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root/group/trunk/OOPSE/libmdtools/TraPPE_ExFF.cpp
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Comparing trunk/OOPSE/libmdtools/TraPPE_ExFF.cpp (file contents):
Revision 420 by mmeineke, Thu Mar 27 17:32:03 2003 UTC vs.
Revision 442 by mmeineke, Wed Apr 2 15:01:06 2003 UTC

# Line 99 | Line 99 | namespace TPE {  // restrict the access of the folowin
99        return NULL;
100      }
101      
102 +    void printMe( void ){
103 +      
104 +      std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n";
105 +      if( next != NULL ) next->printMe();
106 +
107 +    }
108 +
109      void add( atomStruct &info ){
110  
111        // check for duplicates
# Line 114 | Line 121 | namespace TPE {  // restrict the access of the folowin
121  
122        if( next != NULL ) next->add(info);
123        else{
124 <        next = new LinkedType();
124 >        next = new LinkedAtomType();
125          strcpy(next->name, info.name);
126          next->isDipole = info.isDipole;
127          next->isSSD    = info.isSSD;
# Line 140 | Line 147 | namespace TPE {  // restrict the access of the folowin
147        info.dipole   = dipole;
148        info.w0       = w0;
149        info.v0       = v0;
150 +      info.ident    = ident;
151        info.last     = 0;
152      }
153  
# Line 197 | Line 205 | namespace TPE {  // restrict the access of the folowin
205          
206        if( next != NULL ) next->add(info);
207        else{
208 <        next = new LinkedType();
208 >        next = new LinkedBondType();
209          strcpy(next->nameA, info.nameA);
210          strcpy(next->nameB, info.nameB);
211          strcpy(next->type,  info.type);
# Line 266 | Line 274 | namespace TPE {  // restrict the access of the folowin
274  
275        if( next != NULL ) next->add(info);
276        else{
277 <        next = new LinkedType();
277 >        next = new LinkedBendType();
278          strcpy(next->nameA, info.nameA);
279          strcpy(next->nameB, info.nameB);
280          strcpy(next->nameC, info.nameC);
# Line 350 | Line 358 | namespace TPE {  // restrict the access of the folowin
358  
359        if( next != NULL ) next->add(info);
360        else{
361 <        next = new LinkedType();
361 >        next = new LinkedTorsionType();
362          strcpy(next->nameA, info.nameA);
363          strcpy(next->nameB, info.nameB);
364          strcpy(next->nameC, info.nameC);
# Line 621 | Line 629 | void TraPPE_ExFF::readParams( void ){
629  
630   void TraPPE_ExFF::readParams( void ){
631  
632 <  int i;
632 >  int i, a, b, c, d;
633    int identNum;
634 +  char* atomA;
635 +  char* atomB;
636 +  char* atomC;
637 +  char* atomD;
638    
639    atomStruct atomInfo;
640    bondStruct bondInfo;
641    bendStruct bendInfo;
642    torsionStruct torsionInfo;
643    
644 <  
644 >  bigSigma = 0.0;
645 >
646    atomInfo.last = 1;
647    bondInfo.last = 1;
648    bendInfo.last = 1;
# Line 715 | Line 728 | void TraPPE_ExFF::readParams( void ){
728      
729      MPIcheckPoint();
730  
731 <    headAtomType = new LinkedType;
731 >    headAtomType = new LinkedAtomType;
732      recieveFrcStruct( &atomInfo, mpiAtomStructType );
733      
734      while( !atomInfo.last ){
# Line 729 | Line 742 | void TraPPE_ExFF::readParams( void ){
742        recieveFrcStruct( &atomInfo, mpiAtomStructType );
743      }
744    }
745 +
746   #endif // is_mpi
747  
748 +
749 +
750    // call new A_types in fortran
751    
752    int isError;
# Line 787 | Line 803 | void TraPPE_ExFF::readParams( void ){
803    
804  
805    // read in the bonds
790 –
806    
807 <  
808 <  
809 < }
807 > #ifdef IS_MPI
808 >  if( worldRank == 0 ){
809 > #endif
810 >    
811 >    // read in the bond types.
812 >    
813 >    headBondType = new LinkedBondType;
814 >    
815 >    fastForward( "BondTypes", "initializeBonds" );
816  
817 +    // we are now at the bondTypes section
818  
819 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
820 +    lineNum++;
821 +    
822 +    
823 +    // read a line, and start parseing out the atom types
824  
825 < void TraPPE_ExFF::initializeAtoms( void ){
826 <  
825 >    if( eof_test == NULL ){
826 >      sprintf( painCave.errMsg,
827 >               "Error in reading bonds from force file at line %d.\n",
828 >               lineNum );
829 >      painCave.isFatal = 1;
830 >      simError();
831 >    }
832 >    
833 >    // stop reading at end of file, or at next section
834 >    while( readLine[0] != '#' && eof_test != NULL ){
835 >
836 >      // toss comment lines
837 >      if( readLine[0] != '!' ){
838 >        
839 >        // the parser returns 0 if the line was blank
840 >        if( parseBond( readLine, lineNum, bondInfo ) ){
841 >          headBondType->add( bondInfo );
842 >        }
843 >      }
844 >      eof_test = fgets( readLine, sizeof(readLine), frcFile );
845 >      lineNum++;
846 >    }
847 >        
848 > #ifdef IS_MPI
849 >    
850 >    // send out the linked list to all the other processes
851 >    
852 >    sprintf( checkPointMsg,
853 >             "TraPPE_Ex bond structures read successfully." );
854 >    MPIcheckPoint();
855 >    
856 >    currentBondType = headBondType->next;
857 >    while( currentBondType != NULL ){
858 >      currentBondType->duplicate( bondInfo );
859 >      sendFrcStruct( &bondInfo, mpiBondStructType );
860 >      currentBondType = currentBondType->next;
861 >    }
862 >    bondInfo.last = 1;
863 >    sendFrcStruct( &bondInfo, mpiBondStructType );
864 >    
865 >  }
866  
867 +  else{
868 +    
869 +    // listen for node 0 to send out the force params
870 +    
871 +    MPIcheckPoint();
872 +
873 +    headBondType = new LinkedBondType;
874 +    recieveFrcStruct( &bondInfo, mpiBondStructType );
875 +    while( !bondInfo.last ){
876 +
877 +      headBondType->add( bondInfo );
878 +      recieveFrcStruct( &bondInfo, mpiBondStructType );
879 +    }
880 +  }
881 + #endif // is_mpi
882    
883 +
884 +  // read in the bends
885 +
886 + #ifdef IS_MPI
887 +  if( worldRank == 0 ){
888 + #endif
889 +
890 +    // read in the bend types.
891 +
892 +    headBendType = new LinkedBendType;
893 +    
894 +    fastForward( "BendTypes", "initializeBends" );
895 +
896 +    // we are now at the bendTypes section
897 +
898 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
899 +    lineNum++;
900 +        
901 +    // read a line, and start parseing out the bend types
902 +
903 +    if( eof_test == NULL ){
904 +      sprintf( painCave.errMsg,
905 +               "Error in reading bends from force file at line %d.\n",
906 +               lineNum );
907 +      painCave.isFatal = 1;
908 +      simError();
909 +    }
910 +    
911 +    // stop reading at end of file, or at next section
912 +    while( readLine[0] != '#' && eof_test != NULL ){
913 +      
914 +      // toss comment lines
915 +      if( readLine[0] != '!' ){
916 +        
917 +        // the parser returns 0 if the line was blank
918 +        if( parseBend( readLine, lineNum, bendInfo ) ){
919 +          headBendType->add( bendInfo );
920 +        }
921 +      }
922 +      eof_test = fgets( readLine, sizeof(readLine), frcFile );
923 +      lineNum++;
924 +    }
925 +    
926 + #ifdef IS_MPI
927 +    
928 +    // send out the linked list to all the other processes
929 +
930 +    sprintf( checkPointMsg,
931 +             "TraPPE_Ex bend structures read successfully." );
932 +    MPIcheckPoint();
933 +
934 +    currentBendType = headBendType->next;
935 +    while( currentBendType != NULL ){
936 +      currentBendType->duplicate( bendInfo );
937 +      sendFrcStruct( &bendInfo, mpiBendStructType );
938 +      currentBendType = currentBendType->next;
939 +    }
940 +    bendInfo.last = 1;
941 +    sendFrcStruct( &bendInfo, mpiBendStructType );
942 +    
943 +  }
944  
945 +  else{
946 +    
947 +    // listen for node 0 to send out the force params
948 +    
949 +    MPIcheckPoint();
950  
951 +    headBendType = new LinkedBendType;
952 +    recieveFrcStruct( &bendInfo, mpiBendStructType );
953 +    while( !bendInfo.last ){
954 +
955 +      headBendType->add( bendInfo );
956 +      recieveFrcStruct( &bendInfo, mpiBendStructType );
957 +    }
958 +  }
959 + #endif // is_mpi
960 +
961 +
962 +  // read in the torsions
963 +
964 + #ifdef IS_MPI
965 +  if( worldRank == 0 ){
966 + #endif
967 +
968 +    // read in the torsion types.
969 +
970 +    headTorsionType = new LinkedTorsionType;
971 +    
972 +    fastForward( "TorsionTypes", "initializeTorsions" );
973 +
974 +    // we are now at the torsionTypes section
975 +
976 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
977 +    lineNum++;
978 +    
979 +    
980 +    // read a line, and start parseing out the atom types
981 +
982 +    if( eof_test == NULL ){
983 +      sprintf( painCave.errMsg,
984 +               "Error in reading torsions from force file at line %d.\n",
985 +               lineNum );
986 +      painCave.isFatal = 1;
987 +      simError();
988 +    }
989 +    
990 +    // stop reading at end of file, or at next section
991 +    while( readLine[0] != '#' && eof_test != NULL ){
992 +
993 +      // toss comment lines
994 +      if( readLine[0] != '!' ){
995 +        
996 +        // the parser returns 0 if the line was blank
997 +        if( parseTorsion( readLine, lineNum, torsionInfo ) ){
998 +          headTorsionType->add( torsionInfo );
999 +
1000 +        }
1001 +      }
1002 +      eof_test = fgets( readLine, sizeof(readLine), frcFile );
1003 +      lineNum++;
1004 +    }
1005 +
1006 + #ifdef IS_MPI
1007 +    
1008 +    // send out the linked list to all the other processes
1009 +    
1010 +    sprintf( checkPointMsg,
1011 +             "TraPPE_Ex torsion structures read successfully." );
1012 +    MPIcheckPoint();
1013 +    
1014 +    currentTorsionType = headTorsionType->next;
1015 +    while( currentTorsionType != NULL ){
1016 +      currentTorsionType->duplicate( torsionInfo );
1017 +      sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1018 +      currentTorsionType = currentTorsionType->next;
1019 +    }
1020 +    torsionInfo.last = 1;
1021 +    sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1022 +    
1023 +  }
1024 +
1025 +  else{
1026 +    
1027 +    // listen for node 0 to send out the force params
1028 +    
1029 +    MPIcheckPoint();
1030 +
1031 +    headTorsionType = new LinkedTorsionType;
1032 +    recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1033 +    while( !torsionInfo.last ){
1034 +
1035 +      headTorsionType->add( torsionInfo );
1036 +      recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1037 +    }
1038 +  }
1039 + #endif // is_mpi
1040 +
1041 +  entry_plug->useLJ = 1;
1042 + }
1043 +
1044 +
1045 +
1046 + void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
1047    
805 –  Atom** the_atoms;
806 –  int nAtoms;
807 –  the_atoms = entry_plug->atoms;
808 –  nAtoms = entry_plug->n_atoms;
1048    
1049    //////////////////////////////////////////////////
1050    // a quick water fix
# Line 837 | Line 1076 | void TraPPE_ExFF::initializeAtoms( void ){
1076    headI[2][1] = 0.0;
1077    headI[2][2] = 250;
1078  
840 –  
841 –
1079    //////////////////////////////////////////////////
1080  
844 –
845 –
1081    
1082    // initialize the atoms
1083    
849 –  double bigSigma = 0.0;
1084    DirectionalAtom* dAtom;
1085  
1086 <  for( i=0; i<nAtoms; i++ ){
1086 >  for(int i=0; i<nAtoms; i++ ){
1087  
854 –    
1088      currentAtomType = headAtomType->find( the_atoms[i]->getType() );
1089      if( currentAtomType == NULL ){
1090        sprintf( painCave.errMsg,
# Line 917 | Line 1150 | void TraPPE_ExFF::initializeAtoms( void ){
1150        }
1151      }
1152    }
920 –
921 – #ifdef IS_MPI
922 –  double tempBig = bigSigma;
923 –  MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX );
924 – #endif  //is_mpi
925 –
926 –  //calc rCut and rList
927 –
928 –  entry_plug->rCut = 2.5 * bigSigma;
929 –  
930 –  if(entry_plug->rCut > (entry_plug->box_x / 2.0))
931 –    entry_plug->rCut = entry_plug->box_x / 2.0;
932 –  
933 –  if(entry_plug->rCut > (entry_plug->box_y / 2.0))
934 –    entry_plug->rCut = entry_plug->box_y / 2.0;
935 –  
936 –  if(entry_plug->rCut > (entry_plug->box_z / 2.0))
937 –    entry_plug->rCut = entry_plug->box_z / 2.0;
938 –
939 –  entry_plug->rList = entry_plug->rCut + 1.0;
940 –
941 –  entry_plug->useLJ = 1; // use Lennard Jones is on by default
942 –
943 –  // clean up the memory
944 –  
945 –  delete headAtomType;
946 –
947 – #ifdef IS_MPI
948 –  sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" );
949 –  MPIcheckPoint();
950 – #endif // is_mpi
951 –
1153   }
1154  
1155 < void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){
1155 > void TraPPE_ExFF::initializeBonds( int nBonds, Bond** bondArray,
1156 >                                   bond_pair* the_bonds ){
1157 >  int i,a,b;
1158 >  char* atomA;
1159 >  char* atomB;
1160    
956 –
957 –
958 –
959 –  
960 –
961 –
962 –  info.last = 1; // initialize last to have the last set.
963 –                 // if things go well, last will be set to 0
964 –
965 –  SRI **the_sris;
1161    Atom** the_atoms;
967 –  int nBonds;
968 –  the_sris = entry_plug->sr_interactions;
1162    the_atoms = entry_plug->atoms;
970 –  nBonds = entry_plug->n_bonds;
971 –
972 –  int i, a, b;
973 –  char* atomA;
974 –  char* atomB;
1163    
976 – #ifdef IS_MPI
977 –  if( worldRank == 0 ){
978 – #endif
979 –    
980 –    // read in the bond types.
981 –    
982 –    headBondType = new LinkedType;
983 –    
984 –    fastForward( "BondTypes", "initializeBonds" );
1164  
986 –    // we are now at the bondTypes section
987 –
988 –    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
989 –    lineNum++;
990 –    
991 –    
992 –    // read a line, and start parseing out the atom types
993 –
994 –    if( eof_test == NULL ){
995 –      sprintf( painCave.errMsg,
996 –               "Error in reading bonds from force file at line %d.\n",
997 –               lineNum );
998 –      painCave.isFatal = 1;
999 –      simError();
1000 –    }
1001 –    
1002 –    // stop reading at end of file, or at next section
1003 –    while( readLine[0] != '#' && eof_test != NULL ){
1004 –
1005 –      // toss comment lines
1006 –      if( readLine[0] != '!' ){
1007 –        
1008 –        // the parser returns 0 if the line was blank
1009 –        if( parseBond( readLine, lineNum, info ) ){
1010 –          headBondType->add( info );
1011 –        }
1012 –      }
1013 –      eof_test = fgets( readLine, sizeof(readLine), frcFile );
1014 –      lineNum++;
1015 –    }
1016 –        
1017 – #ifdef IS_MPI
1018 –    
1019 –    // send out the linked list to all the other processes
1020 –    
1021 –    sprintf( checkPointMsg,
1022 –             "TraPPE_Ex bond structures read successfully." );
1023 –    MPIcheckPoint();
1024 –    
1025 –    currentBondType = headBondType;
1026 –    while( currentBondType != NULL ){
1027 –      currentBondType->duplicate( info );
1028 –      sendFrcStruct( &info, mpiBondStructType );
1029 –      currentBondType = currentBondType->next;
1030 –    }
1031 –    info.last = 1;
1032 –    sendFrcStruct( &info, mpiBondStructType );
1033 –    
1034 –  }
1035 –
1036 –  else{
1037 –    
1038 –    // listen for node 0 to send out the force params
1039 –    
1040 –    MPIcheckPoint();
1041 –
1042 –    headBondType = new LinkedType;
1043 –    recieveFrcStruct( &info, mpiBondStructType );
1044 –    while( !info.last ){
1045 –
1046 –      headBondType->add( info );
1047 –      recieveFrcStruct( &info, mpiBondStructType );
1048 –    }
1049 –  }
1050 – #endif // is_mpi
1051 –  
1052 –  
1165    // initialize the Bonds
1166    
1055 –
1167    for( i=0; i<nBonds; i++ ){
1168      
1169      a = the_bonds[i].a;
# Line 1071 | Line 1182 | void TraPPE_ExFF::initializeBonds( bond_pair* the_bond
1182      
1183      if( !strcmp( currentBondType->type, "fixed" ) ){
1184        
1185 <      the_sris[i] = new ConstrainedBond( *the_atoms[a],
1186 <                                         *the_atoms[b],
1187 <                                         currentBondType->d0 );
1185 >      bondArray[i] = new ConstrainedBond( *the_atoms[a],
1186 >                                          *the_atoms[b],
1187 >                                          currentBondType->d0 );
1188        entry_plug->n_constraints++;
1189      }
1190    }
1080 –
1081 –
1082 –  // clean up the memory
1083 –  
1084 –  delete headBondType;
1085 –
1086 – #ifdef IS_MPI
1087 –  sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" );
1088 –  MPIcheckPoint();
1089 – #endif // is_mpi
1090 –
1191   }
1192  
1193 < void TraPPE_ExFF::initializeBends( bend_set* the_bends ){
1193 > void TraPPE_ExFF::initializeBends( int nBends, Bend** bendArray,
1194 >                                   bend_set* the_bends ){
1195    
1095 –
1096 –  
1097 –
1098 –  bendStruct info;
1099 –  info.last = 1; // initialize last to have the last set.
1100 –                 // if things go well, last will be set to 0
1101 –
1196    QuadraticBend* qBend;
1197    GhostBend* gBend;
1104 –  SRI **the_sris;
1198    Atom** the_atoms;
1106 –  int nBends;
1107 –  the_sris = entry_plug->sr_interactions;
1199    the_atoms = entry_plug->atoms;
1200 <  nBends = entry_plug->n_bends;
1110 <
1200 >  
1201    int i, a, b, c;
1202    char* atomA;
1203    char* atomB;
1204    char* atomC;
1115 –
1116 –
1117 – #ifdef IS_MPI
1118 –  if( worldRank == 0 ){
1119 – #endif
1120 –
1121 –    // read in the bend types.
1122 –
1123 –    headBendType = new LinkedType;
1124 –    
1125 –    fastForward( "BendTypes", "initializeBends" );
1126 –
1127 –    // we are now at the bendTypes section
1128 –
1129 –    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
1130 –    lineNum++;
1131 –        
1132 –    // read a line, and start parseing out the bend types
1133 –
1134 –    if( eof_test == NULL ){
1135 –      sprintf( painCave.errMsg,
1136 –               "Error in reading bends from force file at line %d.\n",
1137 –               lineNum );
1138 –      painCave.isFatal = 1;
1139 –      simError();
1140 –    }
1141 –    
1142 –    // stop reading at end of file, or at next section
1143 –    while( readLine[0] != '#' && eof_test != NULL ){
1144 –      
1145 –      // toss comment lines
1146 –      if( readLine[0] != '!' ){
1147 –        
1148 –        // the parser returns 0 if the line was blank
1149 –        if( parseBend( readLine, lineNum, info ) ){
1150 –          headBendType->add( info );
1151 –        }
1152 –      }
1153 –      eof_test = fgets( readLine, sizeof(readLine), frcFile );
1154 –      lineNum++;
1155 –    }
1156 –    
1157 – #ifdef IS_MPI
1158 –    
1159 –    // send out the linked list to all the other processes
1160 –
1161 –    sprintf( checkPointMsg,
1162 –             "TraPPE_Ex bend structures read successfully." );
1163 –    MPIcheckPoint();
1164 –
1165 –    currentBendType = headBendType;
1166 –    while( currentBendType != NULL ){
1167 –      currentBendType->duplicate( info );
1168 –      sendFrcStruct( &info, mpiBendStructType );
1169 –      currentBendType = currentBendType->next;
1170 –    }
1171 –    info.last = 1;
1172 –    sendFrcStruct( &info, mpiBendStructType );
1173 –    
1174 –  }
1175 –
1176 –  else{
1177 –    
1178 –    // listen for node 0 to send out the force params
1179 –    
1180 –    MPIcheckPoint();
1181 –
1182 –    headBendType = new LinkedType;
1183 –    recieveFrcStruct( &info, mpiBendStructType );
1184 –    while( !info.last ){
1185 –
1186 –      headBendType->add( info );
1187 –      recieveFrcStruct( &info, mpiBendStructType );
1188 –    }
1189 –  }
1190 – #endif // is_mpi
1205    
1206    // initialize the Bends
1193 –  
1194 –  int index;
1207  
1208    for( i=0; i<nBends; i++ ){
1209      
# Line 1216 | Line 1228 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1228      
1229      if( !strcmp( currentBendType->type, "quadratic" ) ){
1230        
1219 –      index = i + entry_plug->n_bonds;
1220 –      
1231        if( the_bends[i].isGhost){
1232          
1233          if( the_bends[i].ghost == b ){
# Line 1245 | Line 1255 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1255                               currentBendType->k2,
1256                               currentBendType->k3,
1257                               currentBendType->t0 );
1258 <        the_sris[index] = gBend;
1258 >        bendArray[i] = gBend;
1259        }
1260        else{
1261          qBend = new QuadraticBend( *the_atoms[a],
# Line 1255 | Line 1265 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1265                               currentBendType->k2,
1266                               currentBendType->k3,
1267                               currentBendType->t0 );
1268 <        the_sris[index] = qBend;
1268 >        bendArray[i] = qBend;
1269        }
1270      }
1271    }
1262 –
1263 –
1264 –  // clean up the memory
1265 –  
1266 –  delete headBendType;
1267 –
1268 – #ifdef IS_MPI
1269 –  sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" );
1270 –  MPIcheckPoint();
1271 – #endif // is_mpi
1272 –
1272   }
1273  
1274 < void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){
1274 > void TraPPE_ExFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
1275 >                                      torsion_set* the_torsions ){
1276  
1277 <
1278 <  
1279 <
1280 <  torsionStruct info;
1281 <  info.last = 1; // initialize last to have the last set.
1282 <                 // if things go well, last will be set to 0
1283 <
1284 <  int i, a, b, c, d, index;
1277 >  int i, a, b, c, d;
1278    char* atomA;
1279    char* atomB;
1280    char* atomC;
1281    char* atomD;
1289 –  CubicTorsion* cTors;
1282  
1283 <  SRI **the_sris;
1283 >  CubicTorsion* cTors;
1284    Atom** the_atoms;
1293 –  int nTorsions;
1294 –  the_sris = entry_plug->sr_interactions;
1285    the_atoms = entry_plug->atoms;
1296 –  nTorsions = entry_plug->n_torsions;
1286  
1298 – #ifdef IS_MPI
1299 –  if( worldRank == 0 ){
1300 – #endif
1301 –
1302 –    // read in the torsion types.
1303 –
1304 –    headTorsionType = new LinkedType;
1305 –    
1306 –    fastForward( "TorsionTypes", "initializeTorsions" );
1307 –
1308 –    // we are now at the torsionTypes section
1309 –
1310 –    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
1311 –    lineNum++;
1312 –    
1313 –    
1314 –    // read a line, and start parseing out the atom types
1315 –
1316 –    if( eof_test == NULL ){
1317 –      sprintf( painCave.errMsg,
1318 –               "Error in reading torsions from force file at line %d.\n",
1319 –               lineNum );
1320 –      painCave.isFatal = 1;
1321 –      simError();
1322 –    }
1323 –    
1324 –    // stop reading at end of file, or at next section
1325 –    while( readLine[0] != '#' && eof_test != NULL ){
1326 –
1327 –      // toss comment lines
1328 –      if( readLine[0] != '!' ){
1329 –        
1330 –        // the parser returns 0 if the line was blank
1331 –        if( parseTorsion( readLine, lineNum, info ) ){
1332 –          headTorsionType->add( info );
1333 –
1334 –        }
1335 –      }
1336 –      eof_test = fgets( readLine, sizeof(readLine), frcFile );
1337 –      lineNum++;
1338 –    }
1339 –
1340 – #ifdef IS_MPI
1341 –    
1342 –    // send out the linked list to all the other processes
1343 –    
1344 –    sprintf( checkPointMsg,
1345 –             "TraPPE_Ex torsion structures read successfully." );
1346 –    MPIcheckPoint();
1347 –    
1348 –    currentTorsionType = headTorsionType;
1349 –    while( currentTorsionType != NULL ){
1350 –      currentTorsionType->duplicate( info );
1351 –      sendFrcStruct( &info, mpiTorsionStructType );
1352 –      currentTorsionType = currentTorsionType->next;
1353 –    }
1354 –    info.last = 1;
1355 –    sendFrcStruct( &info, mpiTorsionStructType );
1356 –    
1357 –  }
1358 –
1359 –  else{
1360 –    
1361 –    // listen for node 0 to send out the force params
1362 –    
1363 –    MPIcheckPoint();
1364 –
1365 –    headTorsionType = new LinkedType;
1366 –    recieveFrcStruct( &info, mpiTorsionStructType );
1367 –    while( !info.last ){
1368 –
1369 –      headTorsionType->add( info );
1370 –      recieveFrcStruct( &info, mpiTorsionStructType );
1371 –    }
1372 –  }
1373 – #endif // is_mpi
1374 –  
1287    // initialize the Torsions
1288  
1289    for( i=0; i<nTorsions; i++ ){
# Line 1396 | Line 1308 | void TraPPE_ExFF::initializeTorsions( torsion_set* the
1308      }
1309      
1310      if( !strcmp( currentTorsionType->type, "cubic" ) ){
1399 –      index = i + entry_plug->n_bonds + entry_plug->n_bends;
1311        
1312        cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b],
1313                                  *the_atoms[c], *the_atoms[d] );
1314        cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2,
1315                             currentTorsionType->k3, currentTorsionType->k4 );
1316 <      the_sris[index] = cTors;
1316 >      torsionArray[i] = cTors;
1317      }
1318    }
1408 –
1409 –
1410 –  // clean up the memory
1411 –  
1412 –  delete headTorsionType;
1413 –
1414 – #ifdef IS_MPI
1415 –  sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" );
1416 –  MPIcheckPoint();
1417 – #endif // is_mpi
1418 –
1319   }
1320  
1321   void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){

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