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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 463 by gezelter, Sat Apr 5 03:39:25 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;
764 <    if(currentAtomType->isSSD)    entry_plug->useSticky = 1;
764 >    if(currentAtomType->isSSD) {
765 >      entry_plug->useSticky = 1;
766 >      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0));
767 >    }
768  
769      if( currentAtomType->name[0] != '\0' ){
770        isError = 0;
# Line 758 | Line 776 | void TraPPE_ExFF::readParams( void ){
776                   &(currentAtomType->epslon),
777                   &(currentAtomType->sigma),
778                   &(currentAtomType->dipole),
761 –                 &(currentAtomType->w0),
762 –                 &(currentAtomType->v0),
763 –                 &GB_dummy,
764 –                 &GB_dummy,
765 –                 &GB_dummy,
766 –                 &GB_dummy,
767 –                 &GB_dummy,
768 –                 &GB_dummy,
779                   &isError );
780        if( isError ){
781          sprintf( painCave.errMsg,
# Line 787 | Line 797 | void TraPPE_ExFF::readParams( void ){
797    
798  
799    // read in the bonds
790 –
800    
801 <  
802 <  
803 < }
801 > #ifdef IS_MPI
802 >  if( worldRank == 0 ){
803 > #endif
804 >    
805 >    // read in the bond types.
806 >    
807 >    headBondType = new LinkedBondType;
808 >    
809 >    fastForward( "BondTypes", "initializeBonds" );
810  
811 +    // we are now at the bondTypes section
812  
813 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
814 +    lineNum++;
815 +    
816 +    
817 +    // read a line, and start parseing out the atom types
818  
819 < void TraPPE_ExFF::initializeAtoms( void ){
820 <  
819 >    if( eof_test == NULL ){
820 >      sprintf( painCave.errMsg,
821 >               "Error in reading bonds from force file at line %d.\n",
822 >               lineNum );
823 >      painCave.isFatal = 1;
824 >      simError();
825 >    }
826 >    
827 >    // stop reading at end of file, or at next section
828 >    while( readLine[0] != '#' && eof_test != NULL ){
829 >
830 >      // toss comment lines
831 >      if( readLine[0] != '!' ){
832 >        
833 >        // the parser returns 0 if the line was blank
834 >        if( parseBond( readLine, lineNum, bondInfo ) ){
835 >          headBondType->add( bondInfo );
836 >        }
837 >      }
838 >      eof_test = fgets( readLine, sizeof(readLine), frcFile );
839 >      lineNum++;
840 >    }
841 >        
842 > #ifdef IS_MPI
843 >    
844 >    // send out the linked list to all the other processes
845 >    
846 >    sprintf( checkPointMsg,
847 >             "TraPPE_Ex bond structures read successfully." );
848 >    MPIcheckPoint();
849 >    
850 >    currentBondType = headBondType->next;
851 >    while( currentBondType != NULL ){
852 >      currentBondType->duplicate( bondInfo );
853 >      sendFrcStruct( &bondInfo, mpiBondStructType );
854 >      currentBondType = currentBondType->next;
855 >    }
856 >    bondInfo.last = 1;
857 >    sendFrcStruct( &bondInfo, mpiBondStructType );
858 >    
859 >  }
860  
861 +  else{
862 +    
863 +    // listen for node 0 to send out the force params
864 +    
865 +    MPIcheckPoint();
866 +
867 +    headBondType = new LinkedBondType;
868 +    recieveFrcStruct( &bondInfo, mpiBondStructType );
869 +    while( !bondInfo.last ){
870 +
871 +      headBondType->add( bondInfo );
872 +      recieveFrcStruct( &bondInfo, mpiBondStructType );
873 +    }
874 +  }
875 + #endif // is_mpi
876    
877 +
878 +  // read in the bends
879 +
880 + #ifdef IS_MPI
881 +  if( worldRank == 0 ){
882 + #endif
883 +
884 +    // read in the bend types.
885 +
886 +    headBendType = new LinkedBendType;
887 +    
888 +    fastForward( "BendTypes", "initializeBends" );
889 +
890 +    // we are now at the bendTypes section
891 +
892 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
893 +    lineNum++;
894 +        
895 +    // read a line, and start parseing out the bend types
896 +
897 +    if( eof_test == NULL ){
898 +      sprintf( painCave.errMsg,
899 +               "Error in reading bends from force file at line %d.\n",
900 +               lineNum );
901 +      painCave.isFatal = 1;
902 +      simError();
903 +    }
904 +    
905 +    // stop reading at end of file, or at next section
906 +    while( readLine[0] != '#' && eof_test != NULL ){
907 +      
908 +      // toss comment lines
909 +      if( readLine[0] != '!' ){
910 +        
911 +        // the parser returns 0 if the line was blank
912 +        if( parseBend( readLine, lineNum, bendInfo ) ){
913 +          headBendType->add( bendInfo );
914 +        }
915 +      }
916 +      eof_test = fgets( readLine, sizeof(readLine), frcFile );
917 +      lineNum++;
918 +    }
919 +    
920 + #ifdef IS_MPI
921 +    
922 +    // send out the linked list to all the other processes
923  
924 +    sprintf( checkPointMsg,
925 +             "TraPPE_Ex bend structures read successfully." );
926 +    MPIcheckPoint();
927  
928 +    currentBendType = headBendType->next;
929 +    while( currentBendType != NULL ){
930 +      currentBendType->duplicate( bendInfo );
931 +      sendFrcStruct( &bendInfo, mpiBendStructType );
932 +      currentBendType = currentBendType->next;
933 +    }
934 +    bendInfo.last = 1;
935 +    sendFrcStruct( &bendInfo, mpiBendStructType );
936 +    
937 +  }
938 +
939 +  else{
940 +    
941 +    // listen for node 0 to send out the force params
942 +    
943 +    MPIcheckPoint();
944 +
945 +    headBendType = new LinkedBendType;
946 +    recieveFrcStruct( &bendInfo, mpiBendStructType );
947 +    while( !bendInfo.last ){
948 +
949 +      headBendType->add( bendInfo );
950 +      recieveFrcStruct( &bendInfo, mpiBendStructType );
951 +    }
952 +  }
953 + #endif // is_mpi
954 +
955 +
956 +  // read in the torsions
957 +
958 + #ifdef IS_MPI
959 +  if( worldRank == 0 ){
960 + #endif
961 +
962 +    // read in the torsion types.
963 +
964 +    headTorsionType = new LinkedTorsionType;
965 +    
966 +    fastForward( "TorsionTypes", "initializeTorsions" );
967 +
968 +    // we are now at the torsionTypes section
969 +
970 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
971 +    lineNum++;
972 +    
973 +    
974 +    // read a line, and start parseing out the atom types
975 +
976 +    if( eof_test == NULL ){
977 +      sprintf( painCave.errMsg,
978 +               "Error in reading torsions from force file at line %d.\n",
979 +               lineNum );
980 +      painCave.isFatal = 1;
981 +      simError();
982 +    }
983 +    
984 +    // stop reading at end of file, or at next section
985 +    while( readLine[0] != '#' && eof_test != NULL ){
986 +
987 +      // toss comment lines
988 +      if( readLine[0] != '!' ){
989 +        
990 +        // the parser returns 0 if the line was blank
991 +        if( parseTorsion( readLine, lineNum, torsionInfo ) ){
992 +          headTorsionType->add( torsionInfo );
993 +
994 +        }
995 +      }
996 +      eof_test = fgets( readLine, sizeof(readLine), frcFile );
997 +      lineNum++;
998 +    }
999 +
1000 + #ifdef IS_MPI
1001 +    
1002 +    // send out the linked list to all the other processes
1003 +    
1004 +    sprintf( checkPointMsg,
1005 +             "TraPPE_Ex torsion structures read successfully." );
1006 +    MPIcheckPoint();
1007 +    
1008 +    currentTorsionType = headTorsionType->next;
1009 +    while( currentTorsionType != NULL ){
1010 +      currentTorsionType->duplicate( torsionInfo );
1011 +      sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1012 +      currentTorsionType = currentTorsionType->next;
1013 +    }
1014 +    torsionInfo.last = 1;
1015 +    sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1016 +    
1017 +  }
1018 +
1019 +  else{
1020 +    
1021 +    // listen for node 0 to send out the force params
1022 +    
1023 +    MPIcheckPoint();
1024 +
1025 +    headTorsionType = new LinkedTorsionType;
1026 +    recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1027 +    while( !torsionInfo.last ){
1028 +
1029 +      headTorsionType->add( torsionInfo );
1030 +      recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1031 +    }
1032 +  }
1033 + #endif // is_mpi
1034 +
1035 +  entry_plug->useLJ = 1;
1036 + }
1037 +
1038 +
1039 +
1040 + void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
1041    
805 –  Atom** the_atoms;
806 –  int nAtoms;
807 –  the_atoms = entry_plug->atoms;
808 –  nAtoms = entry_plug->n_atoms;
1042    
1043    //////////////////////////////////////////////////
1044    // a quick water fix
# Line 837 | Line 1070 | void TraPPE_ExFF::initializeAtoms( void ){
1070    headI[2][1] = 0.0;
1071    headI[2][2] = 250;
1072  
840 –  
841 –
1073    //////////////////////////////////////////////////
1074  
844 –
845 –
1075    
1076    // initialize the atoms
1077    
849 –  double bigSigma = 0.0;
1078    DirectionalAtom* dAtom;
1079  
1080 <  for( i=0; i<nAtoms; i++ ){
1080 >  for(int i=0; i<nAtoms; i++ ){
1081  
854 –    
1082      currentAtomType = headAtomType->find( the_atoms[i]->getType() );
1083      if( currentAtomType == NULL ){
1084        sprintf( painCave.errMsg,
# Line 917 | Line 1144 | void TraPPE_ExFF::initializeAtoms( void ){
1144        }
1145      }
1146    }
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 –
1147   }
1148  
1149 < void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){
1150 <  
1151 <
1152 <
1153 <
1149 > void TraPPE_ExFF::initializeBonds( int nBonds, Bond** bondArray,
1150 >                                   bond_pair* the_bonds ){
1151 >  int i,a,b;
1152 >  char* atomA;
1153 >  char* atomB;
1154    
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;
1155    Atom** the_atoms;
967 –  int nBonds;
968 –  the_sris = entry_plug->sr_interactions;
1156    the_atoms = entry_plug->atoms;
970 –  nBonds = entry_plug->n_bonds;
971 –
972 –  int i, a, b;
973 –  char* atomA;
974 –  char* atomB;
1157    
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" );
1158  
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 –  
1159    // initialize the Bonds
1160    
1055 –
1161    for( i=0; i<nBonds; i++ ){
1162      
1163      a = the_bonds[i].a;
# Line 1071 | Line 1176 | void TraPPE_ExFF::initializeBonds( bond_pair* the_bond
1176      
1177      if( !strcmp( currentBondType->type, "fixed" ) ){
1178        
1179 <      the_sris[i] = new ConstrainedBond( *the_atoms[a],
1180 <                                         *the_atoms[b],
1181 <                                         currentBondType->d0 );
1179 >      bondArray[i] = new ConstrainedBond( *the_atoms[a],
1180 >                                          *the_atoms[b],
1181 >                                          currentBondType->d0 );
1182        entry_plug->n_constraints++;
1183      }
1184    }
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 –
1185   }
1186  
1187 < void TraPPE_ExFF::initializeBends( bend_set* the_bends ){
1187 > void TraPPE_ExFF::initializeBends( int nBends, Bend** bendArray,
1188 >                                   bend_set* the_bends ){
1189    
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 –
1190    QuadraticBend* qBend;
1191    GhostBend* gBend;
1104 –  SRI **the_sris;
1192    Atom** the_atoms;
1106 –  int nBends;
1107 –  the_sris = entry_plug->sr_interactions;
1193    the_atoms = entry_plug->atoms;
1194 <  nBends = entry_plug->n_bends;
1110 <
1194 >  
1195    int i, a, b, c;
1196    char* atomA;
1197    char* atomB;
1198    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
1199    
1200    // initialize the Bends
1193 –  
1194 –  int index;
1201  
1202    for( i=0; i<nBends; i++ ){
1203      
# Line 1216 | Line 1222 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1222      
1223      if( !strcmp( currentBendType->type, "quadratic" ) ){
1224        
1219 –      index = i + entry_plug->n_bonds;
1220 –      
1225        if( the_bends[i].isGhost){
1226          
1227          if( the_bends[i].ghost == b ){
# Line 1245 | Line 1249 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1249                               currentBendType->k2,
1250                               currentBendType->k3,
1251                               currentBendType->t0 );
1252 <        the_sris[index] = gBend;
1252 >        bendArray[i] = gBend;
1253        }
1254        else{
1255          qBend = new QuadraticBend( *the_atoms[a],
# Line 1255 | Line 1259 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1259                               currentBendType->k2,
1260                               currentBendType->k3,
1261                               currentBendType->t0 );
1262 <        the_sris[index] = qBend;
1262 >        bendArray[i] = qBend;
1263        }
1264      }
1265    }
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 –
1266   }
1267  
1268 < void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){
1268 > void TraPPE_ExFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
1269 >                                      torsion_set* the_torsions ){
1270  
1271 <
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;
1271 >  int i, a, b, c, d;
1272    char* atomA;
1273    char* atomB;
1274    char* atomC;
1275    char* atomD;
1289 –  CubicTorsion* cTors;
1276  
1277 <  SRI **the_sris;
1277 >  CubicTorsion* cTors;
1278    Atom** the_atoms;
1293 –  int nTorsions;
1294 –  the_sris = entry_plug->sr_interactions;
1279    the_atoms = entry_plug->atoms;
1296 –  nTorsions = entry_plug->n_torsions;
1280  
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 –  
1281    // initialize the Torsions
1282  
1283    for( i=0; i<nTorsions; i++ ){
# Line 1396 | Line 1302 | void TraPPE_ExFF::initializeTorsions( torsion_set* the
1302      }
1303      
1304      if( !strcmp( currentTorsionType->type, "cubic" ) ){
1399 –      index = i + entry_plug->n_bonds + entry_plug->n_bends;
1305        
1306        cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b],
1307                                  *the_atoms[c], *the_atoms[d] );
1308        cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2,
1309                             currentTorsionType->k3, currentTorsionType->k4 );
1310 <      the_sris[index] = cTors;
1310 >      torsionArray[i] = cTors;
1311      }
1312    }
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 –
1313   }
1314  
1315   void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){

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