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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 419 by mmeineke, Wed Mar 26 22:02:36 2003 UTC vs.
Revision 420 by mmeineke, Thu Mar 27 17:32:03 2003 UTC

# Line 910 | Line 910 | void SimSetup::makeMolecules( void ){
910    }
911  
912    // clean up the forcefield
913 <
913 >  the_ff->calcRcut();
914    the_ff->cleanMe();
915 – }
916 –
917 –
918 –
919 – void SimSetup::makeAtoms( void ){
920 –
921 –  int i, j, k, index;
922 –  double ux, uy, uz, uSqr, u;
923 –  AtomStamp* current_atom;
924 –
925 –  DirectionalAtom* dAtom;
926 –  int molIndex, molStart, molEnd, nMemb, lMolIndex;
927 –
928 –  lMolIndex = 0;
929 –  molIndex = 0;
930 –  index = 0;
931 –  for( i=0; i<n_components; i++ ){
932 –
933 –    for( j=0; j<components_nmol[i]; j++ ){
934 –
935 – #ifdef IS_MPI
936 –      if( mpiSim->getMyMolStart() <= molIndex &&
937 –          molIndex <= mpiSim->getMyMolEnd() ){
938 – #endif // is_mpi        
939 –
940 –        molStart = index;
941 –        nMemb = comp_stamps[i]->getNAtoms();
942 –        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
943 –          
944 –          current_atom = comp_stamps[i]->getAtom( k );
945 –          if( current_atom->haveOrientation() ){
946 –            
947 –            dAtom = new DirectionalAtom(index);
948 –            simnfo->n_oriented++;
949 –            the_atoms[index] = dAtom;
950 –            
951 –            ux = current_atom->getOrntX();
952 –            uy = current_atom->getOrntY();
953 –            uz = current_atom->getOrntZ();
954 –            
955 –            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
956 –            
957 –            u = sqrt( uSqr );
958 –            ux = ux / u;
959 –            uy = uy / u;
960 –            uz = uz / u;
961 –            
962 –            dAtom->setSUx( ux );
963 –            dAtom->setSUy( uy );
964 –            dAtom->setSUz( uz );
965 –          }
966 –          else{
967 –            the_atoms[index] = new GeneralAtom(index);
968 –          }
969 –          the_atoms[index]->setType( current_atom->getType() );
970 –          the_atoms[index]->setIndex( index );
971 –          
972 –          // increment the index and repeat;
973 –          index++;
974 –        }
975 –        
976 –        molEnd = index -1;
977 –        the_molecules[lMolIndex].setNMembers( nMemb );
978 –        the_molecules[lMolIndex].setStartAtom( molStart );
979 –        the_molecules[lMolIndex].setEndAtom( molEnd );
980 –        the_molecules[lMolIndex].setStampID( i );
981 –        lMolIndex++;
982 –
983 – #ifdef IS_MPI
984 –      }
985 – #endif //is_mpi
986 –      
987 –      molIndex++;
988 –    }
989 –  }
990 –
991 – #ifdef IS_MPI
992 –    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
993 –    
994 –    delete[] globalIndex;
995 –
996 –    mpiSim->mpiRefresh();
997 – #endif //IS_MPI
998 –          
999 –  the_ff->initializeAtoms();
1000 – }
1001 –
1002 – void SimSetup::makeBonds( void ){
1003 –
1004 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1005 –  bond_pair* the_bonds;
1006 –  BondStamp* current_bond;
1007 –
1008 –  the_bonds = new bond_pair[tot_bonds];
1009 –  index = 0;
1010 –  offset = 0;
1011 –  molIndex = 0;
1012 –
1013 –  for( i=0; i<n_components; i++ ){
1014 –
1015 –    for( j=0; j<components_nmol[i]; j++ ){
1016 –
1017 – #ifdef IS_MPI
1018 –      if( mpiSim->getMyMolStart() <= molIndex &&
1019 –          molIndex <= mpiSim->getMyMolEnd() ){
1020 – #endif // is_mpi        
1021 –        
1022 –        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1023 –          
1024 –          current_bond = comp_stamps[i]->getBond( k );
1025 –          the_bonds[index].a = current_bond->getA() + offset;
1026 –          the_bonds[index].b = current_bond->getB() + offset;
1027 –
1028 –          exI = the_bonds[index].a;
1029 –          exJ = the_bonds[index].b;
1030 –
1031 –          // exclude_I must always be the smaller of the pair
1032 –          if( exI > exJ ){
1033 –            tempEx = exI;
1034 –            exI = exJ;
1035 –            exJ = tempEx;
1036 –          }
1037 –
1038 –          
1039 – #ifdef IS_MPI
1040 –
1041 –          the_excludes[index*2] =    
1042 –            the_atoms[exI]->getGlobalIndex() + 1;
1043 –          the_excludes[index*2 + 1] =
1044 –            the_atoms[exJ]->getGlobalIndex() + 1;
1045 –
1046 – #else  // isn't MPI
1047 –          
1048 –          the_excludes[index*2] =     exI + 1;
1049 –          the_excludes[index*2 + 1] = exJ + 1;
1050 –          // fortran index from 1 (hence the +1 in the indexing)
1051 – #endif  //is_mpi
1052 –          
1053 –          // increment the index and repeat;
1054 –          index++;
1055 –        }
1056 –        offset += comp_stamps[i]->getNAtoms();
1057 –        
1058 – #ifdef IS_MPI
1059 –      }
1060 – #endif //is_mpi
1061 –      
1062 –      molIndex++;
1063 –    }      
1064 –  }
1065 –
1066 –  the_ff->initializeBonds( the_bonds );
1067 – }
1068 –
1069 – void SimSetup::makeBends( void ){
1070 –
1071 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1072 –  bend_set* the_bends;
1073 –  BendStamp* current_bend;
1074 –  LinkedAssign* extras;
1075 –  LinkedAssign* current_extra;
1076 –  
1077 –
1078 –  the_bends = new bend_set[tot_bends];
1079 –  index = 0;
1080 –  offset = 0;
1081 –  molIndex = 0;
1082 –  for( i=0; i<n_components; i++ ){
1083 –
1084 –    for( j=0; j<components_nmol[i]; j++ ){
1085 –
1086 – #ifdef IS_MPI
1087 –      if( mpiSim->getMyMolStart() <= molIndex &&
1088 –          molIndex <= mpiSim->getMyMolEnd() ){
1089 – #endif // is_mpi        
1090 –
1091 –        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1092 –          
1093 –          current_bend = comp_stamps[i]->getBend( k );
1094 –          the_bends[index].a = current_bend->getA() + offset;
1095 –          the_bends[index].b = current_bend->getB() + offset;
1096 –          the_bends[index].c = current_bend->getC() + offset;
1097 –          
1098 –          if( current_bend->haveExtras() ){
1099 –            
1100 –            extras = current_bend->getExtras();
1101 –            current_extra = extras;
1102 –            
1103 –            while( current_extra != NULL ){
1104 –              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1105 –                
1106 –                switch( current_extra->getType() ){
1107 –                  
1108 –                case 0:
1109 –                  the_bends[index].ghost =
1110 –                    current_extra->getInt() + offset;
1111 –                  the_bends[index].isGhost = 1;
1112 –                  break;
1113 –                  
1114 –                case 1:
1115 –                  the_bends[index].ghost =
1116 –                    (int)current_extra->getDouble() + offset;
1117 –                  the_bends[index].isGhost = 1;
1118 –                  break;
1119 –                  
1120 –                default:
1121 –                  sprintf( painCave.errMsg,
1122 –                           "SimSetup Error: ghostVectorSource was neiter a "
1123 –                           "double nor an int.\n"
1124 –                           "-->Bend[%d] in %s\n",
1125 –                           k, comp_stamps[i]->getID() );
1126 –                  painCave.isFatal = 1;
1127 –                  simError();
1128 –                }
1129 –              }
1130 –              
1131 –              else{
1132 –                
1133 –                sprintf( painCave.errMsg,
1134 –                         "SimSetup Error: unhandled bend assignment:\n"
1135 –                         "    -->%s in Bend[%d] in %s\n",
1136 –                         current_extra->getlhs(),
1137 –                         k, comp_stamps[i]->getID() );
1138 –                painCave.isFatal = 1;
1139 –                simError();
1140 –              }
1141 –              
1142 –              current_extra = current_extra->getNext();
1143 –            }
1144 –          }
1145 –          
1146 –          if( !the_bends[index].isGhost ){
1147 –            
1148 –            exI = the_bends[index].a;
1149 –            exJ = the_bends[index].c;
1150 –          }
1151 –          else{
1152 –            
1153 –            exI = the_bends[index].a;
1154 –            exJ = the_bends[index].b;
1155 –          }
1156 –          
1157 –          // exclude_I must always be the smaller of the pair
1158 –          if( exI > exJ ){
1159 –            tempEx = exI;
1160 –            exI = exJ;
1161 –            exJ = tempEx;
1162 –          }
1163 –
1164 –
1165 – #ifdef IS_MPI
1166 –
1167 –          the_excludes[(index + tot_bonds)*2] =    
1168 –            the_atoms[exI]->getGlobalIndex() + 1;
1169 –          the_excludes[(index + tot_bonds)*2 + 1] =
1170 –            the_atoms[exJ]->getGlobalIndex() + 1;
1171 –          
1172 – #else  // isn't MPI
1173 –          
1174 –          the_excludes[(index + tot_bonds)*2] =     exI + 1;
1175 –          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1176 –          // fortran index from 1 (hence the +1 in the indexing)
1177 – #endif  //is_mpi
1178 –          
1179 –          
1180 –          // increment the index and repeat;
1181 –          index++;
1182 –        }
1183 –        offset += comp_stamps[i]->getNAtoms();
1184 –        
1185 – #ifdef IS_MPI
1186 –      }
1187 – #endif //is_mpi
1188 –
1189 –      molIndex++;
1190 –    }
1191 –  }
1192 –
1193 – #ifdef IS_MPI
1194 –  sprintf( checkPointMsg,
1195 –           "Successfully created the bends list.\n" );
1196 –  MPIcheckPoint();
1197 – #endif // is_mpi
1198 –  
1199 –
1200 –  the_ff->initializeBends( the_bends );
915   }
916  
1203 – void SimSetup::makeTorsions( void ){
1204 –
1205 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1206 –  torsion_set* the_torsions;
1207 –  TorsionStamp* current_torsion;
1208 –
1209 –  the_torsions = new torsion_set[tot_torsions];
1210 –  index = 0;
1211 –  offset = 0;
1212 –  molIndex = 0;
1213 –  for( i=0; i<n_components; i++ ){
1214 –
1215 –    for( j=0; j<components_nmol[i]; j++ ){
1216 –
1217 – #ifdef IS_MPI
1218 –      if( mpiSim->getMyMolStart() <= molIndex &&
1219 –          molIndex <= mpiSim->getMyMolEnd() ){
1220 – #endif // is_mpi        
1221 –
1222 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1223 –
1224 –        current_torsion = comp_stamps[i]->getTorsion( k );
1225 –        the_torsions[index].a = current_torsion->getA() + offset;
1226 –        the_torsions[index].b = current_torsion->getB() + offset;
1227 –        the_torsions[index].c = current_torsion->getC() + offset;
1228 –        the_torsions[index].d = current_torsion->getD() + offset;
1229 –
1230 –        exI = the_torsions[index].a;
1231 –        exJ = the_torsions[index].d;
1232 –
1233 –        
1234 –        // exclude_I must always be the smaller of the pair
1235 –        if( exI > exJ ){
1236 –          tempEx = exI;
1237 –          exI = exJ;
1238 –          exJ = tempEx;
1239 –        }
1240 –
1241 –
1242 – #ifdef IS_MPI
1243 –        
1244 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1245 –          the_atoms[exI]->getGlobalIndex() + 1;
1246 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1247 –          the_atoms[exJ]->getGlobalIndex() + 1;
1248 –        
1249 – #else  // isn't MPI
1250 –        
1251 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1252 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1253 –        // fortran indexes from 1 (hence the +1 in the indexing)
1254 – #endif  //is_mpi
1255 –        
1256 –
1257 –        // increment the index and repeat;
1258 –        index++;
1259 –      }
1260 –      offset += comp_stamps[i]->getNAtoms();
1261 –
1262 – #ifdef IS_MPI
1263 –      }
1264 – #endif //is_mpi      
1265 –
1266 –      molIndex++;
1267 –    }
1268 –  }
1269 –
1270 –  the_ff->initializeTorsions( the_torsions );
1271 – }
1272 –
917   void SimSetup::initFromBass( void ){
918  
919    int i, j, k;

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