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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 1767 by gezelter, Fri Jul 6 22:01:58 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;
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;
# Line 246 | Line 250 | namespace OpenMD {
250              ndf_local += 3;
251            }
252          }
253 <            
253 >      }
254 >      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255 >           atom = mol->nextFluctuatingCharge(k)) {
256 >        if (atom->isFluctuatingCharge()) {
257 >          nfq_local++;
258 >        }
259        }
260      }
261      
262 +    ndfLocal_ = ndf_local;
263 +
264      // n_constraints is local, so subtract them on each processor
265      ndf_local -= nConstraints_;
266  
267   #ifdef IS_MPI
268      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270   #else
271      ndf_ = ndf_local;
272 +    nGlobalFluctuatingCharges_ = nfq_local;
273   #endif
274  
275      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 777 | Line 790 | namespace OpenMD {
790      set<AtomType*>::iterator i;
791      set<AtomType*> atomTypes;
792      atomTypes = getSimulatedAtomTypes();    
793 <    int usesElectrostatic = 0;
794 <    int usesMetallic = 0;
795 <    int usesDirectional = 0;
793 >    bool usesElectrostatic = false;
794 >    bool usesMetallic = false;
795 >    bool usesDirectional = false;
796 >    bool usesFluctuatingCharges =  false;
797      //loop over all of the atom types
798      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799        usesElectrostatic |= (*i)->isElectrostatic();
800        usesMetallic |= (*i)->isMetal();
801        usesDirectional |= (*i)->isDirectional();
802 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
803      }
804 <    
805 < #ifdef IS_MPI    
806 <    int temp;
807 <    temp = usesDirectional;
808 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
809 <    
804 >
805 > #ifdef IS_MPI
806 >    bool temp;
807 >    temp = usesDirectional;
808 >    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
809 >                              MPI::LOR);
810 >        
811      temp = usesMetallic;
812 <    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
812 >    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
813 >                              MPI::LOR);
814      
815      temp = usesElectrostatic;
816 <    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816 >    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
817 >                              MPI::LOR);
818 >
819 >    temp = usesFluctuatingCharges;
820 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
821 >                              MPI::LOR);
822   #else
823  
824      usesDirectionalAtoms_ = usesDirectional;
825      usesMetallicAtoms_ = usesMetallic;
826      usesElectrostaticAtoms_ = usesElectrostatic;
827 +    usesFluctuatingCharges_ = usesFluctuatingCharges;
828  
829   #endif
830      
# Line 968 | Line 991 | namespace OpenMD {
991        }
992      }    
993      
971 –  }
972 –
973 –  Vector3d SimInfo::getComVel(){
974 –    SimInfo::MoleculeIterator i;
975 –    Molecule* mol;
976 –
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;
994    }
995  
999 –  Vector3d SimInfo::getCom(){
1000 –    SimInfo::MoleculeIterator i;
1001 –    Molecule* mol;
996  
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 –
997    ostream& operator <<(ostream& o, SimInfo& info) {
998  
999      return o;
1000    }
1001    
1002 <  
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 <  
1002 >  
1003    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1004      return IOIndexToIntegrableObject.at(index);
1005    }
# Line 1175 | Line 1007 | namespace OpenMD {
1007    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1008      IOIndexToIntegrableObject= v;
1009    }
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 –  }
1010   /*
1011     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1012        assert( v.size() == nAtoms_ + nRigidBodies_);

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