
1107 <         xz += thisq[0]*thisq[2]*thisMass;
1108 <         yz += thisq[1]*thisq[2]*thisMass;
1109 <            
1110 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1111 <            
1112 <      }  
1113 <      
1114 <      
1115 <      inertiaTensor(0,0) = yy + zz;
1116 <      inertiaTensor(0,1) = -xy;
1117 <      inertiaTensor(0,2) = -xz;
1118 <      inertiaTensor(1,0) = -xy;
1119 <      inertiaTensor(1,1) = xx + zz;
1120 <      inertiaTensor(1,2) = -yz;
1121 <      inertiaTensor(2,0) = -xz;
1122 <      inertiaTensor(2,1) = -yz;
1123 <      inertiaTensor(2,2) = xx + yy;
1124 <      
1125 < #ifdef IS_MPI
1126 <      Mat3x3d tmpI(inertiaTensor);
1127 <      Vector3d tmpAngMom;
1128 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1129 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1130 < #endif
1131 <              
1132 <      return;
1133 <   }
1134 <
1135 <   //Returns the angular momentum of the system
1136 <   Vector3d SimInfo::getAngularMomentum(){
1137 <      
1138 <      Vector3d com(0.0);
1139 <      Vector3d comVel(0.0);
1140 <      Vector3d angularMomentum(0.0);
1141 <      
1142 <      getComAll(com,comVel);
1143 <      
1144 <      SimInfo::MoleculeIterator i;
1145 <      Molecule* mol;
1146 <      
1147 <      Vector3d thisr(0.0);
1148 <      Vector3d thisp(0.0);
1149 <      
1150 <      RealType thisMass;
1151 <      
1152 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1153 <        thisMass = mol->getMass();
1154 <        thisr = mol->getCom()-com;
1155 <        thisp = (mol->getComVel()-comVel)*thisMass;
1156 <        
1157 <        angularMomentum += cross( thisr, thisp );
1158 <        
1159 <      }  
1160 <      
1161 < #ifdef IS_MPI
1162 <      Vector3d tmpAngMom;
1163 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1164 < #endif
1165 <      
1166 <      return angularMomentum;
1167 <   }
1168 <  
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  
1177 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1178 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1179 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1180 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1181 –  */
1182 –  void SimInfo::getGyrationalVolume(RealType &volume){
1183 –    Mat3x3d intTensor;
1184 –    RealType det;
1185 –    Vector3d dummyAngMom;
1186 –    RealType sysconstants;
1187 –    RealType geomCnst;
1188 –
1189 –    geomCnst = 3.0/2.0;
1190 –    /* Get the inertial tensor and angular momentum for free*/
1191 –    getInertiaTensor(intTensor,dummyAngMom);
1192 –    
1193 –    det = intTensor.determinant();
1194 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1195 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1196 –    return;
1197 –  }
1198 –
1199 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1200 –    Mat3x3d intTensor;
1201 –    Vector3d dummyAngMom;
1202 –    RealType sysconstants;
1203 –    RealType geomCnst;
1204 –
1205 –    geomCnst = 3.0/2.0;
1206 –    /* Get the inertial tensor and angular momentum for free*/
1207 –    getInertiaTensor(intTensor,dummyAngMom);
1208 –    
1209 –    detI = intTensor.determinant();
1210 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1211 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1212 –    return;
1213 –  }
1214 – /*
1215 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1216 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1217 –      sdByGlobalIndex_ = v;
1218 –    }
1219 –
1220 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1221 –      //assert(index < nAtoms_ + nRigidBodies_);
1222 –      return sdByGlobalIndex_.at(index);
1223 –    }  
1224 – */  
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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