| 51 |
|
|
| 52 |
|
void RigidBody::setPrevA(const RotMat3x3d& a) { |
| 53 |
|
((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
| 54 |
– |
//((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
| 54 |
|
|
| 55 |
|
for (int i =0 ; i < atoms_.size(); ++i){ |
| 56 |
|
if (atoms_[i]->isDirectional()) { |
| 57 |
< |
atoms_[i]->setPrevA(a * refOrients_[i]); |
| 57 |
> |
atoms_[i]->setPrevA(refOrients_[i].transpose() * a); |
| 58 |
|
} |
| 59 |
|
} |
| 60 |
|
|
| 63 |
|
|
| 64 |
|
void RigidBody::setA(const RotMat3x3d& a) { |
| 65 |
|
((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
| 67 |
– |
//((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
| 66 |
|
|
| 67 |
|
for (int i =0 ; i < atoms_.size(); ++i){ |
| 68 |
|
if (atoms_[i]->isDirectional()) { |
| 69 |
< |
atoms_[i]->setA(a * refOrients_[i]); |
| 69 |
> |
atoms_[i]->setA(refOrients_[i].transpose() * a); |
| 70 |
|
} |
| 71 |
|
} |
| 72 |
|
} |
| 77 |
|
|
| 78 |
|
for (int i =0 ; i < atoms_.size(); ++i){ |
| 79 |
|
if (atoms_[i]->isDirectional()) { |
| 80 |
< |
atoms_[i]->setA(a * refOrients_[i], snapshotNo); |
| 80 |
> |
atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo); |
| 81 |
|
} |
| 82 |
|
} |
| 83 |
|
|
| 87 |
|
return inertiaTensor_; |
| 88 |
|
} |
| 89 |
|
|
| 90 |
< |
std::vector<double> RigidBody::getGrad() { |
| 91 |
< |
std::vector<double> grad(6, 0.0); |
| 90 |
> |
std::vector<RealType> RigidBody::getGrad() { |
| 91 |
> |
std::vector<RealType> grad(6, 0.0); |
| 92 |
|
Vector3d force; |
| 93 |
|
Vector3d torque; |
| 94 |
|
Vector3d myEuler; |
| 95 |
< |
double phi, theta, psi; |
| 96 |
< |
double cphi, sphi, ctheta, stheta; |
| 95 |
> |
RealType phi, theta, psi; |
| 96 |
> |
RealType cphi, sphi, ctheta, stheta; |
| 97 |
|
Vector3d ephi; |
| 98 |
|
Vector3d etheta; |
| 99 |
|
Vector3d epsi; |
| 146 |
|
|
| 147 |
|
/**@todo need modification */ |
| 148 |
|
void RigidBody::calcRefCoords() { |
| 149 |
< |
double mtmp; |
| 149 |
> |
RealType mtmp; |
| 150 |
|
Vector3d refCOM(0.0); |
| 151 |
|
mass_ = 0.0; |
| 152 |
|
for (std::size_t i = 0; i < atoms_.size(); ++i) { |
| 167 |
|
Mat3x3d IAtom(0.0); |
| 168 |
|
mtmp = atoms_[i]->getMass(); |
| 169 |
|
IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp; |
| 170 |
< |
double r2 = refCoords_[i].lengthSquare(); |
| 170 |
> |
RealType r2 = refCoords_[i].lengthSquare(); |
| 171 |
|
IAtom(0, 0) += mtmp * r2; |
| 172 |
|
IAtom(1, 1) += mtmp * r2; |
| 173 |
|
IAtom(2, 2) += mtmp * r2; |
| 179 |
|
} |
| 180 |
|
} |
| 181 |
|
|
| 182 |
+ |
// std::cout << Itmp << std::endl; |
| 183 |
+ |
|
| 184 |
|
//diagonalize |
| 185 |
|
Vector3d evals; |
| 186 |
|
Mat3x3d::diagonalize(Itmp, evals, sU_); |
| 221 |
|
Vector3d apos; |
| 222 |
|
Vector3d rpos; |
| 223 |
|
Vector3d frc(0.0); |
| 224 |
< |
Vector3d trq(0.0); |
| 224 |
> |
Vector3d trq(0.0); |
| 225 |
|
Vector3d pos = this->getPos(); |
| 226 |
|
for (int i = 0; i < atoms_.size(); i++) { |
| 227 |
|
|
| 241 |
|
if (atoms_[i]->isDirectional()) { |
| 242 |
|
atrq = atoms_[i]->getTrq(); |
| 243 |
|
trq += atrq; |
| 244 |
< |
} |
| 244 |
> |
} |
| 245 |
> |
} |
| 246 |
> |
addFrc(frc); |
| 247 |
> |
addTrq(trq); |
| 248 |
> |
} |
| 249 |
> |
|
| 250 |
> |
Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() { |
| 251 |
> |
Vector3d afrc; |
| 252 |
> |
Vector3d atrq; |
| 253 |
> |
Vector3d apos; |
| 254 |
> |
Vector3d rpos; |
| 255 |
> |
Vector3d frc(0.0); |
| 256 |
> |
Vector3d trq(0.0); |
| 257 |
> |
Vector3d pos = this->getPos(); |
| 258 |
> |
Mat3x3d tau_(0.0); |
| 259 |
> |
|
| 260 |
> |
for (int i = 0; i < atoms_.size(); i++) { |
| 261 |
> |
|
| 262 |
> |
afrc = atoms_[i]->getFrc(); |
| 263 |
> |
apos = atoms_[i]->getPos(); |
| 264 |
> |
rpos = apos - pos; |
| 265 |
|
|
| 266 |
< |
} |
| 267 |
< |
|
| 268 |
< |
setFrc(frc); |
| 269 |
< |
setTrq(trq); |
| 270 |
< |
|
| 266 |
> |
frc += afrc; |
| 267 |
> |
|
| 268 |
> |
trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
| 269 |
> |
trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
| 270 |
> |
trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
| 271 |
> |
|
| 272 |
> |
// If the atom has a torque associated with it, then we also need to |
| 273 |
> |
// migrate the torques onto the center of mass: |
| 274 |
> |
|
| 275 |
> |
if (atoms_[i]->isDirectional()) { |
| 276 |
> |
atrq = atoms_[i]->getTrq(); |
| 277 |
> |
trq += atrq; |
| 278 |
> |
} |
| 279 |
> |
|
| 280 |
> |
tau_(0,0) -= rpos[0]*afrc[0]; |
| 281 |
> |
tau_(0,1) -= rpos[0]*afrc[1]; |
| 282 |
> |
tau_(0,2) -= rpos[0]*afrc[2]; |
| 283 |
> |
tau_(1,0) -= rpos[1]*afrc[0]; |
| 284 |
> |
tau_(1,1) -= rpos[1]*afrc[1]; |
| 285 |
> |
tau_(1,2) -= rpos[1]*afrc[2]; |
| 286 |
> |
tau_(2,0) -= rpos[2]*afrc[0]; |
| 287 |
> |
tau_(2,1) -= rpos[2]*afrc[1]; |
| 288 |
> |
tau_(2,2) -= rpos[2]*afrc[2]; |
| 289 |
> |
|
| 290 |
> |
} |
| 291 |
> |
addFrc(frc); |
| 292 |
> |
addTrq(trq); |
| 293 |
> |
return tau_; |
| 294 |
|
} |
| 295 |
|
|
| 296 |
|
void RigidBody::updateAtoms() { |
| 312 |
|
if (atoms_[i]->isDirectional()) { |
| 313 |
|
|
| 314 |
|
dAtom = (DirectionalAtom *) atoms_[i]; |
| 315 |
< |
dAtom->setA(refOrients_[i] * a); |
| 315 |
> |
dAtom->setA(refOrients_[i].transpose() * a); |
| 316 |
|
} |
| 317 |
|
|
| 318 |
|
} |
| 339 |
|
if (atoms_[i]->isDirectional()) { |
| 340 |
|
|
| 341 |
|
dAtom = (DirectionalAtom *) atoms_[i]; |
| 342 |
< |
dAtom->setA(refOrients_[i] * a, frame); |
| 342 |
> |
dAtom->setA(refOrients_[i].transpose() * a, frame); |
| 343 |
|
} |
| 344 |
|
|
| 345 |
|
} |
| 524 |
|
"RigidBody error.\n" |
| 525 |
|
"\tAtom %s does not have a position specified.\n" |
| 526 |
|
"\tThis means RigidBody cannot set up reference coordinates.\n", |
| 527 |
< |
ats->getType() ); |
| 527 |
> |
ats->getType().c_str() ); |
| 528 |
|
painCave.isFatal = 1; |
| 529 |
|
simError(); |
| 530 |
|
} |
| 544 |
|
"RigidBody error.\n" |
| 545 |
|
"\tAtom %s does not have an orientation specified.\n" |
| 546 |
|
"\tThis means RigidBody cannot set up reference orientations.\n", |
| 547 |
< |
ats->getType() ); |
| 547 |
> |
ats->getType().c_str() ); |
| 548 |
|
painCave.isFatal = 1; |
| 549 |
|
simError(); |
| 550 |
|
} |
