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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 451 by mmeineke, Thu Apr 3 22:01:29 2003 UTC

# Line 12 | Line 12 | using namespace std;
12   #include "fortranWrappers.hpp"
13  
14   #ifdef IS_MPI
15 – #include <mpi++.h>
15   #include "mpiForceField.h"
16   #endif // is_mpi
17  
# Line 99 | Line 98 | namespace TPE {  // restrict the access of the folowin
98        return NULL;
99      }
100      
101 +    void printMe( void ){
102 +      
103 +      std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n";
104 +      if( next != NULL ) next->printMe();
105 +
106 +    }
107 +
108      void add( atomStruct &info ){
109  
110        // check for duplicates
# Line 114 | Line 120 | namespace TPE {  // restrict the access of the folowin
120  
121        if( next != NULL ) next->add(info);
122        else{
123 <        next = new LinkedType();
123 >        next = new LinkedAtomType();
124          strcpy(next->name, info.name);
125          next->isDipole = info.isDipole;
126          next->isSSD    = info.isSSD;
# Line 140 | Line 146 | namespace TPE {  // restrict the access of the folowin
146        info.dipole   = dipole;
147        info.w0       = w0;
148        info.v0       = v0;
149 +      info.ident    = ident;
150        info.last     = 0;
151      }
152  
# Line 197 | Line 204 | namespace TPE {  // restrict the access of the folowin
204          
205        if( next != NULL ) next->add(info);
206        else{
207 <        next = new LinkedType();
207 >        next = new LinkedBondType();
208          strcpy(next->nameA, info.nameA);
209          strcpy(next->nameB, info.nameB);
210          strcpy(next->type,  info.type);
# Line 266 | Line 273 | namespace TPE {  // restrict the access of the folowin
273  
274        if( next != NULL ) next->add(info);
275        else{
276 <        next = new LinkedType();
276 >        next = new LinkedBendType();
277          strcpy(next->nameA, info.nameA);
278          strcpy(next->nameB, info.nameB);
279          strcpy(next->nameC, info.nameC);
# Line 350 | Line 357 | namespace TPE {  // restrict the access of the folowin
357  
358        if( next != NULL ) next->add(info);
359        else{
360 <        next = new LinkedType();
360 >        next = new LinkedTorsionType();
361          strcpy(next->nameA, info.nameA);
362          strcpy(next->nameB, info.nameB);
363          strcpy(next->nameC, info.nameC);
# Line 621 | Line 628 | void TraPPE_ExFF::readParams( void ){
628  
629   void TraPPE_ExFF::readParams( void ){
630  
631 <  int i;
631 >  int i, a, b, c, d;
632    int identNum;
633 +  char* atomA;
634 +  char* atomB;
635 +  char* atomC;
636 +  char* atomD;
637    
638    atomStruct atomInfo;
639    bondStruct bondInfo;
640    bendStruct bendInfo;
641    torsionStruct torsionInfo;
642    
643 <  
643 >  bigSigma = 0.0;
644 >
645    atomInfo.last = 1;
646    bondInfo.last = 1;
647    bendInfo.last = 1;
# Line 715 | Line 727 | void TraPPE_ExFF::readParams( void ){
727      
728      MPIcheckPoint();
729  
730 <    headAtomType = new LinkedType;
730 >    headAtomType = new LinkedAtomType;
731      recieveFrcStruct( &atomInfo, mpiAtomStructType );
732      
733      while( !atomInfo.last ){
# Line 729 | Line 741 | void TraPPE_ExFF::readParams( void ){
741        recieveFrcStruct( &atomInfo, mpiAtomStructType );
742      }
743    }
744 +
745   #endif // is_mpi
746  
747 +
748 +
749    // call new A_types in fortran
750    
751    int isError;
# Line 742 | Line 757 | void TraPPE_ExFF::readParams( void ){
757    double GB_dummy = 0.0;
758    
759    
760 <  currentAtomType = headAtomType;
760 >  currentAtomType = headAtomType->next;;
761    while( currentAtomType != NULL ){
762      
763      if(currentAtomType->isDipole) entry_plug->useDipole = 1;
# Line 787 | Line 802 | void TraPPE_ExFF::readParams( void ){
802    
803  
804    // read in the bonds
790 –
805    
806 <  
807 <  
808 < }
806 > #ifdef IS_MPI
807 >  if( worldRank == 0 ){
808 > #endif
809 >    
810 >    // read in the bond types.
811 >    
812 >    headBondType = new LinkedBondType;
813 >    
814 >    fastForward( "BondTypes", "initializeBonds" );
815  
816 +    // we are now at the bondTypes section
817  
818 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
819 +    lineNum++;
820 +    
821 +    
822 +    // read a line, and start parseing out the atom types
823  
824 < void TraPPE_ExFF::initializeAtoms( void ){
825 <  
824 >    if( eof_test == NULL ){
825 >      sprintf( painCave.errMsg,
826 >               "Error in reading bonds from force file at line %d.\n",
827 >               lineNum );
828 >      painCave.isFatal = 1;
829 >      simError();
830 >    }
831 >    
832 >    // stop reading at end of file, or at next section
833 >    while( readLine[0] != '#' && eof_test != NULL ){
834 >
835 >      // toss comment lines
836 >      if( readLine[0] != '!' ){
837 >        
838 >        // the parser returns 0 if the line was blank
839 >        if( parseBond( readLine, lineNum, bondInfo ) ){
840 >          headBondType->add( bondInfo );
841 >        }
842 >      }
843 >      eof_test = fgets( readLine, sizeof(readLine), frcFile );
844 >      lineNum++;
845 >    }
846 >        
847 > #ifdef IS_MPI
848 >    
849 >    // send out the linked list to all the other processes
850 >    
851 >    sprintf( checkPointMsg,
852 >             "TraPPE_Ex bond structures read successfully." );
853 >    MPIcheckPoint();
854 >    
855 >    currentBondType = headBondType->next;
856 >    while( currentBondType != NULL ){
857 >      currentBondType->duplicate( bondInfo );
858 >      sendFrcStruct( &bondInfo, mpiBondStructType );
859 >      currentBondType = currentBondType->next;
860 >    }
861 >    bondInfo.last = 1;
862 >    sendFrcStruct( &bondInfo, mpiBondStructType );
863 >    
864 >  }
865  
866 +  else{
867 +    
868 +    // listen for node 0 to send out the force params
869 +    
870 +    MPIcheckPoint();
871 +
872 +    headBondType = new LinkedBondType;
873 +    recieveFrcStruct( &bondInfo, mpiBondStructType );
874 +    while( !bondInfo.last ){
875 +
876 +      headBondType->add( bondInfo );
877 +      recieveFrcStruct( &bondInfo, mpiBondStructType );
878 +    }
879 +  }
880 + #endif // is_mpi
881    
882  
883 +  // read in the bends
884  
885 + #ifdef IS_MPI
886 +  if( worldRank == 0 ){
887 + #endif
888 +
889 +    // read in the bend types.
890 +
891 +    headBendType = new LinkedBendType;
892 +    
893 +    fastForward( "BendTypes", "initializeBends" );
894 +
895 +    // we are now at the bendTypes section
896 +
897 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
898 +    lineNum++;
899 +        
900 +    // read a line, and start parseing out the bend types
901 +
902 +    if( eof_test == NULL ){
903 +      sprintf( painCave.errMsg,
904 +               "Error in reading bends from force file at line %d.\n",
905 +               lineNum );
906 +      painCave.isFatal = 1;
907 +      simError();
908 +    }
909 +    
910 +    // stop reading at end of file, or at next section
911 +    while( readLine[0] != '#' && eof_test != NULL ){
912 +      
913 +      // toss comment lines
914 +      if( readLine[0] != '!' ){
915 +        
916 +        // the parser returns 0 if the line was blank
917 +        if( parseBend( readLine, lineNum, bendInfo ) ){
918 +          headBendType->add( bendInfo );
919 +        }
920 +      }
921 +      eof_test = fgets( readLine, sizeof(readLine), frcFile );
922 +      lineNum++;
923 +    }
924 +    
925 + #ifdef IS_MPI
926 +    
927 +    // send out the linked list to all the other processes
928 +
929 +    sprintf( checkPointMsg,
930 +             "TraPPE_Ex bend structures read successfully." );
931 +    MPIcheckPoint();
932 +
933 +    currentBendType = headBendType->next;
934 +    while( currentBendType != NULL ){
935 +      currentBendType->duplicate( bendInfo );
936 +      sendFrcStruct( &bendInfo, mpiBendStructType );
937 +      currentBendType = currentBendType->next;
938 +    }
939 +    bendInfo.last = 1;
940 +    sendFrcStruct( &bendInfo, mpiBendStructType );
941 +    
942 +  }
943 +
944 +  else{
945 +    
946 +    // listen for node 0 to send out the force params
947 +    
948 +    MPIcheckPoint();
949 +
950 +    headBendType = new LinkedBendType;
951 +    recieveFrcStruct( &bendInfo, mpiBendStructType );
952 +    while( !bendInfo.last ){
953 +
954 +      headBendType->add( bendInfo );
955 +      recieveFrcStruct( &bendInfo, mpiBendStructType );
956 +    }
957 +  }
958 + #endif // is_mpi
959 +
960 +
961 +  // read in the torsions
962 +
963 + #ifdef IS_MPI
964 +  if( worldRank == 0 ){
965 + #endif
966 +
967 +    // read in the torsion types.
968 +
969 +    headTorsionType = new LinkedTorsionType;
970 +    
971 +    fastForward( "TorsionTypes", "initializeTorsions" );
972 +
973 +    // we are now at the torsionTypes section
974 +
975 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
976 +    lineNum++;
977 +    
978 +    
979 +    // read a line, and start parseing out the atom types
980 +
981 +    if( eof_test == NULL ){
982 +      sprintf( painCave.errMsg,
983 +               "Error in reading torsions from force file at line %d.\n",
984 +               lineNum );
985 +      painCave.isFatal = 1;
986 +      simError();
987 +    }
988 +    
989 +    // stop reading at end of file, or at next section
990 +    while( readLine[0] != '#' && eof_test != NULL ){
991 +
992 +      // toss comment lines
993 +      if( readLine[0] != '!' ){
994 +        
995 +        // the parser returns 0 if the line was blank
996 +        if( parseTorsion( readLine, lineNum, torsionInfo ) ){
997 +          headTorsionType->add( torsionInfo );
998 +
999 +        }
1000 +      }
1001 +      eof_test = fgets( readLine, sizeof(readLine), frcFile );
1002 +      lineNum++;
1003 +    }
1004 +
1005 + #ifdef IS_MPI
1006 +    
1007 +    // send out the linked list to all the other processes
1008 +    
1009 +    sprintf( checkPointMsg,
1010 +             "TraPPE_Ex torsion structures read successfully." );
1011 +    MPIcheckPoint();
1012 +    
1013 +    currentTorsionType = headTorsionType->next;
1014 +    while( currentTorsionType != NULL ){
1015 +      currentTorsionType->duplicate( torsionInfo );
1016 +      sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1017 +      currentTorsionType = currentTorsionType->next;
1018 +    }
1019 +    torsionInfo.last = 1;
1020 +    sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1021 +    
1022 +  }
1023 +
1024 +  else{
1025 +    
1026 +    // listen for node 0 to send out the force params
1027 +    
1028 +    MPIcheckPoint();
1029 +
1030 +    headTorsionType = new LinkedTorsionType;
1031 +    recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1032 +    while( !torsionInfo.last ){
1033 +
1034 +      headTorsionType->add( torsionInfo );
1035 +      recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1036 +    }
1037 +  }
1038 + #endif // is_mpi
1039 +
1040 +  entry_plug->useLJ = 1;
1041 + }
1042 +
1043 +
1044 +
1045 + void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
1046    
805 –  Atom** the_atoms;
806 –  int nAtoms;
807 –  the_atoms = entry_plug->atoms;
808 –  nAtoms = entry_plug->n_atoms;
1047    
1048    //////////////////////////////////////////////////
1049    // a quick water fix
# Line 837 | Line 1075 | void TraPPE_ExFF::initializeAtoms( void ){
1075    headI[2][1] = 0.0;
1076    headI[2][2] = 250;
1077  
840 –  
841 –
1078    //////////////////////////////////////////////////
1079  
844 –
845 –
1080    
1081    // initialize the atoms
1082    
849 –  double bigSigma = 0.0;
1083    DirectionalAtom* dAtom;
1084  
1085 <  for( i=0; i<nAtoms; i++ ){
1085 >  for(int i=0; i<nAtoms; i++ ){
1086  
854 –    
1087      currentAtomType = headAtomType->find( the_atoms[i]->getType() );
1088      if( currentAtomType == NULL ){
1089        sprintf( painCave.errMsg,
# Line 917 | Line 1149 | void TraPPE_ExFF::initializeAtoms( void ){
1149        }
1150      }
1151    }
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 –
1152   }
1153  
1154 < void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){
1154 > void TraPPE_ExFF::initializeBonds( int nBonds, Bond** bondArray,
1155 >                                   bond_pair* the_bonds ){
1156 >  int i,a,b;
1157 >  char* atomA;
1158 >  char* atomB;
1159    
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;
1160    Atom** the_atoms;
967 –  int nBonds;
968 –  the_sris = entry_plug->sr_interactions;
1161    the_atoms = entry_plug->atoms;
970 –  nBonds = entry_plug->n_bonds;
971 –
972 –  int i, a, b;
973 –  char* atomA;
974 –  char* atomB;
1162    
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" );
1163  
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 –  
1164    // initialize the Bonds
1165    
1055 –
1166    for( i=0; i<nBonds; i++ ){
1167      
1168      a = the_bonds[i].a;
# Line 1071 | Line 1181 | void TraPPE_ExFF::initializeBonds( bond_pair* the_bond
1181      
1182      if( !strcmp( currentBondType->type, "fixed" ) ){
1183        
1184 <      the_sris[i] = new ConstrainedBond( *the_atoms[a],
1185 <                                         *the_atoms[b],
1186 <                                         currentBondType->d0 );
1184 >      bondArray[i] = new ConstrainedBond( *the_atoms[a],
1185 >                                          *the_atoms[b],
1186 >                                          currentBondType->d0 );
1187        entry_plug->n_constraints++;
1188      }
1189    }
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 –
1190   }
1191  
1192 < void TraPPE_ExFF::initializeBends( bend_set* the_bends ){
1192 > void TraPPE_ExFF::initializeBends( int nBends, Bend** bendArray,
1193 >                                   bend_set* the_bends ){
1194    
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 –
1195    QuadraticBend* qBend;
1196    GhostBend* gBend;
1104 –  SRI **the_sris;
1197    Atom** the_atoms;
1106 –  int nBends;
1107 –  the_sris = entry_plug->sr_interactions;
1198    the_atoms = entry_plug->atoms;
1199 <  nBends = entry_plug->n_bends;
1110 <
1199 >  
1200    int i, a, b, c;
1201    char* atomA;
1202    char* atomB;
1203    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
1204    
1205    // initialize the Bends
1193 –  
1194 –  int index;
1206  
1207    for( i=0; i<nBends; i++ ){
1208      
# Line 1216 | Line 1227 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1227      
1228      if( !strcmp( currentBendType->type, "quadratic" ) ){
1229        
1219 –      index = i + entry_plug->n_bonds;
1220 –      
1230        if( the_bends[i].isGhost){
1231          
1232          if( the_bends[i].ghost == b ){
# Line 1245 | Line 1254 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1254                               currentBendType->k2,
1255                               currentBendType->k3,
1256                               currentBendType->t0 );
1257 <        the_sris[index] = gBend;
1257 >        bendArray[i] = gBend;
1258        }
1259        else{
1260          qBend = new QuadraticBend( *the_atoms[a],
# Line 1255 | Line 1264 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1264                               currentBendType->k2,
1265                               currentBendType->k3,
1266                               currentBendType->t0 );
1267 <        the_sris[index] = qBend;
1267 >        bendArray[i] = qBend;
1268        }
1269      }
1270    }
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 –
1271   }
1272  
1273 < void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){
1273 > void TraPPE_ExFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
1274 >                                      torsion_set* the_torsions ){
1275  
1276 <
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;
1276 >  int i, a, b, c, d;
1277    char* atomA;
1278    char* atomB;
1279    char* atomC;
1280    char* atomD;
1289 –  CubicTorsion* cTors;
1281  
1282 <  SRI **the_sris;
1282 >  CubicTorsion* cTors;
1283    Atom** the_atoms;
1293 –  int nTorsions;
1294 –  the_sris = entry_plug->sr_interactions;
1284    the_atoms = entry_plug->atoms;
1296 –  nTorsions = entry_plug->n_torsions;
1297 –
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
1285  
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 –  
1286    // initialize the Torsions
1287  
1288    for( i=0; i<nTorsions; i++ ){
# Line 1396 | Line 1307 | void TraPPE_ExFF::initializeTorsions( torsion_set* the
1307      }
1308      
1309      if( !strcmp( currentTorsionType->type, "cubic" ) ){
1399 –      index = i + entry_plug->n_bonds + entry_plug->n_bends;
1310        
1311        cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b],
1312                                  *the_atoms[c], *the_atoms[d] );
1313        cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2,
1314                             currentTorsionType->k3, currentTorsionType->k4 );
1315 <      the_sris[index] = cTors;
1315 >      torsionArray[i] = cTors;
1316      }
1317    }
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 –
1318   }
1319  
1320   void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){

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