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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1668 by gezelter, Fri Jan 6 19:03:05 2012 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

# Line 59 | 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>
# Line 72 | 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 225 | Line 225 | namespace OpenMD {
225  
226  
227    void SimInfo::calcNdf() {
228 <    int ndf_local;
228 >    int ndf_local, nfq_local;
229      MoleculeIterator i;
230      vector<StuntDouble*>::iterator j;
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)) {
237 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
238 –           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          }
249 –            
254        }
255 +
256 +      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
257 +           atom = mol->nextFluctuatingCharge(k)) {
258 +        if (atom->isFluctuatingCharge()) {
259 +          nfq_local++;
260 +        }
261 +      }
262      }
263      
264 +    ndfLocal_ = ndf_local;
265 +
266      // n_constraints is local, so subtract them on each processor
267      ndf_local -= nConstraints_;
268  
269   #ifdef IS_MPI
270      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
272   #else
273      ndf_ = ndf_local;
274 +    nGlobalFluctuatingCharges_ = nfq_local;
275   #endif
276  
277      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 299 | 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)) {
308 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309 –           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 371 | 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;
378 <         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 389 | 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 524 | 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;
531 <         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 542 | 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 777 | 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;
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();
801        usesMetallic |= (*i)->isMetal();
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::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
822 >                              MPI::LOR);
823   #else
824  
825      usesDirectionalAtoms_ = usesDirectional;
826      usesMetallicAtoms_ = usesMetallic;
827      usesElectrostaticAtoms_ = usesElectrostatic;
828 +    usesFluctuatingCharges_ = usesFluctuatingCharges;
829  
830   #endif
831      
# Line 970 | Line 994 | namespace OpenMD {
994      
995    }
996  
973 –  Vector3d SimInfo::getComVel(){
974 –    SimInfo::MoleculeIterator i;
975 –    Molecule* mol;
997  
977 –    Vector3d comVel(0.0);
978 –    RealType totalMass = 0.0;
979 –    
980 –
981 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
982 –      RealType mass = mol->getMass();
983 –      totalMass += mass;
984 –      comVel += mass * mol->getComVel();
985 –    }  
986 –
987 – #ifdef IS_MPI
988 –    RealType tmpMass = totalMass;
989 –    Vector3d tmpComVel(comVel);    
990 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
992 – #endif
993 –
994 –    comVel /= totalMass;
995 –
996 –    return comVel;
997 –  }
998 –
999 –  Vector3d SimInfo::getCom(){
1000 –    SimInfo::MoleculeIterator i;
1001 –    Molecule* mol;
1002 –
1003 –    Vector3d com(0.0);
1004 –    RealType totalMass = 0.0;
1005 –    
1006 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1007 –      RealType mass = mol->getMass();
1008 –      totalMass += mass;
1009 –      com += mass * mol->getCom();
1010 –    }  
1011 –
1012 – #ifdef IS_MPI
1013 –    RealType tmpMass = totalMass;
1014 –    Vector3d tmpCom(com);    
1015 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1017 – #endif
1018 –
1019 –    com /= totalMass;
1020 –
1021 –    return com;
1022 –
1023 –  }        
1024 –
998    ostream& operator <<(ostream& o, SimInfo& info) {
999  
1000      return o;
1001    }
1002    
1003 <  
1031 <   /*
1032 <   Returns center of mass and center of mass velocity in one function call.
1033 <   */
1034 <  
1035 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1036 <      SimInfo::MoleculeIterator i;
1037 <      Molecule* mol;
1038 <      
1039 <    
1040 <      RealType totalMass = 0.0;
1041 <    
1042 <
1043 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1044 <         RealType mass = mol->getMass();
1045 <         totalMass += mass;
1046 <         com += mass * mol->getCom();
1047 <         comVel += mass * mol->getComVel();          
1048 <      }  
1049 <      
1050 < #ifdef IS_MPI
1051 <      RealType tmpMass = totalMass;
1052 <      Vector3d tmpCom(com);  
1053 <      Vector3d tmpComVel(comVel);
1054 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1057 < #endif
1058 <      
1059 <      com /= totalMass;
1060 <      comVel /= totalMass;
1061 <   }        
1062 <  
1063 <   /*
1064 <   Return intertia tensor for entire system and angular momentum Vector.
1065 <
1066 <
1067 <       [  Ixx -Ixy  -Ixz ]
1068 <    J =| -Iyx  Iyy  -Iyz |
1069 <       [ -Izx -Iyz   Izz ]
1070 <    */
1071 <
1072 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1073 <      
1074 <
1075 <      RealType xx = 0.0;
1076 <      RealType yy = 0.0;
1077 <      RealType zz = 0.0;
1078 <      RealType xy = 0.0;
1079 <      RealType xz = 0.0;
1080 <      RealType yz = 0.0;
1081 <      Vector3d com(0.0);
1082 <      Vector3d comVel(0.0);
1083 <      
1084 <      getComAll(com, comVel);
1085 <      
1086 <      SimInfo::MoleculeIterator i;
1087 <      Molecule* mol;
1088 <      
1089 <      Vector3d thisq(0.0);
1090 <      Vector3d thisv(0.0);
1091 <
1092 <      RealType thisMass = 0.0;
1093 <    
1094 <      
1095 <      
1096 <  
1097 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1098 <        
1099 <         thisq = mol->getCom()-com;
1100 <         thisv = mol->getComVel()-comVel;
1101 <         thisMass = mol->getMass();
1102 <         // Compute moment of intertia coefficients.
1103 <         xx += thisq[0]*thisq[0]*thisMass;
1104 <         yy += thisq[1]*thisq[1]*thisMass;
1105 <         zz += thisq[2]*thisq[2]*thisMass;
1106 <        
1107 <         // compute products of intertia
1108 <         xy += thisq[0]*thisq[1]*thisMass;
1109 <         xz += thisq[0]*thisq[2]*thisMass;
1110 <         yz += thisq[1]*thisq[2]*thisMass;
1111 <            
1112 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1113 <            
1114 <      }  
1115 <      
1116 <      
1117 <      inertiaTensor(0,0) = yy + zz;
1118 <      inertiaTensor(0,1) = -xy;
1119 <      inertiaTensor(0,2) = -xz;
1120 <      inertiaTensor(1,0) = -xy;
1121 <      inertiaTensor(1,1) = xx + zz;
1122 <      inertiaTensor(1,2) = -yz;
1123 <      inertiaTensor(2,0) = -xz;
1124 <      inertiaTensor(2,1) = -yz;
1125 <      inertiaTensor(2,2) = xx + yy;
1126 <      
1127 < #ifdef IS_MPI
1128 <      Mat3x3d tmpI(inertiaTensor);
1129 <      Vector3d tmpAngMom;
1130 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1132 < #endif
1133 <              
1134 <      return;
1135 <   }
1136 <
1137 <   //Returns the angular momentum of the system
1138 <   Vector3d SimInfo::getAngularMomentum(){
1139 <      
1140 <      Vector3d com(0.0);
1141 <      Vector3d comVel(0.0);
1142 <      Vector3d angularMomentum(0.0);
1143 <      
1144 <      getComAll(com,comVel);
1145 <      
1146 <      SimInfo::MoleculeIterator i;
1147 <      Molecule* mol;
1148 <      
1149 <      Vector3d thisr(0.0);
1150 <      Vector3d thisp(0.0);
1151 <      
1152 <      RealType thisMass;
1153 <      
1154 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1155 <        thisMass = mol->getMass();
1156 <        thisr = mol->getCom()-com;
1157 <        thisp = (mol->getComVel()-comVel)*thisMass;
1158 <        
1159 <        angularMomentum += cross( thisr, thisp );
1160 <        
1161 <      }  
1162 <      
1163 < #ifdef IS_MPI
1164 <      Vector3d tmpAngMom;
1165 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1166 < #endif
1167 <      
1168 <      return angularMomentum;
1169 <   }
1170 <  
1003 >  
1004    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005      return IOIndexToIntegrableObject.at(index);
1006    }
# Line 1175 | Line 1008 | namespace OpenMD {
1008    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009      IOIndexToIntegrableObject= v;
1010    }
1178 –
1179 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1180 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1181 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1182 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1183 –  */
1184 –  void SimInfo::getGyrationalVolume(RealType &volume){
1185 –    Mat3x3d intTensor;
1186 –    RealType det;
1187 –    Vector3d dummyAngMom;
1188 –    RealType sysconstants;
1189 –    RealType geomCnst;
1190 –
1191 –    geomCnst = 3.0/2.0;
1192 –    /* Get the inertial tensor and angular momentum for free*/
1193 –    getInertiaTensor(intTensor,dummyAngMom);
1194 –    
1195 –    det = intTensor.determinant();
1196 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1197 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1198 –    return;
1199 –  }
1200 –
1201 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1202 –    Mat3x3d intTensor;
1203 –    Vector3d dummyAngMom;
1204 –    RealType sysconstants;
1205 –    RealType geomCnst;
1206 –
1207 –    geomCnst = 3.0/2.0;
1208 –    /* Get the inertial tensor and angular momentum for free*/
1209 –    getInertiaTensor(intTensor,dummyAngMom);
1210 –    
1211 –    detI = intTensor.determinant();
1212 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1213 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1214 –    return;
1215 –  }
1011   /*
1012     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013        assert( v.size() == nAtoms_ + nRigidBodies_);

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