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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 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstdio>
3 < #include <cstring>
1 > #include <stdlib.h>
2 > #include <stdio.h>
3 > #include <string.h>
4  
5   #include <iostream>
6   using namespace std;
# 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 +
876 +  sprintf( checkPointMsg,
877 +           "TraPPE_ExFF bond structures broadcast successfully." );
878 +  MPIcheckPoint();
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 +
959 +  sprintf( checkPointMsg,
960 +           "TraPPE_ExFF bend structures broadcast successfully." );
961 +  MPIcheckPoint();
962 +
963 + #endif // is_mpi
964 +
965 +
966 +  // read in the torsions
967 +
968 + #ifdef IS_MPI
969 +  if( worldRank == 0 ){
970 + #endif
971 +
972 +    // read in the torsion types.
973 +
974 +    headTorsionType = new LinkedTorsionType;
975 +    
976 +    fastForward( "TorsionTypes", "initializeTorsions" );
977 +
978 +    // we are now at the torsionTypes section
979 +
980 +    eof_test =  fgets( readLine, sizeof(readLine), frcFile );
981 +    lineNum++;
982 +    
983 +    
984 +    // read a line, and start parseing out the atom types
985 +
986 +    if( eof_test == NULL ){
987 +      sprintf( painCave.errMsg,
988 +               "Error in reading torsions from force file at line %d.\n",
989 +               lineNum );
990 +      painCave.isFatal = 1;
991 +      simError();
992 +    }
993 +    
994 +    // stop reading at end of file, or at next section
995 +    while( readLine[0] != '#' && eof_test != NULL ){
996 +
997 +      // toss comment lines
998 +      if( readLine[0] != '!' ){
999 +        
1000 +        // the parser returns 0 if the line was blank
1001 +        if( parseTorsion( readLine, lineNum, torsionInfo ) ){
1002 +          headTorsionType->add( torsionInfo );
1003 +
1004 +        }
1005 +      }
1006 +      eof_test = fgets( readLine, sizeof(readLine), frcFile );
1007 +      lineNum++;
1008 +    }
1009 +
1010 + #ifdef IS_MPI
1011 +    
1012 +    // send out the linked list to all the other processes
1013 +    
1014 +    sprintf( checkPointMsg,
1015 +             "TraPPE_Ex torsion structures read successfully." );
1016 +    MPIcheckPoint();
1017 +    
1018 +    currentTorsionType = headTorsionType->next;
1019 +    while( currentTorsionType != NULL ){
1020 +      currentTorsionType->duplicate( torsionInfo );
1021 +      sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1022 +      currentTorsionType = currentTorsionType->next;
1023 +    }
1024 +    torsionInfo.last = 1;
1025 +    sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1026 +    
1027 +  }
1028 +
1029 +  else{
1030 +    
1031 +    // listen for node 0 to send out the force params
1032 +    
1033 +    MPIcheckPoint();
1034 +
1035 +    headTorsionType = new LinkedTorsionType;
1036 +    recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1037 +    while( !torsionInfo.last ){
1038 +
1039 +      headTorsionType->add( torsionInfo );
1040 +      recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1041 +    }
1042 +  }
1043 +
1044 +  sprintf( checkPointMsg,
1045 +           "TraPPE_ExFF torsion structures broadcast successfully." );
1046 +  MPIcheckPoint();
1047 +
1048 + #endif // is_mpi
1049 +
1050 +  entry_plug->useLJ = 1;
1051 + }
1052 +
1053 +
1054 +
1055 + void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
1056    
805 –  Atom** the_atoms;
806 –  int nAtoms;
807 –  the_atoms = entry_plug->atoms;
808 –  nAtoms = entry_plug->n_atoms;
1057    
1058    //////////////////////////////////////////////////
1059    // a quick water fix
# Line 837 | Line 1085 | void TraPPE_ExFF::initializeAtoms( void ){
1085    headI[2][1] = 0.0;
1086    headI[2][2] = 250;
1087  
840 –  
841 –
1088    //////////////////////////////////////////////////
1089  
844 –
845 –
1090    
1091    // initialize the atoms
1092    
849 –  double bigSigma = 0.0;
1093    DirectionalAtom* dAtom;
1094  
1095 <  for( i=0; i<nAtoms; i++ ){
1095 >  for(int i=0; i<nAtoms; i++ ){
1096  
854 –    
1097      currentAtomType = headAtomType->find( the_atoms[i]->getType() );
1098      if( currentAtomType == NULL ){
1099        sprintf( painCave.errMsg,
# Line 917 | Line 1159 | void TraPPE_ExFF::initializeAtoms( void ){
1159        }
1160      }
1161    }
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 –
1162   }
1163  
1164 < void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){
1164 > void TraPPE_ExFF::initializeBonds( int nBonds, Bond** bondArray,
1165 >                                   bond_pair* the_bonds ){
1166 >  int i,a,b;
1167 >  char* atomA;
1168 >  char* atomB;
1169    
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;
1170    Atom** the_atoms;
967 –  int nBonds;
968 –  the_sris = entry_plug->sr_interactions;
1171    the_atoms = entry_plug->atoms;
970 –  nBonds = entry_plug->n_bonds;
971 –
972 –  int i, a, b;
973 –  char* atomA;
974 –  char* atomB;
1172    
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" );
1173  
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 –  
1174    // initialize the Bonds
1175    
1055 –
1176    for( i=0; i<nBonds; i++ ){
1177      
1178      a = the_bonds[i].a;
# Line 1071 | Line 1191 | void TraPPE_ExFF::initializeBonds( bond_pair* the_bond
1191      
1192      if( !strcmp( currentBondType->type, "fixed" ) ){
1193        
1194 <      the_sris[i] = new ConstrainedBond( *the_atoms[a],
1195 <                                         *the_atoms[b],
1196 <                                         currentBondType->d0 );
1194 >      bondArray[i] = new ConstrainedBond( *the_atoms[a],
1195 >                                          *the_atoms[b],
1196 >                                          currentBondType->d0 );
1197        entry_plug->n_constraints++;
1198      }
1199    }
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 –
1200   }
1201  
1202 < void TraPPE_ExFF::initializeBends( bend_set* the_bends ){
1202 > void TraPPE_ExFF::initializeBends( int nBends, Bend** bendArray,
1203 >                                   bend_set* the_bends ){
1204    
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 –
1205    QuadraticBend* qBend;
1206    GhostBend* gBend;
1104 –  SRI **the_sris;
1207    Atom** the_atoms;
1106 –  int nBends;
1107 –  the_sris = entry_plug->sr_interactions;
1208    the_atoms = entry_plug->atoms;
1209 <  nBends = entry_plug->n_bends;
1110 <
1209 >  
1210    int i, a, b, c;
1211    char* atomA;
1212    char* atomB;
1213    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
1214    
1215    // initialize the Bends
1193 –  
1194 –  int index;
1216  
1217    for( i=0; i<nBends; i++ ){
1218      
# Line 1216 | Line 1237 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1237      
1238      if( !strcmp( currentBendType->type, "quadratic" ) ){
1239        
1219 –      index = i + entry_plug->n_bonds;
1220 –      
1240        if( the_bends[i].isGhost){
1241          
1242          if( the_bends[i].ghost == b ){
# Line 1226 | Line 1245 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1245          else if( the_bends[i].ghost == a ){
1246            c = a;
1247            a = b;
1248 <          b = a;
1248 >          b = c;
1249          }
1250          else{
1251            sprintf( painCave.errMsg,
# Line 1245 | Line 1264 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1264                               currentBendType->k2,
1265                               currentBendType->k3,
1266                               currentBendType->t0 );
1267 <        the_sris[index] = gBend;
1267 >        bendArray[i] = gBend;
1268        }
1269        else{
1270          qBend = new QuadraticBend( *the_atoms[a],
# Line 1255 | Line 1274 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1274                               currentBendType->k2,
1275                               currentBendType->k3,
1276                               currentBendType->t0 );
1277 <        the_sris[index] = qBend;
1277 >        bendArray[i] = qBend;
1278        }
1279      }
1280    }
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 –
1281   }
1282  
1283 < void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){
1283 > void TraPPE_ExFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
1284 >                                      torsion_set* the_torsions ){
1285  
1286 <
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;
1286 >  int i, a, b, c, d;
1287    char* atomA;
1288    char* atomB;
1289    char* atomC;
1290    char* atomD;
1289 –  CubicTorsion* cTors;
1291  
1292 <  SRI **the_sris;
1292 >  CubicTorsion* cTors;
1293    Atom** the_atoms;
1293 –  int nTorsions;
1294 –  the_sris = entry_plug->sr_interactions;
1294    the_atoms = entry_plug->atoms;
1296 –  nTorsions = entry_plug->n_torsions;
1295  
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 –  
1296    // initialize the Torsions
1297  
1298    for( i=0; i<nTorsions; i++ ){
# Line 1396 | Line 1317 | void TraPPE_ExFF::initializeTorsions( torsion_set* the
1317      }
1318      
1319      if( !strcmp( currentTorsionType->type, "cubic" ) ){
1399 –      index = i + entry_plug->n_bonds + entry_plug->n_bends;
1320        
1321        cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b],
1322                                  *the_atoms[c], *the_atoms[d] );
1323        cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2,
1324                             currentTorsionType->k3, currentTorsionType->k4 );
1325 <      the_sris[index] = cTors;
1325 >      torsionArray[i] = cTors;
1326      }
1327    }
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 –
1328   }
1329  
1330   void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){

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