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Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 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>
# Line 71 | 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 224 | 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)) {
236 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
237 –           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          }
248 –            
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 298 | 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)) {
307 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
308 –           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 370 | 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;
377 <         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 388 | 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 523 | Line 539 | namespace OpenMD {
539      Molecule::RigidBodyIterator rbIter;
540      RigidBody* rb;
541      Molecule::IntegrableObjectIterator ii;
542 <    StuntDouble* integrableObject;
543 <    
544 <    for (integrableObject = mol->beginIntegrableObject(ii);
545 <         integrableObject != NULL;
530 <         integrableObject = mol->nextIntegrableObject(ii)) {
542 >    StuntDouble* sd;
543 >    
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 541 | 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 776 | 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 969 | Line 994 | namespace OpenMD {
994      
995    }
996  
972 –  Vector3d SimInfo::getComVel(){
973 –    SimInfo::MoleculeIterator i;
974 –    Molecule* mol;
997  
976 –    Vector3d comVel(0.0);
977 –    RealType totalMass = 0.0;
978 –    
979 –
980 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
981 –      RealType mass = mol->getMass();
982 –      totalMass += mass;
983 –      comVel += mass * mol->getComVel();
984 –    }  
985 –
986 – #ifdef IS_MPI
987 –    RealType tmpMass = totalMass;
988 –    Vector3d tmpComVel(comVel);    
989 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
990 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991 – #endif
992 –
993 –    comVel /= totalMass;
994 –
995 –    return comVel;
996 –  }
997 –
998 –  Vector3d SimInfo::getCom(){
999 –    SimInfo::MoleculeIterator i;
1000 –    Molecule* mol;
1001 –
1002 –    Vector3d com(0.0);
1003 –    RealType totalMass = 0.0;
1004 –    
1005 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1006 –      RealType mass = mol->getMass();
1007 –      totalMass += mass;
1008 –      com += mass * mol->getCom();
1009 –    }  
1010 –
1011 – #ifdef IS_MPI
1012 –    RealType tmpMass = totalMass;
1013 –    Vector3d tmpCom(com);    
1014 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1015 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016 – #endif
1017 –
1018 –    com /= totalMass;
1019 –
1020 –    return com;
1021 –
1022 –  }        
1023 –
998    ostream& operator <<(ostream& o, SimInfo& info) {
999  
1000      return o;
1001    }
1002    
1003 <  
1030 <   /*
1031 <   Returns center of mass and center of mass velocity in one function call.
1032 <   */
1033 <  
1034 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1035 <      SimInfo::MoleculeIterator i;
1036 <      Molecule* mol;
1037 <      
1038 <    
1039 <      RealType totalMass = 0.0;
1040 <    
1041 <
1042 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1043 <         RealType mass = mol->getMass();
1044 <         totalMass += mass;
1045 <         com += mass * mol->getCom();
1046 <         comVel += mass * mol->getComVel();          
1047 <      }  
1048 <      
1049 < #ifdef IS_MPI
1050 <      RealType tmpMass = totalMass;
1051 <      Vector3d tmpCom(com);  
1052 <      Vector3d tmpComVel(comVel);
1053 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1054 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056 < #endif
1057 <      
1058 <      com /= totalMass;
1059 <      comVel /= totalMass;
1060 <   }        
1061 <  
1062 <   /*
1063 <   Return intertia tensor for entire system and angular momentum Vector.
1064 <
1065 <
1066 <       [  Ixx -Ixy  -Ixz ]
1067 <    J =| -Iyx  Iyy  -Iyz |
1068 <       [ -Izx -Iyz   Izz ]
1069 <    */
1070 <
1071 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1072 <      
1073 <
1074 <      RealType xx = 0.0;
1075 <      RealType yy = 0.0;
1076 <      RealType zz = 0.0;
1077 <      RealType xy = 0.0;
1078 <      RealType xz = 0.0;
1079 <      RealType yz = 0.0;
1080 <      Vector3d com(0.0);
1081 <      Vector3d comVel(0.0);
1082 <      
1083 <      getComAll(com, comVel);
1084 <      
1085 <      SimInfo::MoleculeIterator i;
1086 <      Molecule* mol;
1087 <      
1088 <      Vector3d thisq(0.0);
1089 <      Vector3d thisv(0.0);
1090 <
1091 <      RealType thisMass = 0.0;
1092 <    
1093 <      
1094 <      
1095 <  
1096 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1097 <        
1098 <         thisq = mol->getCom()-com;
1099 <         thisv = mol->getComVel()-comVel;
1100 <         thisMass = mol->getMass();
1101 <         // Compute moment of intertia coefficients.
1102 <         xx += thisq[0]*thisq[0]*thisMass;
1103 <         yy += thisq[1]*thisq[1]*thisMass;
1104 <         zz += thisq[2]*thisq[2]*thisMass;
1105 <        
1106 <         // compute products of intertia
1107 <         xy += thisq[0]*thisq[1]*thisMass;
1108 <         xz += thisq[0]*thisq[2]*thisMass;
1109 <         yz += thisq[1]*thisq[2]*thisMass;
1110 <            
1111 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1112 <            
1113 <      }  
1114 <      
1115 <      
1116 <      inertiaTensor(0,0) = yy + zz;
1117 <      inertiaTensor(0,1) = -xy;
1118 <      inertiaTensor(0,2) = -xz;
1119 <      inertiaTensor(1,0) = -xy;
1120 <      inertiaTensor(1,1) = xx + zz;
1121 <      inertiaTensor(1,2) = -yz;
1122 <      inertiaTensor(2,0) = -xz;
1123 <      inertiaTensor(2,1) = -yz;
1124 <      inertiaTensor(2,2) = xx + yy;
1125 <      
1126 < #ifdef IS_MPI
1127 <      Mat3x3d tmpI(inertiaTensor);
1128 <      Vector3d tmpAngMom;
1129 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1130 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131 < #endif
1132 <              
1133 <      return;
1134 <   }
1135 <
1136 <   //Returns the angular momentum of the system
1137 <   Vector3d SimInfo::getAngularMomentum(){
1138 <      
1139 <      Vector3d com(0.0);
1140 <      Vector3d comVel(0.0);
1141 <      Vector3d angularMomentum(0.0);
1142 <      
1143 <      getComAll(com,comVel);
1144 <      
1145 <      SimInfo::MoleculeIterator i;
1146 <      Molecule* mol;
1147 <      
1148 <      Vector3d thisr(0.0);
1149 <      Vector3d thisp(0.0);
1150 <      
1151 <      RealType thisMass;
1152 <      
1153 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1154 <        thisMass = mol->getMass();
1155 <        thisr = mol->getCom()-com;
1156 <        thisp = (mol->getComVel()-comVel)*thisMass;
1157 <        
1158 <        angularMomentum += cross( thisr, thisp );
1159 <        
1160 <      }  
1161 <      
1162 < #ifdef IS_MPI
1163 <      Vector3d tmpAngMom;
1164 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1165 < #endif
1166 <      
1167 <      return angularMomentum;
1168 <   }
1169 <  
1003 >  
1004    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005      return IOIndexToIntegrableObject.at(index);
1006    }
# Line 1174 | Line 1008 | namespace OpenMD {
1008    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009      IOIndexToIntegrableObject= v;
1010    }
1177 –
1178 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1179 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1180 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1181 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1182 –  */
1183 –  void SimInfo::getGyrationalVolume(RealType &volume){
1184 –    Mat3x3d intTensor;
1185 –    RealType det;
1186 –    Vector3d dummyAngMom;
1187 –    RealType sysconstants;
1188 –    RealType geomCnst;
1189 –
1190 –    geomCnst = 3.0/2.0;
1191 –    /* Get the inertial tensor and angular momentum for free*/
1192 –    getInertiaTensor(intTensor,dummyAngMom);
1193 –    
1194 –    det = intTensor.determinant();
1195 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1196 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1197 –    return;
1198 –  }
1199 –
1200 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1201 –    Mat3x3d intTensor;
1202 –    Vector3d dummyAngMom;
1203 –    RealType sysconstants;
1204 –    RealType geomCnst;
1205 –
1206 –    geomCnst = 3.0/2.0;
1207 –    /* Get the inertial tensor and angular momentum for free*/
1208 –    getInertiaTensor(intTensor,dummyAngMom);
1209 –    
1210 –    detI = intTensor.determinant();
1211 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1212 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1213 –    return;
1214 –  }
1011   /*
1012     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013        assert( v.size() == nAtoms_ + nRigidBodies_);

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