257 |
|
} |
258 |
|
|
259 |
|
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) { |
260 |
< |
BendType* bendType; |
261 |
< |
Atom* atomA; |
262 |
< |
Atom* atomB; |
263 |
< |
Atom* atomC; |
264 |
< |
|
265 |
< |
//need to consider the ghost bend |
266 |
< |
atomA = mol->getAtomAt(stamp->getA()); |
267 |
< |
atomB = mol->getAtomAt(stamp->getB()); |
268 |
< |
atomC = mol->getAtomAt(stamp->getC()); |
260 |
> |
bool isGhostBend = false; |
261 |
> |
int ghostIndex; |
262 |
|
|
270 |
– |
assert( atomA && atomB && atomC); |
263 |
|
|
264 |
< |
bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType()); |
264 |
> |
// |
265 |
> |
if (stamp->haveExtras()){ |
266 |
> |
LinkedAssign* extras = currentBend->getExtras(); |
267 |
> |
LinkedAssign* currentExtra = extras; |
268 |
|
|
269 |
< |
if (bendType == NULL) { |
270 |
< |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
271 |
< |
atomA->getType().c_str(), |
272 |
< |
atomB->getType().c_str(), |
273 |
< |
atomC->getType().c_str()); |
269 |
> |
while (currentExtra != NULL){ |
270 |
> |
if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){ |
271 |
> |
switch (currentExtra->getType()){ |
272 |
> |
case 0: |
273 |
> |
ghostIndex = currentExtra->getInt(); |
274 |
> |
isGhostBend = true; |
275 |
> |
break; |
276 |
|
|
277 |
< |
painCave.isFatal = 1; |
278 |
< |
simError(); |
277 |
> |
default: |
278 |
> |
sprintf(painCave.errMsg, |
279 |
> |
"SimSetup Error: ghostVectorSource must be an int.\n"); |
280 |
> |
painCave.isFatal = 1; |
281 |
> |
simError(); |
282 |
> |
} |
283 |
> |
} else{ |
284 |
> |
sprintf(painCave.errMsg, |
285 |
> |
"SimSetup Error: unhandled bend assignment:\n"); |
286 |
> |
painCave.isFatal = 1; |
287 |
> |
simError(); |
288 |
> |
} |
289 |
> |
currentExtra = currentExtra->getNext(); |
290 |
> |
} |
291 |
> |
|
292 |
|
} |
293 |
|
|
294 |
< |
return new Bond(atomA, atomB, bendType); |
294 |
> |
if (isGhostBend) { |
295 |
|
|
296 |
+ |
int indexA = stamp->getA(); |
297 |
+ |
int indexB= stamp->getB(); |
298 |
+ |
|
299 |
+ |
assert(indexA != indexB); |
300 |
+ |
|
301 |
+ |
int normalIndex; |
302 |
+ |
if (indexA == ghostIndex) { |
303 |
+ |
normalIndex = indexB; |
304 |
+ |
} else if (indexB == ghostIndex) { |
305 |
+ |
normalIndex = indexA; |
306 |
+ |
} |
307 |
+ |
|
308 |
+ |
Atom* normalAtom = mol->getAtomAt(normalIndex) ; |
309 |
+ |
Atom* ghostAtom = mol->getAtomAt(ghostIndex); |
310 |
+ |
|
311 |
+ |
BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST"); |
312 |
+ |
|
313 |
+ |
if (bendType == NULL) { |
314 |
+ |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
315 |
+ |
normalAtom->getType().c_str(), |
316 |
+ |
ghostAtom->getType().c_str(), |
317 |
+ |
"GHOST"); |
318 |
+ |
|
319 |
+ |
painCave.isFatal = 1; |
320 |
+ |
simError(); |
321 |
+ |
} |
322 |
+ |
|
323 |
+ |
return new GhostBend(normalAtom, ghostAtom, bendType); |
324 |
+ |
|
325 |
+ |
} else { |
326 |
+ |
|
327 |
+ |
Atom* atomA = mol->getAtomAt(stamp->getA()); |
328 |
+ |
Atom* atomB = mol->getAtomAt(stamp->getB()); |
329 |
+ |
Atom* atomC = mol->getAtomAt(stamp->getC()); |
330 |
+ |
|
331 |
+ |
assert( atomA && atomB && atomC); |
332 |
+ |
|
333 |
+ |
BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType()); |
334 |
+ |
|
335 |
+ |
if (bendType == NULL) { |
336 |
+ |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
337 |
+ |
atomA->getType().c_str(), |
338 |
+ |
atomB->getType().c_str(), |
339 |
+ |
atomC->getType().c_str()); |
340 |
+ |
|
341 |
+ |
painCave.isFatal = 1; |
342 |
+ |
simError(); |
343 |
+ |
} |
344 |
+ |
|
345 |
+ |
return new Bend(atomA, atomB, atomC, bendType); |
346 |
+ |
} |
347 |
|
} |
348 |
|
|
349 |
|
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) { |