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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 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

# Line 231 | Line 231 | namespace OpenMD {
231      vector<Atom*>::iterator k;
232  
233      Molecule* mol;
234 <    StuntDouble* integrableObject;
234 >    StuntDouble* sd;
235      Atom* atom;
236  
237      ndf_local = 0;
238      nfq_local = 0;
239      
240      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242 –           integrableObject = mol->nextIntegrableObject(j)) {
241  
242 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
243 +           sd = mol->nextIntegrableObject(j)) {
244 +
245          ndf_local += 3;
246  
247 <        if (integrableObject->isDirectional()) {
248 <          if (integrableObject->isLinear()) {
247 >        if (sd->isDirectional()) {
248 >          if (sd->isLinear()) {
249              ndf_local += 2;
250            } else {
251              ndf_local += 3;
252            }
253          }
254        }
255 +
256        for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
257             atom = mol->nextFluctuatingCharge(k)) {
258          if (atom->isFluctuatingCharge()) {
# Line 312 | Line 314 | namespace OpenMD {
314      MoleculeIterator i;
315      vector<StuntDouble*>::iterator j;
316      Molecule* mol;
317 <    StuntDouble* integrableObject;
317 >    StuntDouble* sd;
318  
319      // Raw degrees of freedom that we have to set
320      ndfRaw_local = 0;
321      
322      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
321 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
322 –           integrableObject = mol->nextIntegrableObject(j)) {
323  
324 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
325 +           sd = mol->nextIntegrableObject(j)) {
326 +
327          ndfRaw_local += 3;
328  
329 <        if (integrableObject->isDirectional()) {
330 <          if (integrableObject->isLinear()) {
329 >        if (sd->isDirectional()) {
330 >          if (sd->isLinear()) {
331              ndfRaw_local += 2;
332            } else {
333              ndfRaw_local += 3;
# Line 384 | Line 387 | namespace OpenMD {
387      Molecule::RigidBodyIterator rbIter;
388      RigidBody* rb;
389      Molecule::IntegrableObjectIterator ii;
390 <    StuntDouble* integrableObject;
390 >    StuntDouble* sd;
391      
392 <    for (integrableObject = mol->beginIntegrableObject(ii);
393 <         integrableObject != NULL;
391 <         integrableObject = mol->nextIntegrableObject(ii)) {
392 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
393 >         sd = mol->nextIntegrableObject(ii)) {
394        
395 <      if (integrableObject->isRigidBody()) {
396 <        rb = static_cast<RigidBody*>(integrableObject);
395 >      if (sd->isRigidBody()) {
396 >        rb = static_cast<RigidBody*>(sd);
397          vector<Atom*> atoms = rb->getAtoms();
398          set<int> rigidAtoms;
399          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 402 | Line 404 | namespace OpenMD {
404          }      
405        } else {
406          set<int> oneAtomSet;
407 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
408 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
407 >        oneAtomSet.insert(sd->getGlobalIndex());
408 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
409        }
410      }  
411            
# Line 537 | Line 539 | namespace OpenMD {
539      Molecule::RigidBodyIterator rbIter;
540      RigidBody* rb;
541      Molecule::IntegrableObjectIterator ii;
542 <    StuntDouble* integrableObject;
542 >    StuntDouble* sd;
543      
544 <    for (integrableObject = mol->beginIntegrableObject(ii);
545 <         integrableObject != NULL;
544 <         integrableObject = mol->nextIntegrableObject(ii)) {
544 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
545 >         sd = mol->nextIntegrableObject(ii)) {
546        
547 <      if (integrableObject->isRigidBody()) {
548 <        rb = static_cast<RigidBody*>(integrableObject);
547 >      if (sd->isRigidBody()) {
548 >        rb = static_cast<RigidBody*>(sd);
549          vector<Atom*> atoms = rb->getAtoms();
550          set<int> rigidAtoms;
551          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 555 | Line 556 | namespace OpenMD {
556          }      
557        } else {
558          set<int> oneAtomSet;
559 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
560 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
559 >        oneAtomSet.insert(sd->getGlobalIndex());
560 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
561        }
562      }  
563  
# Line 790 | Line 791 | namespace OpenMD {
791      set<AtomType*>::iterator i;
792      set<AtomType*> atomTypes;
793      atomTypes = getSimulatedAtomTypes();    
794 <    int usesElectrostatic = 0;
795 <    int usesMetallic = 0;
796 <    int usesDirectional = 0;
797 <    int usesFluctuatingCharges =  0;
794 >    bool usesElectrostatic = false;
795 >    bool usesMetallic = false;
796 >    bool usesDirectional = false;
797 >    bool usesFluctuatingCharges =  false;
798      //loop over all of the atom types
799      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800        usesElectrostatic |= (*i)->isElectrostatic();
# Line 801 | Line 802 | namespace OpenMD {
802        usesDirectional |= (*i)->isDirectional();
803        usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804      }
805 <    
806 < #ifdef IS_MPI    
807 <    int temp;
805 >
806 > #ifdef IS_MPI
807 >    bool temp;
808      temp = usesDirectional;
809 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
810 <    
809 >    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
810 >                              MPI::LOR);
811 >        
812      temp = usesMetallic;
813 <    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
813 >    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
814 >                              MPI::LOR);
815      
816      temp = usesElectrostatic;
817 <    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817 >    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
818 >                              MPI::LOR);
819  
820      temp = usesFluctuatingCharges;
821 <    MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
822 >                              MPI::LOR);
823   #else
824  
825      usesDirectionalAtoms_ = usesDirectional;
# Line 989 | Line 994 | namespace OpenMD {
994      
995    }
996  
992 –  Vector3d SimInfo::getComVel(){
993 –    SimInfo::MoleculeIterator i;
994 –    Molecule* mol;
997  
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 –
998    ostream& operator <<(ostream& o, SimInfo& info) {
999  
1000      return o;
1001    }
1002    
1003 <  
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 <  
1003 >  
1004    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005      return IOIndexToIntegrableObject.at(index);
1006    }
# Line 1194 | Line 1008 | namespace OpenMD {
1008    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009      IOIndexToIntegrableObject= v;
1010    }
1197 –
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 –  }
1011   /*
1012     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013        assert( v.size() == nAtoms_ + nRigidBodies_);

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