114 |
|
|
115 |
|
if( next != NULL ) next->add(info); |
116 |
|
else{ |
117 |
< |
next = new LinkedType(); |
117 |
> |
next = new LinkedAtomType(); |
118 |
|
strcpy(next->name, info.name); |
119 |
|
next->isDipole = info.isDipole; |
120 |
|
next->isSSD = info.isSSD; |
197 |
|
|
198 |
|
if( next != NULL ) next->add(info); |
199 |
|
else{ |
200 |
< |
next = new LinkedType(); |
200 |
> |
next = new LinkedBondType(); |
201 |
|
strcpy(next->nameA, info.nameA); |
202 |
|
strcpy(next->nameB, info.nameB); |
203 |
|
strcpy(next->type, info.type); |
266 |
|
|
267 |
|
if( next != NULL ) next->add(info); |
268 |
|
else{ |
269 |
< |
next = new LinkedType(); |
269 |
> |
next = new LinkedBendType(); |
270 |
|
strcpy(next->nameA, info.nameA); |
271 |
|
strcpy(next->nameB, info.nameB); |
272 |
|
strcpy(next->nameC, info.nameC); |
350 |
|
|
351 |
|
if( next != NULL ) next->add(info); |
352 |
|
else{ |
353 |
< |
next = new LinkedType(); |
353 |
> |
next = new LinkedTorsionType(); |
354 |
|
strcpy(next->nameA, info.nameA); |
355 |
|
strcpy(next->nameB, info.nameB); |
356 |
|
strcpy(next->nameC, info.nameC); |
842 |
|
"TraPPE_Ex bond structures read successfully." ); |
843 |
|
MPIcheckPoint(); |
844 |
|
|
845 |
< |
currentBondType = headBondType; |
845 |
> |
currentBondType = headBondType->next; |
846 |
|
while( currentBondType != NULL ){ |
847 |
|
currentBondType->duplicate( bondInfo ); |
848 |
|
sendFrcStruct( &bondInfo, mpiBondStructType ); |
857 |
|
|
858 |
|
// listen for node 0 to send out the force params |
859 |
|
|
860 |
< |
MPIcheckPoint(); |
860 |
> |
MPIcheckPoint(); |
861 |
|
|
862 |
|
headBondType = new LinkedBondType; |
863 |
|
recieveFrcStruct( &bondInfo, mpiBondStructType ); |
920 |
|
"TraPPE_Ex bend structures read successfully." ); |
921 |
|
MPIcheckPoint(); |
922 |
|
|
923 |
< |
currentBendType = headBendType; |
923 |
> |
currentBendType = headBendType->next; |
924 |
|
while( currentBendType != NULL ){ |
925 |
|
currentBendType->duplicate( bendInfo ); |
926 |
|
sendFrcStruct( &bendInfo, mpiBendStructType ); |
1000 |
|
"TraPPE_Ex torsion structures read successfully." ); |
1001 |
|
MPIcheckPoint(); |
1002 |
|
|
1003 |
< |
currentTorsionType = headTorsionType; |
1003 |
> |
currentTorsionType = headTorsionType->next; |
1004 |
|
while( currentTorsionType != NULL ){ |
1005 |
|
currentTorsionType->duplicate( torsionInfo ); |
1006 |
|
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1027 |
|
} |
1028 |
|
#endif // is_mpi |
1029 |
|
|
1030 |
+ |
entry_plug->useLJ = 1; |
1031 |
|
} |
1032 |
|
|
1033 |
|
|
1072 |
|
|
1073 |
|
DirectionalAtom* dAtom; |
1074 |
|
|
1075 |
< |
for( i=0; i<nAtoms; i++ ){ |
1075 |
> |
for(int i=0; i<nAtoms; i++ ){ |
1076 |
|
|
1077 |
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
1078 |
|
if( currentAtomType == NULL ){ |
1139 |
|
} |
1140 |
|
} |
1141 |
|
} |
1141 |
– |
|
1142 |
– |
|
1143 |
– |
#ifdef IS_MPI |
1144 |
– |
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
1145 |
– |
MPIcheckPoint(); |
1146 |
– |
#endif // is_mpi |
1147 |
– |
|
1142 |
|
} |
1143 |
|
|
1144 |
|
void TraPPE_ExFF::initializeBonds( int nBonds, Bond** bondArray, |
1177 |
|
entry_plug->n_constraints++; |
1178 |
|
} |
1179 |
|
} |
1186 |
– |
|
1187 |
– |
#ifdef IS_MPI |
1188 |
– |
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
1189 |
– |
MPIcheckPoint(); |
1190 |
– |
#endif // is_mpi |
1191 |
– |
|
1180 |
|
} |
1181 |
|
|
1182 |
|
void TraPPE_ExFF::initializeBends( int nBends, Bend** bendArray, |
1258 |
|
} |
1259 |
|
} |
1260 |
|
} |
1273 |
– |
|
1274 |
– |
#ifdef IS_MPI |
1275 |
– |
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1276 |
– |
MPIcheckPoint(); |
1277 |
– |
#endif // is_mpi |
1278 |
– |
|
1261 |
|
} |
1262 |
|
|
1263 |
|
void TraPPE_ExFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1305 |
|
torsionArray[i] = cTors; |
1306 |
|
} |
1307 |
|
} |
1326 |
– |
|
1327 |
– |
#ifdef IS_MPI |
1328 |
– |
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1329 |
– |
MPIcheckPoint(); |
1330 |
– |
#endif // is_mpi |
1331 |
– |
|
1308 |
|
} |
1309 |
|
|
1310 |
|
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |