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 |
|
|
922 |
|
fastForward( "BendTypes", "initializeBends" ); |
923 |
|
|
924 |
|
// we are now at the bendTypes section |
925 |
< |
|
925 |
> |
|
926 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
927 |
|
lineNum++; |
928 |
|
|
1120 |
|
// initialize the atoms |
1121 |
|
|
1122 |
|
DirectionalAtom* dAtom; |
1123 |
+ |
double ji[3]; |
1124 |
|
|
1125 |
|
for(int i=0; i<nAtoms; i++ ){ |
1126 |
|
|
1134 |
|
} |
1135 |
|
|
1136 |
|
the_atoms[i]->setMass( currentAtomType->mass ); |
1136 |
– |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
1137 |
– |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
1137 |
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
1139 |
– |
the_atoms[i]->setLJ(); |
1138 |
|
|
1139 |
|
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
1140 |
|
|
1142 |
|
if( the_atoms[i]->isDirectional() ){ |
1143 |
|
|
1144 |
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
1147 |
– |
dAtom->setMu( currentAtomType->dipole ); |
1145 |
|
dAtom->setHasDipole( 1 ); |
1146 |
< |
dAtom->setJx( 0.0 ); |
1147 |
< |
dAtom->setJy( 0.0 ); |
1148 |
< |
dAtom->setJz( 0.0 ); |
1146 |
> |
|
1147 |
> |
ji[0] = 0.0; |
1148 |
> |
ji[1] = 0.0; |
1149 |
> |
ji[2] = 0.0; |
1150 |
> |
|
1151 |
> |
dAtom->setJ( ji ); |
1152 |
|
|
1153 |
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
1154 |
|
dAtom->setI( waterI ); |
1155 |
– |
dAtom->setSSD( 1 ); |
1155 |
|
} |
1156 |
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
1157 |
|
dAtom->setI( headI ); |
1159 |
– |
dAtom->setSSD( 0 ); |
1158 |
|
} |
1159 |
|
else{ |
1160 |
|
sprintf(painCave.errMsg, |
1178 |
|
else{ |
1179 |
|
if( the_atoms[i]->isDirectional() ){ |
1180 |
|
sprintf( painCave.errMsg, |
1181 |
< |
"DUFF error: Atom \"%s\" was given a standard" |
1181 |
> |
"DUFF error: Atom \"%s\" was given a standard " |
1182 |
|
"orientation in the BASS file, yet it is not a dipole.\n", |
1183 |
|
currentAtomType->name); |
1184 |
|
painCave.isFatal = 1; |