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root/group/trunk/OOPSE/libmdtools/DUFF.cpp
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Comparing trunk/OOPSE/libmdtools/DUFF.cpp (file contents):
Revision 559 by mmeineke, Thu Jun 19 22:02:44 2003 UTC vs.
Revision 976 by chrisfen, Thu Jan 22 17:34:20 2004 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 15 | Line 15 | namespace TPE {  // restrict the access of the folowin
15   #include "mpiForceField.h"
16   #endif // is_mpi
17  
18 – namespace TPE {  // restrict the access of the folowing to this file only.
18  
19 + // define some bond Types
20  
21 + #define FIXED_BOND    0
22 + #define HARMONIC_BOND 1
23 +
24 +
25 + namespace DUFF_NS {  // restrict the access of the folowing to this file only.
26 +
27 +
28    // Declare the structures that will be passed by MPI
29    
30    typedef struct{
# Line 25 | Line 32 | namespace TPE {  // restrict the access of the folowin
32      double mass;
33      double epslon;
34      double sigma;
35 +    double charge;
36      double dipole;
37      double w0;
38      double v0;
39 +    double v0p;
40 +    double rl;
41 +    double ru;
42 +    double rlp;
43 +    double rup;
44      int isSSD;
45 +    int isCharge;
46      int isDipole;
47      int ident;
48      int last;      //  0  -> default
# Line 39 | Line 53 | namespace TPE {  // restrict the access of the folowin
53    typedef struct{
54      char nameA[15];
55      char nameB[15];
42 –    char type[30];
56      double d0;
57 +    double k0;
58      int last;      //  0  -> default
59                     //  1  -> tells nodes to stop listening
60 +    int type;
61    } bondStruct;
62    
63    
# Line 111 | Line 126 | namespace TPE {  // restrict the access of the folowin
126        
127        if( !strcmp( info.name, name ) ){
128          sprintf( painCave.errMsg,
129 <                 "Duplicate TraPPE_Ex atom type \"%s\" found in "
130 <                 "the TraPPE_ExFF param file./n",
129 >                 "Duplicate DUFF atom type \"%s\" found in "
130 >                 "the DUFF param file./n",
131                   name );
132          painCave.isFatal = 1;
133          simError();
# Line 130 | Line 145 | namespace TPE {  // restrict the access of the folowin
145          next->dipole   = info.dipole;
146          next->w0       = info.w0;
147          next->v0       = info.v0;
148 +        next->v0p      = info.v0p;
149 +        next->rl       = info.rl;
150 +        next->ru       = info.ru;
151 +        next->rlp      = info.rlp;
152 +        next->rup      = info.rup;
153          next->ident    = info.ident;
154        }
155      }
# Line 146 | Line 166 | namespace TPE {  // restrict the access of the folowin
166        info.dipole   = dipole;
167        info.w0       = w0;
168        info.v0       = v0;
169 +      info.v0p      = v0p;
170 +      info.rl       = rl;
171 +      info.ru       = ru;
172 +      info.rlp      = rlp;
173 +      info.rup      = rup;
174        info.ident    = ident;
175        info.last     = 0;
176      }
# Line 162 | Line 187 | namespace TPE {  // restrict the access of the folowin
187      double dipole;
188      double w0;
189      double v0;
190 +    double v0p;
191 +    double rl;
192 +    double ru;
193 +    double rlp;
194 +    double rup;
195      int ident;
196      LinkedAtomType* next;
197    };
# Line 172 | Line 202 | namespace TPE {  // restrict the access of the folowin
202        next = NULL;
203        nameA[0] = '\0';
204        nameB[0] = '\0';
175 –      type[0] = '\0';
205      }
206      ~LinkedBondType(){ if( next != NULL ) delete next; }
207  
# Line 194 | Line 223 | namespace TPE {  // restrict the access of the folowin
223        
224        if(dup){
225          sprintf( painCave.errMsg,
226 <                 "Duplicate TraPPE_Ex bond type \"%s - %s\" found in "
227 <                 "the TraPPE_ExFF param file./n",
226 >                 "Duplicate DUFF bond type \"%s - %s\" found in "
227 >                 "the DUFF param file./n",
228                   nameA, nameB );
229          painCave.isFatal = 1;
230          simError();
# Line 207 | Line 236 | namespace TPE {  // restrict the access of the folowin
236          next = new LinkedBondType();
237          strcpy(next->nameA, info.nameA);
238          strcpy(next->nameB, info.nameB);
239 <        strcpy(next->type,  info.type);
239 >        next->type = info.type;
240          next->d0 = info.d0;
241 +        next->k0 = info.k0;
242        }
243      }
244      
# Line 216 | Line 246 | namespace TPE {  // restrict the access of the folowin
246      void duplicate( bondStruct &info ){
247        strcpy(info.nameA, nameA);
248        strcpy(info.nameB, nameB);
249 <      strcpy(info.type,  type);
249 >      info.type = type;
250        info.d0   = d0;
251 +      info.k0   = k0;
252        info.last = 0;
253      }
254  
# Line 226 | Line 257 | namespace TPE {  // restrict the access of the folowin
257  
258      char nameA[15];
259      char nameB[15];
260 <    char type[30];
260 >    int type;
261      double d0;
262 +    double k0;
263  
264      LinkedBondType* next;
265    };
# Line 264 | Line 296 | namespace TPE {  // restrict the access of the folowin
296  
297        if(dup){
298          sprintf( painCave.errMsg,
299 <                 "Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in "
300 <                 "the TraPPE_ExFF param file./n",
299 >                 "Duplicate DUFF bend type \"%s - %s - %s\" found in "
300 >                 "the DUFF param file./n",
301                   nameA, nameB, nameC );
302          painCave.isFatal = 1;
303          simError();
# Line 349 | Line 381 | namespace TPE {  // restrict the access of the folowin
381        
382        if(dup){
383          sprintf( painCave.errMsg,
384 <                 "Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in "
385 <                 "the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD );
384 >                 "Duplicate DUFF torsion type \"%s - %s - %s - %s\" found in "
385 >                 "the DUFF param file./n", nameA, nameB, nameC, nameD );
386          painCave.isFatal = 1;
387          simError();
388        }
# Line 410 | Line 442 | using namespace TPE;
442  
443   } // namespace
444  
445 < using namespace TPE;
445 > using namespace DUFF_NS;
446  
447  
448   //****************************************************************
# Line 418 | Line 450 | TraPPE_ExFF::TraPPE_ExFF(){
450   //****************************************************************
451  
452  
453 < TraPPE_ExFF::TraPPE_ExFF(){
453 > DUFF::DUFF(){
454  
455    char fileName[200];
456    char* ffPath_env = "FORCE_PARAM_PATH";
457    char* ffPath;
458    char temp[200];
427 –  char errMsg[1000];
459  
460    headAtomType       = NULL;
461    currentAtomType    = NULL;
# Line 446 | Line 477 | TraPPE_ExFF::TraPPE_ExFF(){
477    // Init the atomStruct mpi type
478  
479    atomStruct atomProto; // mpiPrototype
480 <  int atomBC[3] = {15,6,4};  // block counts
480 >  int atomBC[3] = {15,12,5};  // block counts
481    MPI_Aint atomDspls[3];           // displacements
482    MPI_Datatype atomMbrTypes[3];    // member mpi types
483  
# Line 468 | Line 499 | TraPPE_ExFF::TraPPE_ExFF(){
499    // Init the bondStruct mpi type
500    
501    bondStruct bondProto; // mpiPrototype
502 <  int bondBC[3] = {60,1,1};  // block counts
502 >  int bondBC[3] = {30,2,2};  // block counts
503    MPI_Aint bondDspls[3];           // displacements
504    MPI_Datatype bondMbrTypes[3];    // member mpi types
505    
# Line 537 | Line 568 | TraPPE_ExFF::TraPPE_ExFF(){
568      
569      // generate the force file name
570      
571 <    strcpy( fileName, "TraPPE_Ex.frc" );
571 >    strcpy( fileName, "DUFF.frc" );
572      //    fprintf( stderr,"Trying to open %s\n", fileName );
573      
574      // attempt to open the file in the current directory first.
# Line 576 | Line 607 | TraPPE_ExFF::TraPPE_ExFF(){
607   #ifdef IS_MPI
608    }
609    
610 <  sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." );
610 >  sprintf( checkPointMsg, "DUFF file opened sucessfully." );
611    MPIcheckPoint();
612    
613   #endif // is_mpi
614   }
615  
616  
617 < TraPPE_ExFF::~TraPPE_ExFF(){
617 > DUFF::~DUFF(){
618  
619    if( headAtomType != NULL ) delete headAtomType;
620    if( headBondType != NULL ) delete headBondType;
# Line 601 | Line 632 | void TraPPE_ExFF::cleanMe( void ){
632   #endif // is_mpi
633   }
634  
635 < void TraPPE_ExFF::cleanMe( void ){
635 > void DUFF::cleanMe( void ){
636  
637   #ifdef IS_MPI
638    
# Line 620 | Line 651 | void TraPPE_ExFF::initForceField( int ljMixRule ){
651   }
652  
653  
654 < void TraPPE_ExFF::initForceField( int ljMixRule ){
654 > void DUFF::initForceField( int ljMixRule ){
655    
656    initFortran( ljMixRule, entry_plug->useReactionField );
657   }
658  
659  
660 < void TraPPE_ExFF::readParams( void ){
660 > void DUFF::readParams( void ){
661  
631 –  int i, a, b, c, d;
662    int identNum;
633 –  char* atomA;
634 –  char* atomB;
635 –  char* atomC;
636 –  char* atomD;
663    
664    atomStruct atomInfo;
665    bondStruct bondInfo;
# Line 698 | Line 724 | void TraPPE_ExFF::readParams( void ){
724      // send out the linked list to all the other processes
725  
726      sprintf( checkPointMsg,
727 <             "TraPPE_ExFF atom structures read successfully." );
727 >             "DUFF atom structures read successfully." );
728      MPIcheckPoint();
729  
730      currentAtomType = headAtomType->next; //skip the first element who is a place holder.
731      while( currentAtomType != NULL ){
732        currentAtomType->duplicate( atomInfo );
733  
708 –
709 –
734        sendFrcStruct( &atomInfo, mpiAtomStructType );
735  
736        sprintf( checkPointMsg,
737 <               "successfully sent TraPPE_Ex force type: \"%s\"\n",
737 >               "successfully sent DUFF force type: \"%s\"\n",
738                 atomInfo.name );
739        MPIcheckPoint();
740  
# Line 724 | Line 748 | void TraPPE_ExFF::readParams( void ){
748    else{
749      
750      // listen for node 0 to send out the force params
751 <    
751 >
752      MPIcheckPoint();
753  
754      headAtomType = new LinkedAtomType;
755 <    recieveFrcStruct( &atomInfo, mpiAtomStructType );
755 >    receiveFrcStruct( &atomInfo, mpiAtomStructType );
756      
757      while( !atomInfo.last ){
758  
735 –
736 –
759        headAtomType->add( atomInfo );
760        
761        MPIcheckPoint();
762  
763 <      recieveFrcStruct( &atomInfo, mpiAtomStructType );
763 >      receiveFrcStruct( &atomInfo, mpiAtomStructType );
764      }
765    }
766  
# Line 754 | Line 776 | void TraPPE_ExFF::readParams( void ){
776    
777    int isGB = 0;
778    int isLJ = 1;
779 <  double GB_dummy = 0.0;
780 <  
781 <  
779 >  int isEAM =0;
780 >  int isCharge = 0;
781 >  double charge=0.0;
782 >    
783    currentAtomType = headAtomType->next;;
784    while( currentAtomType != NULL ){
785      
786 <    if(currentAtomType->isDipole) entry_plug->useDipole = 1;
786 >    if(currentAtomType->isDipole) entry_plug->useDipoles = 1;
787      if(currentAtomType->isSSD) {
788        entry_plug->useSticky = 1;
789 <      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0));
789 >      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0),
790 >                         &(currentAtomType->v0p),
791 >                         &(currentAtomType->rl), &(currentAtomType->ru),
792 >                         &(currentAtomType->rlp), &(currentAtomType->rup));
793      }
794  
795      if( currentAtomType->name[0] != '\0' ){
# Line 773 | Line 799 | void TraPPE_ExFF::readParams( void ){
799                   &(currentAtomType->isSSD),
800                   &(currentAtomType->isDipole),
801                   &isGB,
802 +                 &isEAM,
803 +                 &isCharge,
804                   &(currentAtomType->epslon),
805                   &(currentAtomType->sigma),
806 +                 &charge,
807                   &(currentAtomType->dipole),
808                   &isError );
809        if( isError ){
# Line 790 | Line 819 | void TraPPE_ExFF::readParams( void ){
819        
820   #ifdef IS_MPI
821    sprintf( checkPointMsg,
822 <           "TraPPE_ExFF atom structures successfully sent to fortran\n" );
822 >           "DUFF atom structures successfully sent to fortran\n" );
823    MPIcheckPoint();
824   #endif // is_mpi
825  
# Line 844 | Line 873 | void TraPPE_ExFF::readParams( void ){
873      // send out the linked list to all the other processes
874      
875      sprintf( checkPointMsg,
876 <             "TraPPE_Ex bond structures read successfully." );
876 >             "DUFF bond structures read successfully." );
877      MPIcheckPoint();
878      
879      currentBondType = headBondType->next;
# Line 865 | Line 894 | void TraPPE_ExFF::readParams( void ){
894      MPIcheckPoint();
895  
896      headBondType = new LinkedBondType;
897 <    recieveFrcStruct( &bondInfo, mpiBondStructType );
897 >    receiveFrcStruct( &bondInfo, mpiBondStructType );
898      while( !bondInfo.last ){
899  
900        headBondType->add( bondInfo );
901 <      recieveFrcStruct( &bondInfo, mpiBondStructType );
901 >      receiveFrcStruct( &bondInfo, mpiBondStructType );
902      }
903    }
904  
905    sprintf( checkPointMsg,
906 <           "TraPPE_ExFF bond structures broadcast successfully." );
906 >           "DUFF bond structures broadcast successfully." );
907    MPIcheckPoint();
908  
909   #endif // is_mpi
# Line 927 | Line 956 | void TraPPE_ExFF::readParams( void ){
956      // send out the linked list to all the other processes
957  
958      sprintf( checkPointMsg,
959 <             "TraPPE_Ex bend structures read successfully." );
959 >             "DUFF bend structures read successfully." );
960      MPIcheckPoint();
961  
962      currentBendType = headBendType->next;
# Line 948 | Line 977 | void TraPPE_ExFF::readParams( void ){
977      MPIcheckPoint();
978  
979      headBendType = new LinkedBendType;
980 <    recieveFrcStruct( &bendInfo, mpiBendStructType );
980 >    receiveFrcStruct( &bendInfo, mpiBendStructType );
981      while( !bendInfo.last ){
982  
983        headBendType->add( bendInfo );
984 <      recieveFrcStruct( &bendInfo, mpiBendStructType );
984 >      receiveFrcStruct( &bendInfo, mpiBendStructType );
985      }
986    }
987  
988    sprintf( checkPointMsg,
989 <           "TraPPE_ExFF bend structures broadcast successfully." );
989 >           "DUFF bend structures broadcast successfully." );
990    MPIcheckPoint();
991  
992   #endif // is_mpi
# Line 1012 | Line 1041 | void TraPPE_ExFF::readParams( void ){
1041      // send out the linked list to all the other processes
1042      
1043      sprintf( checkPointMsg,
1044 <             "TraPPE_Ex torsion structures read successfully." );
1044 >             "DUFF torsion structures read successfully." );
1045      MPIcheckPoint();
1046      
1047      currentTorsionType = headTorsionType->next;
# Line 1033 | Line 1062 | void TraPPE_ExFF::readParams( void ){
1062      MPIcheckPoint();
1063  
1064      headTorsionType = new LinkedTorsionType;
1065 <    recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1065 >    receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1066      while( !torsionInfo.last ){
1067  
1068        headTorsionType->add( torsionInfo );
1069 <      recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1069 >      receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1070      }
1071    }
1072  
1073    sprintf( checkPointMsg,
1074 <           "TraPPE_ExFF torsion structures broadcast successfully." );
1074 >           "DUFF torsion structures broadcast successfully." );
1075    MPIcheckPoint();
1076  
1077   #endif // is_mpi
# Line 1052 | Line 1081 | void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom**
1081  
1082  
1083  
1084 < void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
1084 > void DUFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
1085    
1086    
1087    //////////////////////////////////////////////////
# Line 1141 | Line 1170 | void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom**
1170        else{
1171          
1172          sprintf( painCave.errMsg,
1173 <                "TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard"
1173 >                "DUFF error: Atom \"%s\" is a dipole, yet no standard"
1174                   " orientation was specifed in the BASS file.\n",
1175                   currentAtomType->name );
1176          painCave.isFatal = 1;
# Line 1151 | Line 1180 | void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom**
1180      else{
1181        if( the_atoms[i]->isDirectional() ){
1182          sprintf( painCave.errMsg,
1183 <                 "TraPPE_ExFF error: Atom \"%s\" was given a standard"
1183 >                 "DUFF error: Atom \"%s\" was given a standard"
1184                   "orientation in the BASS file, yet it is not a dipole.\n",
1185                   currentAtomType->name);
1186          painCave.isFatal = 1;
# Line 1161 | Line 1190 | void TraPPE_ExFF::initializeBonds( int nBonds, Bond**
1190    }
1191   }
1192  
1193 < void TraPPE_ExFF::initializeBonds( int nBonds, Bond** bondArray,
1193 > void DUFF::initializeBonds( int nBonds, Bond** bondArray,
1194                                     bond_pair* the_bonds ){
1195    int i,a,b;
1196    char* atomA;
# Line 1189 | Line 1218 | void TraPPE_ExFF::initializeBonds( int nBonds, Bond**
1218        simError();
1219      }
1220      
1221 <    if( !strcmp( currentBondType->type, "fixed" ) ){
1222 <      
1221 >    switch( currentBondType->type ){
1222 >
1223 >    case FIXED_BOND:
1224 >            
1225        bondArray[i] = new ConstrainedBond( *the_atoms[a],
1226                                            *the_atoms[b],
1227                                            currentBondType->d0 );
1228        entry_plug->n_constraints++;
1229 +      break;
1230 +
1231 +    case HARMONIC_BOND:
1232 +      
1233 +      bondArray[i] = new HarmonicBond( *the_atoms[a],
1234 +                                       *the_atoms[b],
1235 +                                       currentBondType->d0,
1236 +                                       currentBondType->k0 );
1237 +      break;
1238 +      
1239 +    default:
1240 +
1241 +      break;
1242 +      // do nothing
1243      }
1244    }
1245   }
1246  
1247 < void TraPPE_ExFF::initializeBends( int nBends, Bend** bendArray,
1247 > void DUFF::initializeBends( int nBends, Bend** bendArray,
1248                                     bend_set* the_bends ){
1249    
1250    QuadraticBend* qBend;
# Line 1259 | Line 1304 | void TraPPE_ExFF::initializeBends( int nBends, Bend**
1304          }
1305          
1306          gBend = new GhostBend( *the_atoms[a],
1307 <                               *the_atoms[b] );                        
1307 >                               *the_atoms[b]);
1308 >                                                                      
1309          gBend->setConstants( currentBendType->k1,
1310                               currentBendType->k2,
1311                               currentBendType->k3,
# Line 1275 | Line 1321 | void TraPPE_ExFF::initializeBends( int nBends, Bend**
1321                               currentBendType->k3,
1322                               currentBendType->t0 );
1323          bendArray[i] = qBend;
1324 <      }
1324 >      }      
1325      }
1326    }
1327   }
1328  
1329 < void TraPPE_ExFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
1329 > void DUFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
1330                                        torsion_set* the_torsions ){
1331  
1332    int i, a, b, c, d;
# Line 1327 | Line 1373 | void TraPPE_ExFF::fastForward( char* stopText, char* s
1373    }
1374   }
1375  
1376 < void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){
1376 > void DUFF::fastForward( char* stopText, char* searchOwner ){
1377  
1378    int foundText = 0;
1379    char* the_token;
# Line 1382 | Line 1428 | int TPE::parseAtom( char *lineBuffer, int lineNum, ato
1428   }
1429  
1430  
1431 < int TPE::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
1431 > int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
1432  
1433    char* the_token;
1434    
# Line 1468 | Line 1514 | int TPE::parseAtom( char *lineBuffer, int lineNum, ato
1514        }
1515        
1516        info.v0 = atof( the_token );
1517 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1518 +        sprintf( painCave.errMsg,
1519 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1520 +        painCave.isFatal = 1;
1521 +        simError();
1522 +      }
1523 +      
1524 +      info.v0p = atof( the_token );
1525 +
1526 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1527 +        sprintf( painCave.errMsg,
1528 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1529 +        painCave.isFatal = 1;
1530 +        simError();
1531 +      }
1532 +      
1533 +      info.rl = atof( the_token );
1534 +
1535 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1536 +        sprintf( painCave.errMsg,
1537 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1538 +        painCave.isFatal = 1;
1539 +        simError();
1540 +      }
1541 +      
1542 +      info.ru = atof( the_token );
1543 +
1544 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1545 +        sprintf( painCave.errMsg,
1546 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1547 +        painCave.isFatal = 1;
1548 +        simError();
1549 +      }
1550 +      
1551 +      info.rlp = atof( the_token );
1552 +
1553 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1554 +        sprintf( painCave.errMsg,
1555 +                 "Error parseing AtomTypes: line %d\n", lineNum );
1556 +        painCave.isFatal = 1;
1557 +        simError();
1558 +      }
1559 +      
1560 +      info.rup = atof( the_token );
1561      }
1562 <    else info.v0 = info.w0 = 0.0;
1562 >    else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0;
1563  
1564      return 1;
1565    }
1566    else return 0;
1567   }
1568  
1569 < int TPE::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
1569 > int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
1570  
1571    char* the_token;
1572 +  char bondType[30];
1573    
1574    the_token = strtok( lineBuffer, " \n\t,;" );
1575    if( the_token != NULL ){
# Line 1501 | Line 1592 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
1592        simError();
1593      }
1594      
1595 <    strcpy( info.type, the_token );
1595 >    strcpy( bondType, the_token );
1596      
1597 <    if( !strcmp( info.type, "fixed" ) ){
1597 >    if( !strcmp( bondType, "fixed" ) ){
1598 >      info.type = FIXED_BOND;
1599 >      
1600 >      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1601 >        sprintf( painCave.errMsg,
1602 >                 "Error parseing BondTypes: line %d\n", lineNum );
1603 >        painCave.isFatal = 1;
1604 >        simError();
1605 >      }
1606 >      
1607 >      info.d0 = atof( the_token );
1608 >      
1609 >      info.k0=0.0;
1610 >    }
1611 >    else if( !strcmp( bondType, "harmonic" ) ){
1612 >      info.type = HARMONIC_BOND;
1613 >      
1614        if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1615          sprintf( painCave.errMsg,
1616                   "Error parseing BondTypes: line %d\n", lineNum );
# Line 1512 | Line 1619 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
1619        }
1620        
1621        info.d0 = atof( the_token );
1622 +
1623 +      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1624 +        sprintf( painCave.errMsg,
1625 +                 "Error parseing BondTypes: line %d\n", lineNum );
1626 +        painCave.isFatal = 1;
1627 +        simError();
1628 +      }
1629 +      
1630 +      info.k0 = atof( the_token );
1631      }
1632 +
1633      else{
1634        sprintf( painCave.errMsg,
1635 <               "Unknown TraPPE_Ex bond type \"%s\" at line %d\n",
1636 <               info.type,
1635 >               "Unknown DUFF bond type \"%s\" at line %d\n",
1636 >               bondType,
1637                 lineNum );
1638        painCave.isFatal = 1;
1639        simError();
# Line 1528 | Line 1645 | int TPE::parseBend( char *lineBuffer, int lineNum, ben
1645   }
1646  
1647  
1648 < int TPE::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
1648 > int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
1649  
1650    char* the_token;
1651    
# Line 1604 | Line 1721 | int TPE::parseBend( char *lineBuffer, int lineNum, ben
1721      
1722      else{
1723        sprintf( painCave.errMsg,
1724 <               "Unknown TraPPE_Ex bend type \"%s\" at line %d\n",
1724 >               "Unknown DUFF bend type \"%s\" at line %d\n",
1725                 info.type,
1726                 lineNum );
1727        painCave.isFatal = 1;
# Line 1616 | Line 1733 | int TPE::parseTorsion( char *lineBuffer, int lineNum,
1733    else return 0;
1734   }
1735  
1736 < int TPE::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
1736 > int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
1737    
1738    char*  the_token;
1739  
# Line 1702 | Line 1819 | int TPE::parseTorsion( char *lineBuffer, int lineNum,
1819      
1820      else{
1821        sprintf( painCave.errMsg,
1822 <               "Unknown TraPPE_Ex torsion type \"%s\" at line %d\n",
1822 >               "Unknown DUFF torsion type \"%s\" at line %d\n",
1823                 info.type,
1824                 lineNum );
1825        painCave.isFatal = 1;

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