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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1750 by gezelter, Thu Jun 7 12:53:46 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 312 | 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)) {
321 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
322 –           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 384 | 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;
391 <         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 402 | 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 537 | 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;
544 <         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 555 | 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 780 | 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 790 | 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 801 | 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 974 | 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  
992 –  Vector3d SimInfo::getComVel(){
993 –    SimInfo::MoleculeIterator i;
994 –    Molecule* mol;
1002  
996 –    Vector3d comVel(0.0);
997 –    RealType totalMass = 0.0;
998 –    
999 –
1000 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1001 –      RealType mass = mol->getMass();
1002 –      totalMass += mass;
1003 –      comVel += mass * mol->getComVel();
1004 –    }  
1005 –
1006 – #ifdef IS_MPI
1007 –    RealType tmpMass = totalMass;
1008 –    Vector3d tmpComVel(comVel);    
1009 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1010 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1011 – #endif
1012 –
1013 –    comVel /= totalMass;
1014 –
1015 –    return comVel;
1016 –  }
1017 –
1018 –  Vector3d SimInfo::getCom(){
1019 –    SimInfo::MoleculeIterator i;
1020 –    Molecule* mol;
1021 –
1022 –    Vector3d com(0.0);
1023 –    RealType totalMass = 0.0;
1024 –    
1025 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1026 –      RealType mass = mol->getMass();
1027 –      totalMass += mass;
1028 –      com += mass * mol->getCom();
1029 –    }  
1030 –
1031 – #ifdef IS_MPI
1032 –    RealType tmpMass = totalMass;
1033 –    Vector3d tmpCom(com);    
1034 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1035 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1036 – #endif
1037 –
1038 –    com /= totalMass;
1039 –
1040 –    return com;
1041 –
1042 –  }        
1043 –
1003    ostream& operator <<(ostream& o, SimInfo& info) {
1004  
1005      return o;
1006    }
1007    
1008 <  
1050 <   /*
1051 <   Returns center of mass and center of mass velocity in one function call.
1052 <   */
1053 <  
1054 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1055 <      SimInfo::MoleculeIterator i;
1056 <      Molecule* mol;
1057 <      
1058 <    
1059 <      RealType totalMass = 0.0;
1060 <    
1061 <
1062 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1063 <         RealType mass = mol->getMass();
1064 <         totalMass += mass;
1065 <         com += mass * mol->getCom();
1066 <         comVel += mass * mol->getComVel();          
1067 <      }  
1068 <      
1069 < #ifdef IS_MPI
1070 <      RealType tmpMass = totalMass;
1071 <      Vector3d tmpCom(com);  
1072 <      Vector3d tmpComVel(comVel);
1073 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1075 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1076 < #endif
1077 <      
1078 <      com /= totalMass;
1079 <      comVel /= totalMass;
1080 <   }        
1081 <  
1082 <   /*
1083 <   Return intertia tensor for entire system and angular momentum Vector.
1084 <
1085 <
1086 <       [  Ixx -Ixy  -Ixz ]
1087 <    J =| -Iyx  Iyy  -Iyz |
1088 <       [ -Izx -Iyz   Izz ]
1089 <    */
1090 <
1091 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1092 <      
1093 <
1094 <      RealType xx = 0.0;
1095 <      RealType yy = 0.0;
1096 <      RealType zz = 0.0;
1097 <      RealType xy = 0.0;
1098 <      RealType xz = 0.0;
1099 <      RealType yz = 0.0;
1100 <      Vector3d com(0.0);
1101 <      Vector3d comVel(0.0);
1102 <      
1103 <      getComAll(com, comVel);
1104 <      
1105 <      SimInfo::MoleculeIterator i;
1106 <      Molecule* mol;
1107 <      
1108 <      Vector3d thisq(0.0);
1109 <      Vector3d thisv(0.0);
1110 <
1111 <      RealType thisMass = 0.0;
1112 <    
1113 <      
1114 <      
1115 <  
1116 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1117 <        
1118 <         thisq = mol->getCom()-com;
1119 <         thisv = mol->getComVel()-comVel;
1120 <         thisMass = mol->getMass();
1121 <         // Compute moment of intertia coefficients.
1122 <         xx += thisq[0]*thisq[0]*thisMass;
1123 <         yy += thisq[1]*thisq[1]*thisMass;
1124 <         zz += thisq[2]*thisq[2]*thisMass;
1125 <        
1126 <         // compute products of intertia
1127 <         xy += thisq[0]*thisq[1]*thisMass;
1128 <         xz += thisq[0]*thisq[2]*thisMass;
1129 <         yz += thisq[1]*thisq[2]*thisMass;
1130 <            
1131 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1132 <            
1133 <      }  
1134 <      
1135 <      
1136 <      inertiaTensor(0,0) = yy + zz;
1137 <      inertiaTensor(0,1) = -xy;
1138 <      inertiaTensor(0,2) = -xz;
1139 <      inertiaTensor(1,0) = -xy;
1140 <      inertiaTensor(1,1) = xx + zz;
1141 <      inertiaTensor(1,2) = -yz;
1142 <      inertiaTensor(2,0) = -xz;
1143 <      inertiaTensor(2,1) = -yz;
1144 <      inertiaTensor(2,2) = xx + yy;
1145 <      
1146 < #ifdef IS_MPI
1147 <      Mat3x3d tmpI(inertiaTensor);
1148 <      Vector3d tmpAngMom;
1149 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151 < #endif
1152 <              
1153 <      return;
1154 <   }
1155 <
1156 <   //Returns the angular momentum of the system
1157 <   Vector3d SimInfo::getAngularMomentum(){
1158 <      
1159 <      Vector3d com(0.0);
1160 <      Vector3d comVel(0.0);
1161 <      Vector3d angularMomentum(0.0);
1162 <      
1163 <      getComAll(com,comVel);
1164 <      
1165 <      SimInfo::MoleculeIterator i;
1166 <      Molecule* mol;
1167 <      
1168 <      Vector3d thisr(0.0);
1169 <      Vector3d thisp(0.0);
1170 <      
1171 <      RealType thisMass;
1172 <      
1173 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1174 <        thisMass = mol->getMass();
1175 <        thisr = mol->getCom()-com;
1176 <        thisp = (mol->getComVel()-comVel)*thisMass;
1177 <        
1178 <        angularMomentum += cross( thisr, thisp );
1179 <        
1180 <      }  
1181 <      
1182 < #ifdef IS_MPI
1183 <      Vector3d tmpAngMom;
1184 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1185 < #endif
1186 <      
1187 <      return angularMomentum;
1188 <   }
1189 <  
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  
1198 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1199 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1200 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1201 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1202 –  */
1203 –  void SimInfo::getGyrationalVolume(RealType &volume){
1204 –    Mat3x3d intTensor;
1205 –    RealType det;
1206 –    Vector3d dummyAngMom;
1207 –    RealType sysconstants;
1208 –    RealType geomCnst;
1209 –
1210 –    geomCnst = 3.0/2.0;
1211 –    /* Get the inertial tensor and angular momentum for free*/
1212 –    getInertiaTensor(intTensor,dummyAngMom);
1213 –    
1214 –    det = intTensor.determinant();
1215 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1216 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1217 –    return;
1218 –  }
1219 –
1220 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1221 –    Mat3x3d intTensor;
1222 –    Vector3d dummyAngMom;
1223 –    RealType sysconstants;
1224 –    RealType geomCnst;
1225 –
1226 –    geomCnst = 3.0/2.0;
1227 –    /* Get the inertial tensor and angular momentum for free*/
1228 –    getInertiaTensor(intTensor,dummyAngMom);
1229 –    
1230 –    detI = intTensor.determinant();
1231 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1232 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1233 –    return;
1234 –  }
1235 – /*
1236 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1237 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1238 –      sdByGlobalIndex_ = v;
1239 –    }
1240 –
1241 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1242 –      //assert(index < nAtoms_ + nRigidBodies_);
1243 –      return sdByGlobalIndex_.at(index);
1244 –    }  
1245 – */  
1025    int SimInfo::getNGlobalConstraints() {
1026      int nGlobalConstraints;
1027   #ifdef IS_MPI

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