| 278 |
|
|
| 279 |
|
} |
| 280 |
|
|
| 281 |
+ |
} |
| 282 |
+ |
|
| 283 |
+ |
|
| 284 |
+ |
void RigidBody::updateAtoms(int frame) { |
| 285 |
+ |
unsigned int i; |
| 286 |
+ |
Vector3d ref; |
| 287 |
+ |
Vector3d apos; |
| 288 |
+ |
DirectionalAtom* dAtom; |
| 289 |
+ |
Vector3d pos = getPos(frame); |
| 290 |
+ |
RotMat3x3d a = getA(frame); |
| 291 |
+ |
|
| 292 |
+ |
for (i = 0; i < atoms_.size(); i++) { |
| 293 |
+ |
|
| 294 |
+ |
ref = body2Lab(refCoords_[i]); |
| 295 |
+ |
|
| 296 |
+ |
apos = pos + ref; |
| 297 |
+ |
|
| 298 |
+ |
atoms_[i]->setPos(apos, frame); |
| 299 |
+ |
|
| 300 |
+ |
if (atoms_[i]->isDirectional()) { |
| 301 |
+ |
|
| 302 |
+ |
dAtom = (DirectionalAtom *) atoms_[i]; |
| 303 |
+ |
dAtom->setA(a * refOrients_[i], frame); |
| 304 |
+ |
} |
| 305 |
+ |
|
| 306 |
+ |
} |
| 307 |
+ |
|
| 308 |
+ |
} |
| 309 |
+ |
|
| 310 |
+ |
void RigidBody::updateAtomVel() { |
| 311 |
+ |
Mat3x3d skewMat;; |
| 312 |
+ |
|
| 313 |
+ |
Vector3d ji = getJ(); |
| 314 |
+ |
Mat3x3d I = getI(); |
| 315 |
+ |
|
| 316 |
+ |
skewMat(0, 0) =0; |
| 317 |
+ |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 318 |
+ |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 319 |
+ |
|
| 320 |
+ |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 321 |
+ |
skewMat(1, 1) = 0; |
| 322 |
+ |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 323 |
+ |
|
| 324 |
+ |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 325 |
+ |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 326 |
+ |
skewMat(2, 2) = 0; |
| 327 |
+ |
|
| 328 |
+ |
Mat3x3d mat = (getA() * skewMat).transpose(); |
| 329 |
+ |
Vector3d rbVel = getVel(); |
| 330 |
+ |
|
| 331 |
+ |
|
| 332 |
+ |
Vector3d velRot; |
| 333 |
+ |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 334 |
+ |
atoms_[i]->setVel(rbVel + mat * refCoords_[i]); |
| 335 |
+ |
} |
| 336 |
+ |
|
| 337 |
|
} |
| 338 |
|
|
| 339 |
+ |
void RigidBody::updateAtomVel(int frame) { |
| 340 |
+ |
Mat3x3d skewMat;; |
| 341 |
|
|
| 342 |
+ |
Vector3d ji = getJ(frame); |
| 343 |
+ |
Mat3x3d I = getI(); |
| 344 |
+ |
|
| 345 |
+ |
skewMat(0, 0) =0; |
| 346 |
+ |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 347 |
+ |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 348 |
+ |
|
| 349 |
+ |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 350 |
+ |
skewMat(1, 1) = 0; |
| 351 |
+ |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 352 |
+ |
|
| 353 |
+ |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 354 |
+ |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 355 |
+ |
skewMat(2, 2) = 0; |
| 356 |
+ |
|
| 357 |
+ |
Mat3x3d mat = (getA(frame) * skewMat).transpose(); |
| 358 |
+ |
Vector3d rbVel = getVel(frame); |
| 359 |
+ |
|
| 360 |
+ |
|
| 361 |
+ |
Vector3d velRot; |
| 362 |
+ |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 363 |
+ |
atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame); |
| 364 |
+ |
} |
| 365 |
+ |
|
| 366 |
+ |
} |
| 367 |
+ |
|
| 368 |
+ |
|
| 369 |
+ |
|
| 370 |
|
bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) { |
| 371 |
|
if (index < atoms_.size()) { |
| 372 |
|
|
