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Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC vs.
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 58 | 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>
66 + #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 68 | 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 221 | 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 242 | 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 773 | 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;
804 >
805 > #ifdef IS_MPI
806 >    bool temp;
807      temp = usesDirectional;
808 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
809 <    
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 966 | Line 993 | namespace OpenMD {
993      
994    }
995  
969 –  Vector3d SimInfo::getComVel(){
970 –    SimInfo::MoleculeIterator i;
971 –    Molecule* mol;
996  
973 –    Vector3d comVel(0.0);
974 –    RealType totalMass = 0.0;
975 –    
976 –
977 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
978 –      RealType mass = mol->getMass();
979 –      totalMass += mass;
980 –      comVel += mass * mol->getComVel();
981 –    }  
982 –
983 – #ifdef IS_MPI
984 –    RealType tmpMass = totalMass;
985 –    Vector3d tmpComVel(comVel);    
986 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
987 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
988 – #endif
989 –
990 –    comVel /= totalMass;
991 –
992 –    return comVel;
993 –  }
994 –
995 –  Vector3d SimInfo::getCom(){
996 –    SimInfo::MoleculeIterator i;
997 –    Molecule* mol;
998 –
999 –    Vector3d com(0.0);
1000 –    RealType totalMass = 0.0;
1001 –    
1002 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1003 –      RealType mass = mol->getMass();
1004 –      totalMass += mass;
1005 –      com += mass * mol->getCom();
1006 –    }  
1007 –
1008 – #ifdef IS_MPI
1009 –    RealType tmpMass = totalMass;
1010 –    Vector3d tmpCom(com);    
1011 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1012 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1013 – #endif
1014 –
1015 –    com /= totalMass;
1016 –
1017 –    return com;
1018 –
1019 –  }        
1020 –
997    ostream& operator <<(ostream& o, SimInfo& info) {
998  
999      return o;
1000    }
1001    
1002 <  
1027 <   /*
1028 <   Returns center of mass and center of mass velocity in one function call.
1029 <   */
1030 <  
1031 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1032 <      SimInfo::MoleculeIterator i;
1033 <      Molecule* mol;
1034 <      
1035 <    
1036 <      RealType totalMass = 0.0;
1037 <    
1038 <
1039 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1040 <         RealType mass = mol->getMass();
1041 <         totalMass += mass;
1042 <         com += mass * mol->getCom();
1043 <         comVel += mass * mol->getComVel();          
1044 <      }  
1045 <      
1046 < #ifdef IS_MPI
1047 <      RealType tmpMass = totalMass;
1048 <      Vector3d tmpCom(com);  
1049 <      Vector3d tmpComVel(comVel);
1050 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1051 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1052 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1053 < #endif
1054 <      
1055 <      com /= totalMass;
1056 <      comVel /= totalMass;
1057 <   }        
1058 <  
1059 <   /*
1060 <   Return intertia tensor for entire system and angular momentum Vector.
1061 <
1062 <
1063 <       [  Ixx -Ixy  -Ixz ]
1064 <    J =| -Iyx  Iyy  -Iyz |
1065 <       [ -Izx -Iyz   Izz ]
1066 <    */
1067 <
1068 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1069 <      
1070 <
1071 <      RealType xx = 0.0;
1072 <      RealType yy = 0.0;
1073 <      RealType zz = 0.0;
1074 <      RealType xy = 0.0;
1075 <      RealType xz = 0.0;
1076 <      RealType yz = 0.0;
1077 <      Vector3d com(0.0);
1078 <      Vector3d comVel(0.0);
1079 <      
1080 <      getComAll(com, comVel);
1081 <      
1082 <      SimInfo::MoleculeIterator i;
1083 <      Molecule* mol;
1084 <      
1085 <      Vector3d thisq(0.0);
1086 <      Vector3d thisv(0.0);
1087 <
1088 <      RealType thisMass = 0.0;
1089 <    
1090 <      
1091 <      
1092 <  
1093 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1094 <        
1095 <         thisq = mol->getCom()-com;
1096 <         thisv = mol->getComVel()-comVel;
1097 <         thisMass = mol->getMass();
1098 <         // Compute moment of intertia coefficients.
1099 <         xx += thisq[0]*thisq[0]*thisMass;
1100 <         yy += thisq[1]*thisq[1]*thisMass;
1101 <         zz += thisq[2]*thisq[2]*thisMass;
1102 <        
1103 <         // compute products of intertia
1104 <         xy += thisq[0]*thisq[1]*thisMass;
1105 <         xz += thisq[0]*thisq[2]*thisMass;
1106 <         yz += thisq[1]*thisq[2]*thisMass;
1107 <            
1108 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1109 <            
1110 <      }  
1111 <      
1112 <      
1113 <      inertiaTensor(0,0) = yy + zz;
1114 <      inertiaTensor(0,1) = -xy;
1115 <      inertiaTensor(0,2) = -xz;
1116 <      inertiaTensor(1,0) = -xy;
1117 <      inertiaTensor(1,1) = xx + zz;
1118 <      inertiaTensor(1,2) = -yz;
1119 <      inertiaTensor(2,0) = -xz;
1120 <      inertiaTensor(2,1) = -yz;
1121 <      inertiaTensor(2,2) = xx + yy;
1122 <      
1123 < #ifdef IS_MPI
1124 <      Mat3x3d tmpI(inertiaTensor);
1125 <      Vector3d tmpAngMom;
1126 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1127 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1128 < #endif
1129 <              
1130 <      return;
1131 <   }
1132 <
1133 <   //Returns the angular momentum of the system
1134 <   Vector3d SimInfo::getAngularMomentum(){
1135 <      
1136 <      Vector3d com(0.0);
1137 <      Vector3d comVel(0.0);
1138 <      Vector3d angularMomentum(0.0);
1139 <      
1140 <      getComAll(com,comVel);
1141 <      
1142 <      SimInfo::MoleculeIterator i;
1143 <      Molecule* mol;
1144 <      
1145 <      Vector3d thisr(0.0);
1146 <      Vector3d thisp(0.0);
1147 <      
1148 <      RealType thisMass;
1149 <      
1150 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1151 <        thisMass = mol->getMass();
1152 <        thisr = mol->getCom()-com;
1153 <        thisp = (mol->getComVel()-comVel)*thisMass;
1154 <        
1155 <        angularMomentum += cross( thisr, thisp );
1156 <        
1157 <      }  
1158 <      
1159 < #ifdef IS_MPI
1160 <      Vector3d tmpAngMom;
1161 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1162 < #endif
1163 <      
1164 <      return angularMomentum;
1165 <   }
1166 <  
1002 >  
1003    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1004      return IOIndexToIntegrableObject.at(index);
1005    }
# Line 1171 | Line 1007 | namespace OpenMD {
1007    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1008      IOIndexToIntegrableObject= v;
1009    }
1174 –
1175 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1176 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1177 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1178 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1179 –  */
1180 –  void SimInfo::getGyrationalVolume(RealType &volume){
1181 –    Mat3x3d intTensor;
1182 –    RealType det;
1183 –    Vector3d dummyAngMom;
1184 –    RealType sysconstants;
1185 –    RealType geomCnst;
1186 –
1187 –    geomCnst = 3.0/2.0;
1188 –    /* Get the inertial tensor and angular momentum for free*/
1189 –    getInertiaTensor(intTensor,dummyAngMom);
1190 –    
1191 –    det = intTensor.determinant();
1192 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1193 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1194 –    return;
1195 –  }
1196 –
1197 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1198 –    Mat3x3d intTensor;
1199 –    Vector3d dummyAngMom;
1200 –    RealType sysconstants;
1201 –    RealType geomCnst;
1202 –
1203 –    geomCnst = 3.0/2.0;
1204 –    /* Get the inertial tensor and angular momentum for free*/
1205 –    getInertiaTensor(intTensor,dummyAngMom);
1206 –    
1207 –    detI = intTensor.determinant();
1208 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1209 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1210 –    return;
1211 –  }
1010   /*
1011     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1012        assert( v.size() == nAtoms_ + nRigidBodies_);

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