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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC vs.
Revision 1779 by gezelter, Mon Aug 20 17:51:39 2012 UTC

# Line 88 | Line 88 | namespace OpenMD {
88      
89      vector<Component*> components = simParams->getComponents();
90      
91 <    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91 >    for (vector<Component*>::iterator i = components.begin();
92 >         i !=components.end(); ++i) {
93        molStamp = (*i)->getMoleculeStamp();
94        nMolWithSameStamp = (*i)->getNMol();
95        
# Line 231 | Line 232 | namespace OpenMD {
232      vector<Atom*>::iterator k;
233  
234      Molecule* mol;
235 <    StuntDouble* integrableObject;
235 >    StuntDouble* sd;
236      Atom* atom;
237  
238      ndf_local = 0;
239      nfq_local = 0;
240      
241      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242 –           integrableObject = mol->nextIntegrableObject(j)) {
242  
243 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
244 +           sd = mol->nextIntegrableObject(j)) {
245 +
246          ndf_local += 3;
247  
248 <        if (integrableObject->isDirectional()) {
249 <          if (integrableObject->isLinear()) {
248 >        if (sd->isDirectional()) {
249 >          if (sd->isLinear()) {
250              ndf_local += 2;
251            } else {
252              ndf_local += 3;
253            }
254          }
255        }
256 +
257        for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258             atom = mol->nextFluctuatingCharge(k)) {
259          if (atom->isFluctuatingCharge()) {
# Line 260 | Line 263 | namespace OpenMD {
263      }
264      
265      ndfLocal_ = ndf_local;
263 –    cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
266  
267      // n_constraints is local, so subtract them on each processor
268      ndf_local -= nConstraints_;
# Line 313 | 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)) {
322 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
323 –           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 385 | 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;
392 <         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 403 | 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 538 | Line 540 | namespace OpenMD {
540      Molecule::RigidBodyIterator rbIter;
541      RigidBody* rb;
542      Molecule::IntegrableObjectIterator ii;
543 <    StuntDouble* integrableObject;
544 <    
545 <    for (integrableObject = mol->beginIntegrableObject(ii);
546 <         integrableObject != NULL;
545 <         integrableObject = mol->nextIntegrableObject(ii)) {
543 >    StuntDouble* sd;
544 >    
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 556 | 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 781 | 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 791 | 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;
799 <    int usesFluctuatingCharges =  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();
# Line 802 | Line 804 | namespace OpenMD {
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_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
823 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
824 >                              MPI::LOR);
825   #else
826  
827      usesDirectionalAtoms_ = usesDirectional;
# Line 975 | 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  
993 –  Vector3d SimInfo::getComVel(){
994 –    SimInfo::MoleculeIterator i;
995 –    Molecule* mol;
1002  
997 –    Vector3d comVel(0.0);
998 –    RealType totalMass = 0.0;
999 –    
1000 –
1001 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1002 –      RealType mass = mol->getMass();
1003 –      totalMass += mass;
1004 –      comVel += mass * mol->getComVel();
1005 –    }  
1006 –
1007 – #ifdef IS_MPI
1008 –    RealType tmpMass = totalMass;
1009 –    Vector3d tmpComVel(comVel);    
1010 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1011 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1012 – #endif
1013 –
1014 –    comVel /= totalMass;
1015 –
1016 –    return comVel;
1017 –  }
1018 –
1019 –  Vector3d SimInfo::getCom(){
1020 –    SimInfo::MoleculeIterator i;
1021 –    Molecule* mol;
1022 –
1023 –    Vector3d com(0.0);
1024 –    RealType totalMass = 0.0;
1025 –    
1026 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1027 –      RealType mass = mol->getMass();
1028 –      totalMass += mass;
1029 –      com += mass * mol->getCom();
1030 –    }  
1031 –
1032 – #ifdef IS_MPI
1033 –    RealType tmpMass = totalMass;
1034 –    Vector3d tmpCom(com);    
1035 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1036 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1037 – #endif
1038 –
1039 –    com /= totalMass;
1040 –
1041 –    return com;
1042 –
1043 –  }        
1044 –
1003    ostream& operator <<(ostream& o, SimInfo& info) {
1004  
1005      return o;
1006    }
1049 –  
1050 –  
1051 –   /*
1052 –   Returns center of mass and center of mass velocity in one function call.
1053 –   */
1054 –  
1055 –   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1056 –      SimInfo::MoleculeIterator i;
1057 –      Molecule* mol;
1058 –      
1059 –    
1060 –      RealType totalMass = 0.0;
1061 –    
1062 –
1063 –      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1064 –         RealType mass = mol->getMass();
1065 –         totalMass += mass;
1066 –         com += mass * mol->getCom();
1067 –         comVel += mass * mol->getComVel();          
1068 –      }  
1069 –      
1070 – #ifdef IS_MPI
1071 –      RealType tmpMass = totalMass;
1072 –      Vector3d tmpCom(com);  
1073 –      Vector3d tmpComVel(comVel);
1074 –      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1075 –      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1076 –      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1077 – #endif
1078 –      
1079 –      com /= totalMass;
1080 –      comVel /= totalMass;
1081 –   }        
1007    
1008 <   /*
1084 <   Return intertia tensor for entire system and angular momentum Vector.
1085 <
1086 <
1087 <       [  Ixx -Ixy  -Ixz ]
1088 <    J =| -Iyx  Iyy  -Iyz |
1089 <       [ -Izx -Iyz   Izz ]
1090 <    */
1091 <
1092 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1093 <      
1094 <
1095 <      RealType xx = 0.0;
1096 <      RealType yy = 0.0;
1097 <      RealType zz = 0.0;
1098 <      RealType xy = 0.0;
1099 <      RealType xz = 0.0;
1100 <      RealType yz = 0.0;
1101 <      Vector3d com(0.0);
1102 <      Vector3d comVel(0.0);
1103 <      
1104 <      getComAll(com, comVel);
1105 <      
1106 <      SimInfo::MoleculeIterator i;
1107 <      Molecule* mol;
1108 <      
1109 <      Vector3d thisq(0.0);
1110 <      Vector3d thisv(0.0);
1111 <
1112 <      RealType thisMass = 0.0;
1113 <    
1114 <      
1115 <      
1116 <  
1117 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1118 <        
1119 <         thisq = mol->getCom()-com;
1120 <         thisv = mol->getComVel()-comVel;
1121 <         thisMass = mol->getMass();
1122 <         // Compute moment of intertia coefficients.
1123 <         xx += thisq[0]*thisq[0]*thisMass;
1124 <         yy += thisq[1]*thisq[1]*thisMass;
1125 <         zz += thisq[2]*thisq[2]*thisMass;
1126 <        
1127 <         // compute products of intertia
1128 <         xy += thisq[0]*thisq[1]*thisMass;
1129 <         xz += thisq[0]*thisq[2]*thisMass;
1130 <         yz += thisq[1]*thisq[2]*thisMass;
1131 <            
1132 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1133 <            
1134 <      }  
1135 <      
1136 <      
1137 <      inertiaTensor(0,0) = yy + zz;
1138 <      inertiaTensor(0,1) = -xy;
1139 <      inertiaTensor(0,2) = -xz;
1140 <      inertiaTensor(1,0) = -xy;
1141 <      inertiaTensor(1,1) = xx + zz;
1142 <      inertiaTensor(1,2) = -yz;
1143 <      inertiaTensor(2,0) = -xz;
1144 <      inertiaTensor(2,1) = -yz;
1145 <      inertiaTensor(2,2) = xx + yy;
1146 <      
1147 < #ifdef IS_MPI
1148 <      Mat3x3d tmpI(inertiaTensor);
1149 <      Vector3d tmpAngMom;
1150 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1152 < #endif
1153 <              
1154 <      return;
1155 <   }
1156 <
1157 <   //Returns the angular momentum of the system
1158 <   Vector3d SimInfo::getAngularMomentum(){
1159 <      
1160 <      Vector3d com(0.0);
1161 <      Vector3d comVel(0.0);
1162 <      Vector3d angularMomentum(0.0);
1163 <      
1164 <      getComAll(com,comVel);
1165 <      
1166 <      SimInfo::MoleculeIterator i;
1167 <      Molecule* mol;
1168 <      
1169 <      Vector3d thisr(0.0);
1170 <      Vector3d thisp(0.0);
1171 <      
1172 <      RealType thisMass;
1173 <      
1174 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1175 <        thisMass = mol->getMass();
1176 <        thisr = mol->getCom()-com;
1177 <        thisp = (mol->getComVel()-comVel)*thisMass;
1178 <        
1179 <        angularMomentum += cross( thisr, thisp );
1180 <        
1181 <      }  
1182 <      
1183 < #ifdef IS_MPI
1184 <      Vector3d tmpAngMom;
1185 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1186 < #endif
1187 <      
1188 <      return angularMomentum;
1189 <   }
1190 <  
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  
1199 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1200 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1201 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1202 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1203 –  */
1204 –  void SimInfo::getGyrationalVolume(RealType &volume){
1205 –    Mat3x3d intTensor;
1206 –    RealType det;
1207 –    Vector3d dummyAngMom;
1208 –    RealType sysconstants;
1209 –    RealType geomCnst;
1210 –
1211 –    geomCnst = 3.0/2.0;
1212 –    /* Get the inertial tensor and angular momentum for free*/
1213 –    getInertiaTensor(intTensor,dummyAngMom);
1214 –    
1215 –    det = intTensor.determinant();
1216 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1218 –    return;
1219 –  }
1220 –
1221 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1222 –    Mat3x3d intTensor;
1223 –    Vector3d dummyAngMom;
1224 –    RealType sysconstants;
1225 –    RealType geomCnst;
1226 –
1227 –    geomCnst = 3.0/2.0;
1228 –    /* Get the inertial tensor and angular momentum for free*/
1229 –    getInertiaTensor(intTensor,dummyAngMom);
1230 –    
1231 –    detI = intTensor.determinant();
1232 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1234 –    return;
1235 –  }
1236 – /*
1237 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1238 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1239 –      sdByGlobalIndex_ = v;
1240 –    }
1241 –
1242 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1243 –      //assert(index < nAtoms_ + nRigidBodies_);
1244 –      return sdByGlobalIndex_.at(index);
1245 –    }  
1246 – */  
1025    int SimInfo::getNGlobalConstraints() {
1026      int nGlobalConstraints;
1027   #ifdef IS_MPI

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