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; |