111 |
|
|
112 |
|
if( !strcmp( info.name, name ) ){ |
113 |
|
sprintf( painCave.errMsg, |
114 |
< |
"Duplicate TraPPE_Ex atom type \"%s\" found in " |
115 |
< |
"the TraPPE_ExFF param file./n", |
114 |
> |
"Duplicate DUFF atom type \"%s\" found in " |
115 |
> |
"the DUFF param file./n", |
116 |
|
name ); |
117 |
|
painCave.isFatal = 1; |
118 |
|
simError(); |
194 |
|
|
195 |
|
if(dup){ |
196 |
|
sprintf( painCave.errMsg, |
197 |
< |
"Duplicate TraPPE_Ex bond type \"%s - %s\" found in " |
198 |
< |
"the TraPPE_ExFF param file./n", |
197 |
> |
"Duplicate DUFF bond type \"%s - %s\" found in " |
198 |
> |
"the DUFF param file./n", |
199 |
|
nameA, nameB ); |
200 |
|
painCave.isFatal = 1; |
201 |
|
simError(); |
264 |
|
|
265 |
|
if(dup){ |
266 |
|
sprintf( painCave.errMsg, |
267 |
< |
"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in " |
268 |
< |
"the TraPPE_ExFF param file./n", |
267 |
> |
"Duplicate DUFF bend type \"%s - %s - %s\" found in " |
268 |
> |
"the DUFF param file./n", |
269 |
|
nameA, nameB, nameC ); |
270 |
|
painCave.isFatal = 1; |
271 |
|
simError(); |
349 |
|
|
350 |
|
if(dup){ |
351 |
|
sprintf( painCave.errMsg, |
352 |
< |
"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in " |
353 |
< |
"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD ); |
352 |
> |
"Duplicate DUFF torsion type \"%s - %s - %s - %s\" found in " |
353 |
> |
"the DUFF param file./n", nameA, nameB, nameC, nameD ); |
354 |
|
painCave.isFatal = 1; |
355 |
|
simError(); |
356 |
|
} |
418 |
|
//**************************************************************** |
419 |
|
|
420 |
|
|
421 |
< |
TraPPE_ExFF::TraPPE_ExFF(){ |
421 |
> |
DUFF::DUFF(){ |
422 |
|
|
423 |
|
char fileName[200]; |
424 |
|
char* ffPath_env = "FORCE_PARAM_PATH"; |
537 |
|
|
538 |
|
// generate the force file name |
539 |
|
|
540 |
< |
strcpy( fileName, "TraPPE_Ex.frc" ); |
540 |
> |
strcpy( fileName, "DUFF.frc" ); |
541 |
|
// fprintf( stderr,"Trying to open %s\n", fileName ); |
542 |
|
|
543 |
|
// attempt to open the file in the current directory first. |
576 |
|
#ifdef IS_MPI |
577 |
|
} |
578 |
|
|
579 |
< |
sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." ); |
579 |
> |
sprintf( checkPointMsg, "DUFF file opened sucessfully." ); |
580 |
|
MPIcheckPoint(); |
581 |
|
|
582 |
|
#endif // is_mpi |
583 |
|
} |
584 |
|
|
585 |
|
|
586 |
< |
TraPPE_ExFF::~TraPPE_ExFF(){ |
586 |
> |
DUFF::~DUFF(){ |
587 |
|
|
588 |
|
if( headAtomType != NULL ) delete headAtomType; |
589 |
|
if( headBondType != NULL ) delete headBondType; |
601 |
|
#endif // is_mpi |
602 |
|
} |
603 |
|
|
604 |
< |
void TraPPE_ExFF::cleanMe( void ){ |
604 |
> |
void DUFF::cleanMe( void ){ |
605 |
|
|
606 |
|
#ifdef IS_MPI |
607 |
|
|
620 |
|
} |
621 |
|
|
622 |
|
|
623 |
< |
void TraPPE_ExFF::initForceField( int ljMixRule ){ |
623 |
> |
void DUFF::initForceField( int ljMixRule ){ |
624 |
|
|
625 |
|
initFortran( ljMixRule, entry_plug->useReactionField ); |
626 |
|
} |
627 |
|
|
628 |
|
|
629 |
< |
void TraPPE_ExFF::readParams( void ){ |
629 |
> |
void DUFF::readParams( void ){ |
630 |
|
|
631 |
|
int i, a, b, c, d; |
632 |
|
int identNum; |
698 |
|
// send out the linked list to all the other processes |
699 |
|
|
700 |
|
sprintf( checkPointMsg, |
701 |
< |
"TraPPE_ExFF atom structures read successfully." ); |
701 |
> |
"DUFF atom structures read successfully." ); |
702 |
|
MPIcheckPoint(); |
703 |
|
|
704 |
|
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
710 |
|
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
711 |
|
|
712 |
|
sprintf( checkPointMsg, |
713 |
< |
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
713 |
> |
"successfully sent DUFF force type: \"%s\"\n", |
714 |
|
atomInfo.name ); |
715 |
|
MPIcheckPoint(); |
716 |
|
|
790 |
|
|
791 |
|
#ifdef IS_MPI |
792 |
|
sprintf( checkPointMsg, |
793 |
< |
"TraPPE_ExFF atom structures successfully sent to fortran\n" ); |
793 |
> |
"DUFF atom structures successfully sent to fortran\n" ); |
794 |
|
MPIcheckPoint(); |
795 |
|
#endif // is_mpi |
796 |
|
|
844 |
|
// send out the linked list to all the other processes |
845 |
|
|
846 |
|
sprintf( checkPointMsg, |
847 |
< |
"TraPPE_Ex bond structures read successfully." ); |
847 |
> |
"DUFF bond structures read successfully." ); |
848 |
|
MPIcheckPoint(); |
849 |
|
|
850 |
|
currentBondType = headBondType->next; |
874 |
|
} |
875 |
|
|
876 |
|
sprintf( checkPointMsg, |
877 |
< |
"TraPPE_ExFF bond structures broadcast successfully." ); |
877 |
> |
"DUFF bond structures broadcast successfully." ); |
878 |
|
MPIcheckPoint(); |
879 |
|
|
880 |
|
#endif // is_mpi |
927 |
|
// send out the linked list to all the other processes |
928 |
|
|
929 |
|
sprintf( checkPointMsg, |
930 |
< |
"TraPPE_Ex bend structures read successfully." ); |
930 |
> |
"DUFF bend structures read successfully." ); |
931 |
|
MPIcheckPoint(); |
932 |
|
|
933 |
|
currentBendType = headBendType->next; |
957 |
|
} |
958 |
|
|
959 |
|
sprintf( checkPointMsg, |
960 |
< |
"TraPPE_ExFF bend structures broadcast successfully." ); |
960 |
> |
"DUFF bend structures broadcast successfully." ); |
961 |
|
MPIcheckPoint(); |
962 |
|
|
963 |
|
#endif // is_mpi |
1012 |
|
// send out the linked list to all the other processes |
1013 |
|
|
1014 |
|
sprintf( checkPointMsg, |
1015 |
< |
"TraPPE_Ex torsion structures read successfully." ); |
1015 |
> |
"DUFF torsion structures read successfully." ); |
1016 |
|
MPIcheckPoint(); |
1017 |
|
|
1018 |
|
currentTorsionType = headTorsionType->next; |
1042 |
|
} |
1043 |
|
|
1044 |
|
sprintf( checkPointMsg, |
1045 |
< |
"TraPPE_ExFF torsion structures broadcast successfully." ); |
1045 |
> |
"DUFF torsion structures broadcast successfully." ); |
1046 |
|
MPIcheckPoint(); |
1047 |
|
|
1048 |
|
#endif // is_mpi |
1052 |
|
|
1053 |
|
|
1054 |
|
|
1055 |
< |
void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
1055 |
> |
void DUFF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
1056 |
|
|
1057 |
|
|
1058 |
|
////////////////////////////////////////////////// |
1141 |
|
else{ |
1142 |
|
|
1143 |
|
sprintf( painCave.errMsg, |
1144 |
< |
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
1144 |
> |
"DUFF error: Atom \"%s\" is a dipole, yet no standard" |
1145 |
|
" orientation was specifed in the BASS file.\n", |
1146 |
|
currentAtomType->name ); |
1147 |
|
painCave.isFatal = 1; |
1151 |
|
else{ |
1152 |
|
if( the_atoms[i]->isDirectional() ){ |
1153 |
|
sprintf( painCave.errMsg, |
1154 |
< |
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
1154 |
> |
"DUFF error: Atom \"%s\" was given a standard" |
1155 |
|
"orientation in the BASS file, yet it is not a dipole.\n", |
1156 |
|
currentAtomType->name); |
1157 |
|
painCave.isFatal = 1; |
1161 |
|
} |
1162 |
|
} |
1163 |
|
|
1164 |
< |
void TraPPE_ExFF::initializeBonds( int nBonds, Bond** bondArray, |
1164 |
> |
void DUFF::initializeBonds( int nBonds, Bond** bondArray, |
1165 |
|
bond_pair* the_bonds ){ |
1166 |
|
int i,a,b; |
1167 |
|
char* atomA; |
1199 |
|
} |
1200 |
|
} |
1201 |
|
|
1202 |
< |
void TraPPE_ExFF::initializeBends( int nBends, Bend** bendArray, |
1202 |
> |
void DUFF::initializeBends( int nBends, Bend** bendArray, |
1203 |
|
bend_set* the_bends ){ |
1204 |
|
|
1205 |
|
QuadraticBend* qBend; |
1280 |
|
} |
1281 |
|
} |
1282 |
|
|
1283 |
< |
void TraPPE_ExFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1283 |
> |
void DUFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1284 |
|
torsion_set* the_torsions ){ |
1285 |
|
|
1286 |
|
int i, a, b, c, d; |
1327 |
|
} |
1328 |
|
} |
1329 |
|
|
1330 |
< |
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |
1330 |
> |
void DUFF::fastForward( char* stopText, char* searchOwner ){ |
1331 |
|
|
1332 |
|
int foundText = 0; |
1333 |
|
char* the_token; |
1515 |
|
} |
1516 |
|
else{ |
1517 |
|
sprintf( painCave.errMsg, |
1518 |
< |
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
1518 |
> |
"Unknown DUFF bond type \"%s\" at line %d\n", |
1519 |
|
info.type, |
1520 |
|
lineNum ); |
1521 |
|
painCave.isFatal = 1; |
1604 |
|
|
1605 |
|
else{ |
1606 |
|
sprintf( painCave.errMsg, |
1607 |
< |
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1607 |
> |
"Unknown DUFF bend type \"%s\" at line %d\n", |
1608 |
|
info.type, |
1609 |
|
lineNum ); |
1610 |
|
painCave.isFatal = 1; |
1702 |
|
|
1703 |
|
else{ |
1704 |
|
sprintf( painCave.errMsg, |
1705 |
< |
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1705 |
> |
"Unknown DUFF torsion type \"%s\" at line %d\n", |
1706 |
|
info.type, |
1707 |
|
lineNum ); |
1708 |
|
painCave.isFatal = 1; |