| 76 |
|
std::string line; |
| 77 |
|
char buffer[bufferSize]; |
| 78 |
|
int lineNo = 0; |
| 79 |
< |
int atomIdent = 1; //atom's indent begins from 1 (since only fortran's array begins from 1) |
| 79 |
> |
int atomIdent = getNAtomType() + 1; //atom's indent begins from 1 (since only fortran's array begins from 1) |
| 80 |
|
ParseState currentSection = DUFF::UnknownSection; |
| 81 |
|
|
| 82 |
|
while(ffStream.getline(buffer, bufferSize)){ |
| 198 |
|
atomType->setName(atomTypeName); |
| 199 |
|
atomType->setMass(mass); |
| 200 |
|
|
| 201 |
< |
//by default, all of the properties in AtomTypeProperties is set to 0 |
| 202 |
< |
//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true |
| 203 |
< |
atomType->setLennardJones(); |
| 201 |
> |
if (isLJ) { |
| 202 |
> |
atomType->setLennardJones(); |
| 203 |
> |
} |
| 204 |
|
|
| 205 |
+ |
if (isCharge) { |
| 206 |
+ |
atomType->setCharge(); |
| 207 |
+ |
} |
| 208 |
+ |
|
| 209 |
|
atomType->setIdent(ident); |
| 210 |
|
|
| 211 |
|
atomType->complete(); |
| 265 |
|
|
| 266 |
|
} |
| 267 |
|
|
| 268 |
< |
dAtomType->setDipole(isDipole); |
| 269 |
< |
dAtomType->setSticky(isSticky); |
| 268 |
> |
if (isDipole) { |
| 269 |
> |
dAtomType->setDipole(); |
| 270 |
> |
} |
| 271 |
|
|
| 272 |
+ |
if (isSticky) { |
| 273 |
+ |
dAtomType->setSticky(); |
| 274 |
+ |
} |
| 275 |
+ |
|
| 276 |
|
Mat3x3d inertialMat; |
| 277 |
|
inertialMat(0, 0) = Ixx; |
| 278 |
|
inertialMat(1, 1) = Ixx; |
