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Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC vs.
Revision 1779 by gezelter, Mon Aug 20 17:51:39 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 58 | Line 59
59   #include "utils/simError.h"
60   #include "selection/SelectionManager.hpp"
61   #include "io/ForceFieldOptions.hpp"
62 < #include "UseTheForce/ForceField.hpp"
62 > #include "brains/ForceField.hpp"
63   #include "nonbonded/SwitchingFunction.hpp"
64 + #ifdef IS_MPI
65 + #include <mpi.h>
66 + #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 68 | Line 72 | namespace OpenMD {
72      forceField_(ff), simParams_(simParams),
73      ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75 <    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75 >    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78 <    nConstraints_(0), sman_(NULL), topologyDone_(false),
78 >    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79      calcBoxDipole_(false), useAtomicVirial_(true) {    
80      
81      MoleculeStamp* molStamp;
# Line 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);
272 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
273   #else
274      ndf_ = ndf_local;
275 +    nGlobalFluctuatingCharges_ = nfq_local;
276   #endif
277  
278      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 295 | Line 315 | namespace OpenMD {
315      MoleculeIterator i;
316      vector<StuntDouble*>::iterator j;
317      Molecule* mol;
318 <    StuntDouble* integrableObject;
318 >    StuntDouble* sd;
319  
320      // Raw degrees of freedom that we have to set
321      ndfRaw_local = 0;
322      
323      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
304 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
305 –           integrableObject = mol->nextIntegrableObject(j)) {
324  
325 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
326 +           sd = mol->nextIntegrableObject(j)) {
327 +
328          ndfRaw_local += 3;
329  
330 <        if (integrableObject->isDirectional()) {
331 <          if (integrableObject->isLinear()) {
330 >        if (sd->isDirectional()) {
331 >          if (sd->isLinear()) {
332              ndfRaw_local += 2;
333            } else {
334              ndfRaw_local += 3;
# Line 367 | Line 388 | namespace OpenMD {
388      Molecule::RigidBodyIterator rbIter;
389      RigidBody* rb;
390      Molecule::IntegrableObjectIterator ii;
391 <    StuntDouble* integrableObject;
391 >    StuntDouble* sd;
392      
393 <    for (integrableObject = mol->beginIntegrableObject(ii);
394 <         integrableObject != NULL;
374 <         integrableObject = mol->nextIntegrableObject(ii)) {
393 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
394 >         sd = mol->nextIntegrableObject(ii)) {
395        
396 <      if (integrableObject->isRigidBody()) {
397 <        rb = static_cast<RigidBody*>(integrableObject);
396 >      if (sd->isRigidBody()) {
397 >        rb = static_cast<RigidBody*>(sd);
398          vector<Atom*> atoms = rb->getAtoms();
399          set<int> rigidAtoms;
400          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 385 | Line 405 | namespace OpenMD {
405          }      
406        } else {
407          set<int> oneAtomSet;
408 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
409 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
408 >        oneAtomSet.insert(sd->getGlobalIndex());
409 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
410        }
411      }  
412            
# Line 520 | Line 540 | namespace OpenMD {
540      Molecule::RigidBodyIterator rbIter;
541      RigidBody* rb;
542      Molecule::IntegrableObjectIterator ii;
543 <    StuntDouble* integrableObject;
543 >    StuntDouble* sd;
544      
545 <    for (integrableObject = mol->beginIntegrableObject(ii);
546 <         integrableObject != NULL;
527 <         integrableObject = mol->nextIntegrableObject(ii)) {
545 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
546 >         sd = mol->nextIntegrableObject(ii)) {
547        
548 <      if (integrableObject->isRigidBody()) {
549 <        rb = static_cast<RigidBody*>(integrableObject);
548 >      if (sd->isRigidBody()) {
549 >        rb = static_cast<RigidBody*>(sd);
550          vector<Atom*> atoms = rb->getAtoms();
551          set<int> rigidAtoms;
552          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 538 | Line 557 | namespace OpenMD {
557          }      
558        } else {
559          set<int> oneAtomSet;
560 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
561 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
560 >        oneAtomSet.insert(sd->getGlobalIndex());
561 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
562        }
563      }  
564  
# Line 763 | Line 782 | namespace OpenMD {
782  
783    void SimInfo::setupSimVariables() {
784      useAtomicVirial_ = simParams_->getUseAtomicVirial();
785 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole
786 >    // parameter is true
787      calcBoxDipole_ = false;
788      if ( simParams_->haveAccumulateBoxDipole() )
789        if ( simParams_->getAccumulateBoxDipole() ) {
# Line 773 | Line 793 | namespace OpenMD {
793      set<AtomType*>::iterator i;
794      set<AtomType*> atomTypes;
795      atomTypes = getSimulatedAtomTypes();    
796 <    int usesElectrostatic = 0;
797 <    int usesMetallic = 0;
798 <    int usesDirectional = 0;
796 >    bool usesElectrostatic = false;
797 >    bool usesMetallic = false;
798 >    bool usesDirectional = false;
799 >    bool usesFluctuatingCharges =  false;
800      //loop over all of the atom types
801      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
802        usesElectrostatic |= (*i)->isElectrostatic();
803        usesMetallic |= (*i)->isMetal();
804        usesDirectional |= (*i)->isDirectional();
805 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
806      }
807 <    
808 < #ifdef IS_MPI    
809 <    int temp;
807 >
808 > #ifdef IS_MPI
809 >    bool temp;
810      temp = usesDirectional;
811 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
812 <    
811 >    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
812 >                              MPI::LOR);
813 >        
814      temp = usesMetallic;
815 <    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
815 >    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
816 >                              MPI::LOR);
817      
818      temp = usesElectrostatic;
819 <    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819 >    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
820 >                              MPI::LOR);
821 >
822 >    temp = usesFluctuatingCharges;
823 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
824 >                              MPI::LOR);
825   #else
826  
827      usesDirectionalAtoms_ = usesDirectional;
828      usesMetallicAtoms_ = usesMetallic;
829      usesElectrostaticAtoms_ = usesElectrostatic;
830 +    usesFluctuatingCharges_ = usesFluctuatingCharges;
831  
832   #endif
833      
# Line 951 | Line 981 | namespace OpenMD {
981  
982      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
983          
984 <      for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
984 >      for (atom = mol->beginAtom(atomIter); atom != NULL;
985 >           atom = mol->nextAtom(atomIter)) {
986          atom->setSnapshotManager(sman_);
987        }
988          
989 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
989 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
990 >           rb = mol->nextRigidBody(rbIter)) {
991          rb->setSnapshotManager(sman_);
992        }
993  
994 <      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
994 >      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
995 >           cg = mol->nextCutoffGroup(cgIter)) {
996          cg->setSnapshotManager(sman_);
997        }
998      }    
999      
1000    }
1001  
969 –  Vector3d SimInfo::getComVel(){
970 –    SimInfo::MoleculeIterator i;
971 –    Molecule* mol;
1002  
973 –    Vector3d comVel(0.0);
974 –    RealType totalMass = 0.0;
975 –    
976 –
977 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
978 –      RealType mass = mol->getMass();
979 –      totalMass += mass;
980 –      comVel += mass * mol->getComVel();
981 –    }  
982 –
983 – #ifdef IS_MPI
984 –    RealType tmpMass = totalMass;
985 –    Vector3d tmpComVel(comVel);    
986 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
987 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
988 – #endif
989 –
990 –    comVel /= totalMass;
991 –
992 –    return comVel;
993 –  }
994 –
995 –  Vector3d SimInfo::getCom(){
996 –    SimInfo::MoleculeIterator i;
997 –    Molecule* mol;
998 –
999 –    Vector3d com(0.0);
1000 –    RealType totalMass = 0.0;
1001 –    
1002 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1003 –      RealType mass = mol->getMass();
1004 –      totalMass += mass;
1005 –      com += mass * mol->getCom();
1006 –    }  
1007 –
1008 – #ifdef IS_MPI
1009 –    RealType tmpMass = totalMass;
1010 –    Vector3d tmpCom(com);    
1011 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1012 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1013 – #endif
1014 –
1015 –    com /= totalMass;
1016 –
1017 –    return com;
1018 –
1019 –  }        
1020 –
1003    ostream& operator <<(ostream& o, SimInfo& info) {
1004  
1005      return o;
1006    }
1025 –  
1026 –  
1027 –   /*
1028 –   Returns center of mass and center of mass velocity in one function call.
1029 –   */
1030 –  
1031 –   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1032 –      SimInfo::MoleculeIterator i;
1033 –      Molecule* mol;
1034 –      
1035 –    
1036 –      RealType totalMass = 0.0;
1037 –    
1038 –
1039 –      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1040 –         RealType mass = mol->getMass();
1041 –         totalMass += mass;
1042 –         com += mass * mol->getCom();
1043 –         comVel += mass * mol->getComVel();          
1044 –      }  
1045 –      
1046 – #ifdef IS_MPI
1047 –      RealType tmpMass = totalMass;
1048 –      Vector3d tmpCom(com);  
1049 –      Vector3d tmpComVel(comVel);
1050 –      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1051 –      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1052 –      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1053 – #endif
1054 –      
1055 –      com /= totalMass;
1056 –      comVel /= totalMass;
1057 –   }        
1007    
1008 <   /*
1060 <   Return intertia tensor for entire system and angular momentum Vector.
1061 <
1062 <
1063 <       [  Ixx -Ixy  -Ixz ]
1064 <    J =| -Iyx  Iyy  -Iyz |
1065 <       [ -Izx -Iyz   Izz ]
1066 <    */
1067 <
1068 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1069 <      
1070 <
1071 <      RealType xx = 0.0;
1072 <      RealType yy = 0.0;
1073 <      RealType zz = 0.0;
1074 <      RealType xy = 0.0;
1075 <      RealType xz = 0.0;
1076 <      RealType yz = 0.0;
1077 <      Vector3d com(0.0);
1078 <      Vector3d comVel(0.0);
1079 <      
1080 <      getComAll(com, comVel);
1081 <      
1082 <      SimInfo::MoleculeIterator i;
1083 <      Molecule* mol;
1084 <      
1085 <      Vector3d thisq(0.0);
1086 <      Vector3d thisv(0.0);
1087 <
1088 <      RealType thisMass = 0.0;
1089 <    
1090 <      
1091 <      
1092 <  
1093 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1094 <        
1095 <         thisq = mol->getCom()-com;
1096 <         thisv = mol->getComVel()-comVel;
1097 <         thisMass = mol->getMass();
1098 <         // Compute moment of intertia coefficients.
1099 <         xx += thisq[0]*thisq[0]*thisMass;
1100 <         yy += thisq[1]*thisq[1]*thisMass;
1101 <         zz += thisq[2]*thisq[2]*thisMass;
1102 <        
1103 <         // compute products of intertia
1104 <         xy += thisq[0]*thisq[1]*thisMass;
1105 <         xz += thisq[0]*thisq[2]*thisMass;
1106 <         yz += thisq[1]*thisq[2]*thisMass;
1107 <            
1108 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1109 <            
1110 <      }  
1111 <      
1112 <      
1113 <      inertiaTensor(0,0) = yy + zz;
1114 <      inertiaTensor(0,1) = -xy;
1115 <      inertiaTensor(0,2) = -xz;
1116 <      inertiaTensor(1,0) = -xy;
1117 <      inertiaTensor(1,1) = xx + zz;
1118 <      inertiaTensor(1,2) = -yz;
1119 <      inertiaTensor(2,0) = -xz;
1120 <      inertiaTensor(2,1) = -yz;
1121 <      inertiaTensor(2,2) = xx + yy;
1122 <      
1123 < #ifdef IS_MPI
1124 <      Mat3x3d tmpI(inertiaTensor);
1125 <      Vector3d tmpAngMom;
1126 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1127 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1128 < #endif
1129 <              
1130 <      return;
1131 <   }
1132 <
1133 <   //Returns the angular momentum of the system
1134 <   Vector3d SimInfo::getAngularMomentum(){
1135 <      
1136 <      Vector3d com(0.0);
1137 <      Vector3d comVel(0.0);
1138 <      Vector3d angularMomentum(0.0);
1139 <      
1140 <      getComAll(com,comVel);
1141 <      
1142 <      SimInfo::MoleculeIterator i;
1143 <      Molecule* mol;
1144 <      
1145 <      Vector3d thisr(0.0);
1146 <      Vector3d thisp(0.0);
1147 <      
1148 <      RealType thisMass;
1149 <      
1150 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1151 <        thisMass = mol->getMass();
1152 <        thisr = mol->getCom()-com;
1153 <        thisp = (mol->getComVel()-comVel)*thisMass;
1154 <        
1155 <        angularMomentum += cross( thisr, thisp );
1156 <        
1157 <      }  
1158 <      
1159 < #ifdef IS_MPI
1160 <      Vector3d tmpAngMom;
1161 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1162 < #endif
1163 <      
1164 <      return angularMomentum;
1165 <   }
1166 <  
1008 >  
1009    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1010 <    return IOIndexToIntegrableObject.at(index);
1010 >    if (index >= IOIndexToIntegrableObject.size()) {
1011 >      sprintf(painCave.errMsg,
1012 >              "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1013 >              "\tindex exceeds number of known objects!\n");
1014 >      painCave.isFatal = 1;
1015 >      simError();
1016 >      return NULL;
1017 >    } else
1018 >      return IOIndexToIntegrableObject.at(index);
1019    }
1020    
1021    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1022      IOIndexToIntegrableObject= v;
1023    }
1024  
1175 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1176 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1177 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1178 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1179 –  */
1180 –  void SimInfo::getGyrationalVolume(RealType &volume){
1181 –    Mat3x3d intTensor;
1182 –    RealType det;
1183 –    Vector3d dummyAngMom;
1184 –    RealType sysconstants;
1185 –    RealType geomCnst;
1186 –
1187 –    geomCnst = 3.0/2.0;
1188 –    /* Get the inertial tensor and angular momentum for free*/
1189 –    getInertiaTensor(intTensor,dummyAngMom);
1190 –    
1191 –    det = intTensor.determinant();
1192 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1193 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1194 –    return;
1195 –  }
1196 –
1197 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1198 –    Mat3x3d intTensor;
1199 –    Vector3d dummyAngMom;
1200 –    RealType sysconstants;
1201 –    RealType geomCnst;
1202 –
1203 –    geomCnst = 3.0/2.0;
1204 –    /* Get the inertial tensor and angular momentum for free*/
1205 –    getInertiaTensor(intTensor,dummyAngMom);
1206 –    
1207 –    detI = intTensor.determinant();
1208 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1209 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1210 –    return;
1211 –  }
1212 – /*
1213 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1214 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1215 –      sdByGlobalIndex_ = v;
1216 –    }
1217 –
1218 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1219 –      //assert(index < nAtoms_ + nRigidBodies_);
1220 –      return sdByGlobalIndex_.at(index);
1221 –    }  
1222 – */  
1025    int SimInfo::getNGlobalConstraints() {
1026      int nGlobalConstraints;
1027   #ifdef IS_MPI

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