ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/SimInfo.cpp
(Generate patch)

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1725 by gezelter, Sat May 26 18:13:43 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 259 | Line 261 | namespace OpenMD {
261        }
262      }
263      
264 +    ndfLocal_ = ndf_local;
265 +
266      // n_constraints is local, so subtract them on each processor
267      ndf_local -= nConstraints_;
268  
# Line 310 | 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)) {
319 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
320 –           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 382 | 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;
389 <         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 400 | 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 535 | 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;
542 <         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 553 | 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 788 | 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 799 | 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 987 | Line 994 | namespace OpenMD {
994      
995    }
996  
990 –  Vector3d SimInfo::getComVel(){
991 –    SimInfo::MoleculeIterator i;
992 –    Molecule* mol;
997  
994 –    Vector3d comVel(0.0);
995 –    RealType totalMass = 0.0;
996 –    
997 –
998 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
999 –      RealType mass = mol->getMass();
1000 –      totalMass += mass;
1001 –      comVel += mass * mol->getComVel();
1002 –    }  
1003 –
1004 – #ifdef IS_MPI
1005 –    RealType tmpMass = totalMass;
1006 –    Vector3d tmpComVel(comVel);    
1007 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1008 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1009 – #endif
1010 –
1011 –    comVel /= totalMass;
1012 –
1013 –    return comVel;
1014 –  }
1015 –
1016 –  Vector3d SimInfo::getCom(){
1017 –    SimInfo::MoleculeIterator i;
1018 –    Molecule* mol;
1019 –
1020 –    Vector3d com(0.0);
1021 –    RealType totalMass = 0.0;
1022 –    
1023 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1024 –      RealType mass = mol->getMass();
1025 –      totalMass += mass;
1026 –      com += mass * mol->getCom();
1027 –    }  
1028 –
1029 – #ifdef IS_MPI
1030 –    RealType tmpMass = totalMass;
1031 –    Vector3d tmpCom(com);    
1032 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034 – #endif
1035 –
1036 –    com /= totalMass;
1037 –
1038 –    return com;
1039 –
1040 –  }        
1041 –
998    ostream& operator <<(ostream& o, SimInfo& info) {
999  
1000      return o;
1001    }
1002    
1003 <  
1048 <   /*
1049 <   Returns center of mass and center of mass velocity in one function call.
1050 <   */
1051 <  
1052 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1053 <      SimInfo::MoleculeIterator i;
1054 <      Molecule* mol;
1055 <      
1056 <    
1057 <      RealType totalMass = 0.0;
1058 <    
1059 <
1060 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061 <         RealType mass = mol->getMass();
1062 <         totalMass += mass;
1063 <         com += mass * mol->getCom();
1064 <         comVel += mass * mol->getComVel();          
1065 <      }  
1066 <      
1067 < #ifdef IS_MPI
1068 <      RealType tmpMass = totalMass;
1069 <      Vector3d tmpCom(com);  
1070 <      Vector3d tmpComVel(comVel);
1071 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1072 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1073 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074 < #endif
1075 <      
1076 <      com /= totalMass;
1077 <      comVel /= totalMass;
1078 <   }        
1079 <  
1080 <   /*
1081 <   Return intertia tensor for entire system and angular momentum Vector.
1082 <
1083 <
1084 <       [  Ixx -Ixy  -Ixz ]
1085 <    J =| -Iyx  Iyy  -Iyz |
1086 <       [ -Izx -Iyz   Izz ]
1087 <    */
1088 <
1089 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1090 <      
1091 <
1092 <      RealType xx = 0.0;
1093 <      RealType yy = 0.0;
1094 <      RealType zz = 0.0;
1095 <      RealType xy = 0.0;
1096 <      RealType xz = 0.0;
1097 <      RealType yz = 0.0;
1098 <      Vector3d com(0.0);
1099 <      Vector3d comVel(0.0);
1100 <      
1101 <      getComAll(com, comVel);
1102 <      
1103 <      SimInfo::MoleculeIterator i;
1104 <      Molecule* mol;
1105 <      
1106 <      Vector3d thisq(0.0);
1107 <      Vector3d thisv(0.0);
1108 <
1109 <      RealType thisMass = 0.0;
1110 <    
1111 <      
1112 <      
1113 <  
1114 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1115 <        
1116 <         thisq = mol->getCom()-com;
1117 <         thisv = mol->getComVel()-comVel;
1118 <         thisMass = mol->getMass();
1119 <         // Compute moment of intertia coefficients.
1120 <         xx += thisq[0]*thisq[0]*thisMass;
1121 <         yy += thisq[1]*thisq[1]*thisMass;
1122 <         zz += thisq[2]*thisq[2]*thisMass;
1123 <        
1124 <         // compute products of intertia
1125 <         xy += thisq[0]*thisq[1]*thisMass;
1126 <         xz += thisq[0]*thisq[2]*thisMass;
1127 <         yz += thisq[1]*thisq[2]*thisMass;
1128 <            
1129 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1130 <            
1131 <      }  
1132 <      
1133 <      
1134 <      inertiaTensor(0,0) = yy + zz;
1135 <      inertiaTensor(0,1) = -xy;
1136 <      inertiaTensor(0,2) = -xz;
1137 <      inertiaTensor(1,0) = -xy;
1138 <      inertiaTensor(1,1) = xx + zz;
1139 <      inertiaTensor(1,2) = -yz;
1140 <      inertiaTensor(2,0) = -xz;
1141 <      inertiaTensor(2,1) = -yz;
1142 <      inertiaTensor(2,2) = xx + yy;
1143 <      
1144 < #ifdef IS_MPI
1145 <      Mat3x3d tmpI(inertiaTensor);
1146 <      Vector3d tmpAngMom;
1147 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1148 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149 < #endif
1150 <              
1151 <      return;
1152 <   }
1153 <
1154 <   //Returns the angular momentum of the system
1155 <   Vector3d SimInfo::getAngularMomentum(){
1156 <      
1157 <      Vector3d com(0.0);
1158 <      Vector3d comVel(0.0);
1159 <      Vector3d angularMomentum(0.0);
1160 <      
1161 <      getComAll(com,comVel);
1162 <      
1163 <      SimInfo::MoleculeIterator i;
1164 <      Molecule* mol;
1165 <      
1166 <      Vector3d thisr(0.0);
1167 <      Vector3d thisp(0.0);
1168 <      
1169 <      RealType thisMass;
1170 <      
1171 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1172 <        thisMass = mol->getMass();
1173 <        thisr = mol->getCom()-com;
1174 <        thisp = (mol->getComVel()-comVel)*thisMass;
1175 <        
1176 <        angularMomentum += cross( thisr, thisp );
1177 <        
1178 <      }  
1179 <      
1180 < #ifdef IS_MPI
1181 <      Vector3d tmpAngMom;
1182 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1183 < #endif
1184 <      
1185 <      return angularMomentum;
1186 <   }
1187 <  
1003 >  
1004    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005      return IOIndexToIntegrableObject.at(index);
1006    }
# Line 1192 | Line 1008 | namespace OpenMD {
1008    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009      IOIndexToIntegrableObject= v;
1010    }
1195 –
1196 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1197 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1198 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1199 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1200 –  */
1201 –  void SimInfo::getGyrationalVolume(RealType &volume){
1202 –    Mat3x3d intTensor;
1203 –    RealType det;
1204 –    Vector3d dummyAngMom;
1205 –    RealType sysconstants;
1206 –    RealType geomCnst;
1207 –
1208 –    geomCnst = 3.0/2.0;
1209 –    /* Get the inertial tensor and angular momentum for free*/
1210 –    getInertiaTensor(intTensor,dummyAngMom);
1211 –    
1212 –    det = intTensor.determinant();
1213 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1215 –    return;
1216 –  }
1217 –
1218 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1219 –    Mat3x3d intTensor;
1220 –    Vector3d dummyAngMom;
1221 –    RealType sysconstants;
1222 –    RealType geomCnst;
1223 –
1224 –    geomCnst = 3.0/2.0;
1225 –    /* Get the inertial tensor and angular momentum for free*/
1226 –    getInertiaTensor(intTensor,dummyAngMom);
1227 –    
1228 –    detI = intTensor.determinant();
1229 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1231 –    return;
1232 –  }
1011   /*
1012     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013        assert( v.size() == nAtoms_ + nRigidBodies_);

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines