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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 1224 by gezelter, Wed Jun 2 18:27:52 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 | using namespace std;
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 101 | Line 116 | namespace TPE {  // restrict the access of the folowin
116      void printMe( void ){
117        
118        std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n";
119 <      if( next != NULL ) next->printMe();
119 >      //      if( next != NULL ) next->printMe();
120  
121      }
122  
# 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 | namespace TPE {  // restrict the access of the folowin
442  
443   } // namespace
444  
445 < using namespace TPE;
445 > using namespace DUFF_NS;
446  
447  
448   //****************************************************************
# Line 418 | Line 450 | using namespace TPE;
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 564 | Line 595 | TraPPE_ExFF::TraPPE_ExFF(){
595        if( frcFile == NULL ){
596          
597          sprintf( painCave.errMsg,
598 <                 "Error opening the force field parameter file: %s\n"
599 <                 "Have you tried setting the FORCE_PARAM_PATH environment "
600 <                 "vairable?\n",
598 >                 "Error opening the force field parameter file:\n"
599 >                 "\t%s\n"
600 >                 "\tHave you tried setting the FORCE_PARAM_PATH environment "
601 >                 "variable?\n",
602                   fileName );
603 +        painCave.severity = OOPSE_ERROR;
604          painCave.isFatal = 1;
605          simError();
606        }
# Line 576 | Line 609 | TraPPE_ExFF::TraPPE_ExFF(){
609   #ifdef IS_MPI
610    }
611    
612 <  sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." );
612 >  sprintf( checkPointMsg, "DUFF file opened sucessfully." );
613    MPIcheckPoint();
614    
615   #endif // is_mpi
616   }
617  
618  
619 < TraPPE_ExFF::~TraPPE_ExFF(){
619 > DUFF::~DUFF(){
620  
621    if( headAtomType != NULL ) delete headAtomType;
622    if( headBondType != NULL ) delete headBondType;
# Line 601 | Line 634 | TraPPE_ExFF::~TraPPE_ExFF(){
634   #endif // is_mpi
635   }
636  
637 < void TraPPE_ExFF::cleanMe( void ){
637 > void DUFF::cleanMe( void ){
638  
639   #ifdef IS_MPI
640    
# Line 620 | Line 653 | void TraPPE_ExFF::cleanMe( void ){
653   }
654  
655  
656 < void TraPPE_ExFF::initForceField( int ljMixRule ){
656 > void DUFF::initForceField( int ljMixRule ){
657    
658    initFortran( ljMixRule, entry_plug->useReactionField );
659   }
660  
661  
662 < void TraPPE_ExFF::readParams( void ){
662 > void DUFF::readParams( void ){
663  
631 –  int i, a, b, c, d;
664    int identNum;
633 –  char* atomA;
634 –  char* atomB;
635 –  char* atomC;
636 –  char* atomD;
665    
666    atomStruct atomInfo;
667    bondStruct bondInfo;
# Line 698 | Line 726 | void TraPPE_ExFF::readParams( void ){
726      // send out the linked list to all the other processes
727  
728      sprintf( checkPointMsg,
729 <             "TraPPE_ExFF atom structures read successfully." );
729 >             "DUFF atom structures read successfully." );
730      MPIcheckPoint();
731  
732      currentAtomType = headAtomType->next; //skip the first element who is a place holder.
733      while( currentAtomType != NULL ){
734        currentAtomType->duplicate( atomInfo );
735  
708 –
709 –
736        sendFrcStruct( &atomInfo, mpiAtomStructType );
737  
738        sprintf( checkPointMsg,
739 <               "successfully sent TraPPE_Ex force type: \"%s\"\n",
739 >               "successfully sent DUFF force type: \"%s\"\n",
740                 atomInfo.name );
741        MPIcheckPoint();
742  
# Line 724 | Line 750 | void TraPPE_ExFF::readParams( void ){
750    else{
751      
752      // listen for node 0 to send out the force params
753 <    
753 >
754      MPIcheckPoint();
755  
756      headAtomType = new LinkedAtomType;
757 <    recieveFrcStruct( &atomInfo, mpiAtomStructType );
757 >    receiveFrcStruct( &atomInfo, mpiAtomStructType );
758      
759      while( !atomInfo.last ){
760  
735 –
736 –
761        headAtomType->add( atomInfo );
762        
763        MPIcheckPoint();
764  
765 <      recieveFrcStruct( &atomInfo, mpiAtomStructType );
765 >      receiveFrcStruct( &atomInfo, mpiAtomStructType );
766      }
767    }
768  
# Line 754 | Line 778 | void TraPPE_ExFF::readParams( void ){
778    
779    int isGB = 0;
780    int isLJ = 1;
781 <  double GB_dummy = 0.0;
782 <  
783 <  
781 >  int isEAM =0;
782 >  int isCharge = 0;
783 >  double charge=0.0;
784 >    
785    currentAtomType = headAtomType->next;;
786    while( currentAtomType != NULL ){
787      
788 <    if(currentAtomType->isDipole) entry_plug->useDipole = 1;
788 >    if(currentAtomType->isDipole) entry_plug->useDipoles = 1;
789      if(currentAtomType->isSSD) {
790        entry_plug->useSticky = 1;
791 <      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0));
791 >      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0),
792 >                         &(currentAtomType->v0p),
793 >                         &(currentAtomType->rl), &(currentAtomType->ru),
794 >                         &(currentAtomType->rlp), &(currentAtomType->rup));
795      }
796  
797      if( currentAtomType->name[0] != '\0' ){
# Line 773 | Line 801 | void TraPPE_ExFF::readParams( void ){
801                   &(currentAtomType->isSSD),
802                   &(currentAtomType->isDipole),
803                   &isGB,
804 +                 &isEAM,
805 +                 &isCharge,
806                   &(currentAtomType->epslon),
807                   &(currentAtomType->sigma),
808 +                 &charge,
809                   &(currentAtomType->dipole),
810                   &isError );
811        if( isError ){
# Line 790 | Line 821 | void TraPPE_ExFF::readParams( void ){
821        
822   #ifdef IS_MPI
823    sprintf( checkPointMsg,
824 <           "TraPPE_ExFF atom structures successfully sent to fortran\n" );
824 >           "DUFF atom structures successfully sent to fortran\n" );
825    MPIcheckPoint();
826   #endif // is_mpi
827  
# Line 844 | Line 875 | void TraPPE_ExFF::readParams( void ){
875      // send out the linked list to all the other processes
876      
877      sprintf( checkPointMsg,
878 <             "TraPPE_Ex bond structures read successfully." );
878 >             "DUFF bond structures read successfully." );
879      MPIcheckPoint();
880      
881      currentBondType = headBondType->next;
# Line 865 | Line 896 | void TraPPE_ExFF::readParams( void ){
896      MPIcheckPoint();
897  
898      headBondType = new LinkedBondType;
899 <    recieveFrcStruct( &bondInfo, mpiBondStructType );
899 >    receiveFrcStruct( &bondInfo, mpiBondStructType );
900      while( !bondInfo.last ){
901  
902        headBondType->add( bondInfo );
903 <      recieveFrcStruct( &bondInfo, mpiBondStructType );
903 >      receiveFrcStruct( &bondInfo, mpiBondStructType );
904      }
905    }
906  
907    sprintf( checkPointMsg,
908 <           "TraPPE_ExFF bond structures broadcast successfully." );
908 >           "DUFF bond structures broadcast successfully." );
909    MPIcheckPoint();
910  
911   #endif // is_mpi
# Line 893 | Line 924 | void TraPPE_ExFF::readParams( void ){
924      fastForward( "BendTypes", "initializeBends" );
925  
926      // we are now at the bendTypes section
927 <
927 >    
928      eof_test =  fgets( readLine, sizeof(readLine), frcFile );
929      lineNum++;
930          
# Line 927 | Line 958 | void TraPPE_ExFF::readParams( void ){
958      // send out the linked list to all the other processes
959  
960      sprintf( checkPointMsg,
961 <             "TraPPE_Ex bend structures read successfully." );
961 >             "DUFF bend structures read successfully." );
962      MPIcheckPoint();
963  
964      currentBendType = headBendType->next;
# Line 948 | Line 979 | void TraPPE_ExFF::readParams( void ){
979      MPIcheckPoint();
980  
981      headBendType = new LinkedBendType;
982 <    recieveFrcStruct( &bendInfo, mpiBendStructType );
982 >    receiveFrcStruct( &bendInfo, mpiBendStructType );
983      while( !bendInfo.last ){
984  
985        headBendType->add( bendInfo );
986 <      recieveFrcStruct( &bendInfo, mpiBendStructType );
986 >      receiveFrcStruct( &bendInfo, mpiBendStructType );
987      }
988    }
989  
990    sprintf( checkPointMsg,
991 <           "TraPPE_ExFF bend structures broadcast successfully." );
991 >           "DUFF bend structures broadcast successfully." );
992    MPIcheckPoint();
993  
994   #endif // is_mpi
# Line 1012 | Line 1043 | void TraPPE_ExFF::readParams( void ){
1043      // send out the linked list to all the other processes
1044      
1045      sprintf( checkPointMsg,
1046 <             "TraPPE_Ex torsion structures read successfully." );
1046 >             "DUFF torsion structures read successfully." );
1047      MPIcheckPoint();
1048      
1049      currentTorsionType = headTorsionType->next;
# Line 1033 | Line 1064 | void TraPPE_ExFF::readParams( void ){
1064      MPIcheckPoint();
1065  
1066      headTorsionType = new LinkedTorsionType;
1067 <    recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1067 >    receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1068      while( !torsionInfo.last ){
1069  
1070        headTorsionType->add( torsionInfo );
1071 <      recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
1071 >      receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1072      }
1073    }
1074  
1075    sprintf( checkPointMsg,
1076 <           "TraPPE_ExFF torsion structures broadcast successfully." );
1076 >           "DUFF torsion structures broadcast successfully." );
1077    MPIcheckPoint();
1078  
1079   #endif // is_mpi
# Line 1052 | Line 1083 | void TraPPE_ExFF::readParams( void ){
1083  
1084  
1085  
1086 < void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
1086 > void DUFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
1087    
1088    
1089    //////////////////////////////////////////////////
# Line 1091 | Line 1122 | void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom**
1122    // initialize the atoms
1123    
1124    DirectionalAtom* dAtom;
1125 +  double ji[3];
1126  
1127    for(int i=0; i<nAtoms; i++ ){
1128  
# Line 1104 | Line 1136 | void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom**
1136      }
1137      
1138      the_atoms[i]->setMass( currentAtomType->mass );
1107 –    the_atoms[i]->setEpslon( currentAtomType->epslon );
1108 –    the_atoms[i]->setSigma( currentAtomType->sigma );
1139      the_atoms[i]->setIdent( currentAtomType->ident );
1110 –    the_atoms[i]->setLJ();
1140  
1141      if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
1142  
# Line 1115 | Line 1144 | void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom**
1144        if( the_atoms[i]->isDirectional() ){
1145          
1146          dAtom = (DirectionalAtom *) the_atoms[i];
1118 –        dAtom->setMu( currentAtomType->dipole );
1147          dAtom->setHasDipole( 1 );
1148 <        dAtom->setJx( 0.0 );
1149 <        dAtom->setJy( 0.0 );
1150 <        dAtom->setJz( 0.0 );
1148 >
1149 >        ji[0] = 0.0;
1150 >        ji[1] = 0.0;
1151 >        ji[2] = 0.0;
1152 >
1153 >        dAtom->setJ( ji );
1154          
1155          if(!strcmp("SSD",the_atoms[i]->getType())){
1156            dAtom->setI( waterI );
1126 –          dAtom->setSSD( 1 );
1157          }
1158          else if(!strcmp("HEAD",the_atoms[i]->getType())){
1159            dAtom->setI( headI );
1130 –          dAtom->setSSD( 0 );
1160          }
1161          else{
1162            sprintf(painCave.errMsg,
# 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::initializeAtoms( int nAtoms, Atom**
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::initializeTorsions( int nTorsions, T
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 | void TraPPE_ExFF::fastForward( char* stopText, char* s
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 );
# Line 1512 | Line 1605 | int TPE::parseBond( char *lineBuffer, int lineNum, bon
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 );
1617 +        painCave.isFatal = 1;
1618 +        simError();
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::parseBond( char *lineBuffer, int lineNum, bon
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::parseBend( char *lineBuffer, int lineNum, ben
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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