| 1 | < | /* | 
| 1 | > | /* | 
| 2 |  | * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. | 
| 3 |  | * | 
| 4 |  | * The University of Notre Dame grants you ("Licensee") a | 
| 45 |  | #include "utils/NumericConstant.hpp" | 
| 46 |  | namespace oopse { | 
| 47 |  |  | 
| 48 | < | RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){ | 
| 48 | > | RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){ | 
| 49 |  |  | 
| 50 | < | } | 
| 50 | > | } | 
| 51 |  |  | 
| 52 | < | void RigidBody::setPrevA(const RotMat3x3d& a) { | 
| 52 | > | void RigidBody::setPrevA(const RotMat3x3d& a) { | 
| 53 |  | ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; | 
| 54 |  | //((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; | 
| 55 |  |  | 
| 56 |  | for (int i =0 ; i < atoms_.size(); ++i){ | 
| 57 | < | if (atoms_[i]->isDirectional()) { | 
| 58 | < | atoms_[i]->setPrevA(a * refOrients_[i]); | 
| 59 | < | } | 
| 57 | > | if (atoms_[i]->isDirectional()) { | 
| 58 | > | atoms_[i]->setPrevA(a * refOrients_[i]); | 
| 59 | > | } | 
| 60 |  | } | 
| 61 |  |  | 
| 62 | < | } | 
| 62 | > | } | 
| 63 |  |  | 
| 64 |  |  | 
| 65 | < | void RigidBody::setA(const RotMat3x3d& a) { | 
| 65 | > | void RigidBody::setA(const RotMat3x3d& a) { | 
| 66 |  | ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; | 
| 67 |  | //((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; | 
| 68 |  |  | 
| 69 |  | for (int i =0 ; i < atoms_.size(); ++i){ | 
| 70 | < | if (atoms_[i]->isDirectional()) { | 
| 71 | < | atoms_[i]->setA(a * refOrients_[i]); | 
| 72 | < | } | 
| 70 | > | if (atoms_[i]->isDirectional()) { | 
| 71 | > | atoms_[i]->setA(a * refOrients_[i]); | 
| 72 | > | } | 
| 73 |  | } | 
| 74 | < | } | 
| 74 | > | } | 
| 75 |  |  | 
| 76 | < | void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) { | 
| 76 | > | void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) { | 
| 77 |  | ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; | 
| 78 |  | //((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; | 
| 79 |  |  | 
| 80 |  | for (int i =0 ; i < atoms_.size(); ++i){ | 
| 81 | < | if (atoms_[i]->isDirectional()) { | 
| 82 | < | atoms_[i]->setA(a * refOrients_[i], snapshotNo); | 
| 83 | < | } | 
| 81 | > | if (atoms_[i]->isDirectional()) { | 
| 82 | > | atoms_[i]->setA(a * refOrients_[i], snapshotNo); | 
| 83 | > | } | 
| 84 |  | } | 
| 85 |  |  | 
| 86 | < | } | 
| 86 | > | } | 
| 87 |  |  | 
| 88 | < | Mat3x3d RigidBody::getI() { | 
| 88 | > | Mat3x3d RigidBody::getI() { | 
| 89 |  | return inertiaTensor_; | 
| 90 | < | } | 
| 90 | > | } | 
| 91 |  |  | 
| 92 | < | std::vector<double> RigidBody::getGrad() { | 
| 93 | < | std::vector<double> grad(6, 0.0); | 
| 92 | > | std::vector<double> RigidBody::getGrad() { | 
| 93 | > | std::vector<double> grad(6, 0.0); | 
| 94 |  | Vector3d force; | 
| 95 |  | Vector3d torque; | 
| 96 |  | Vector3d myEuler; | 
| 129 |  |  | 
| 130 |  | //gradient is equal to -force | 
| 131 |  | for (int j = 0 ; j<3; j++) | 
| 132 | < | grad[j] = -force[j]; | 
| 132 | > | grad[j] = -force[j]; | 
| 133 |  |  | 
| 134 |  | for (int j = 0; j < 3; j++ ) { | 
| 135 |  |  | 
| 136 | < | grad[3] += torque[j]*ephi[j]; | 
| 137 | < | grad[4] += torque[j]*etheta[j]; | 
| 138 | < | grad[5] += torque[j]*epsi[j]; | 
| 136 | > | grad[3] += torque[j]*ephi[j]; | 
| 137 | > | grad[4] += torque[j]*etheta[j]; | 
| 138 | > | grad[5] += torque[j]*epsi[j]; | 
| 139 |  |  | 
| 140 |  | } | 
| 141 |  |  | 
| 142 |  | return grad; | 
| 143 | < | } | 
| 143 | > | } | 
| 144 |  |  | 
| 145 | < | void RigidBody::accept(BaseVisitor* v) { | 
| 145 | > | void RigidBody::accept(BaseVisitor* v) { | 
| 146 |  | v->visit(this); | 
| 147 | < | } | 
| 147 | > | } | 
| 148 |  |  | 
| 149 | < | /**@todo need modification */ | 
| 150 | < | void  RigidBody::calcRefCoords() { | 
| 149 | > | /**@todo need modification */ | 
| 150 | > | void  RigidBody::calcRefCoords() { | 
| 151 |  | double mtmp; | 
| 152 |  | Vector3d refCOM(0.0); | 
| 153 |  | mass_ = 0.0; | 
| 154 |  | for (std::size_t i = 0; i < atoms_.size(); ++i) { | 
| 155 | < | mtmp = atoms_[i]->getMass(); | 
| 156 | < | mass_ += mtmp; | 
| 157 | < | refCOM += refCoords_[i]*mtmp; | 
| 155 | > | mtmp = atoms_[i]->getMass(); | 
| 156 | > | mass_ += mtmp; | 
| 157 | > | refCOM += refCoords_[i]*mtmp; | 
| 158 |  | } | 
| 159 |  | refCOM /= mass_; | 
| 160 |  |  | 
| 161 |  | // Next, move the origin of the reference coordinate system to the COM: | 
| 162 |  | for (std::size_t i = 0; i < atoms_.size(); ++i) { | 
| 163 | < | refCoords_[i] -= refCOM; | 
| 163 | > | refCoords_[i] -= refCOM; | 
| 164 |  | } | 
| 165 |  |  | 
| 166 | < | // Moment of Inertia calculation | 
| 167 | < | Mat3x3d Itmp(0.0); | 
| 168 | < |  | 
| 166 | > | // Moment of Inertia calculation | 
| 167 | > | Mat3x3d Itmp(0.0); | 
| 168 |  | for (std::size_t i = 0; i < atoms_.size(); i++) { | 
| 169 | < | mtmp = atoms_[i]->getMass(); | 
| 170 | < | Itmp -= outProduct(refCoords_[i], refCoords_[i]) * mtmp; | 
| 171 | < | double r2 = refCoords_[i].lengthSquare(); | 
| 172 | < | Itmp(0, 0) += mtmp * r2; | 
| 173 | < | Itmp(1, 1) += mtmp * r2; | 
| 174 | < | Itmp(2, 2) += mtmp * r2; | 
| 175 | < | } | 
| 169 | > | Mat3x3d IAtom(0.0); | 
| 170 | > | mtmp = atoms_[i]->getMass(); | 
| 171 | > | IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp; | 
| 172 | > | double r2 = refCoords_[i].lengthSquare(); | 
| 173 | > | IAtom(0, 0) += mtmp * r2; | 
| 174 | > | IAtom(1, 1) += mtmp * r2; | 
| 175 | > | IAtom(2, 2) += mtmp * r2; | 
| 176 | > | Itmp += IAtom; | 
| 177 |  |  | 
| 178 | < | //project the inertial moment of directional atoms into this rigid body | 
| 179 | < | for (std::size_t i = 0; i < atoms_.size(); i++) { | 
| 180 | < | if (atoms_[i]->isDirectional()) { | 
| 181 | < | RectMatrix<double, 3, 3> Iproject = refOrients_[i].transpose() * atoms_[i]->getI(); | 
| 182 | < | Itmp(0, 0) += Iproject(0, 0); | 
| 183 | < | Itmp(1, 1) += Iproject(1, 1); | 
| 184 | < | Itmp(2, 2) += Iproject(2, 2); | 
| 185 | < | } | 
| 178 | > | //project the inertial moment of directional atoms into this rigid body | 
| 179 | > | if (atoms_[i]->isDirectional()) { | 
| 180 | > | Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i]; | 
| 181 | > | } | 
| 182 |  | } | 
| 183 |  |  | 
| 184 | + | std::cout << Itmp << std::endl; | 
| 185 | + |  | 
| 186 |  | //diagonalize | 
| 187 |  | Vector3d evals; | 
| 188 |  | Mat3x3d::diagonalize(Itmp, evals, sU_); | 
| 194 |  |  | 
| 195 |  | int nLinearAxis = 0; | 
| 196 |  | for (int i = 0; i < 3; i++) { | 
| 197 | < | if (fabs(evals[i]) < oopse::epsilon) { | 
| 198 | < | linear_ = true; | 
| 199 | < | linearAxis_ = i; | 
| 200 | < | ++ nLinearAxis; | 
| 201 | < | } | 
| 197 | > | if (fabs(evals[i]) < oopse::epsilon) { | 
| 198 | > | linear_ = true; | 
| 199 | > | linearAxis_ = i; | 
| 200 | > | ++ nLinearAxis; | 
| 201 | > | } | 
| 202 |  | } | 
| 203 |  |  | 
| 204 |  | if (nLinearAxis > 1) { | 
| 205 | < | sprintf( painCave.errMsg, | 
| 206 | < | "RigidBody error.\n" | 
| 207 | < | "\tOOPSE found more than one axis in this rigid body with a vanishing \n" | 
| 208 | < | "\tmoment of inertia.  This can happen in one of three ways:\n" | 
| 209 | < | "\t 1) Only one atom was specified, or \n" | 
| 210 | < | "\t 2) All atoms were specified at the same location, or\n" | 
| 211 | < | "\t 3) The programmers did something stupid.\n" | 
| 212 | < | "\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n" | 
| 213 | < | ); | 
| 214 | < | painCave.isFatal = 1; | 
| 215 | < | simError(); | 
| 205 | > | sprintf( painCave.errMsg, | 
| 206 | > | "RigidBody error.\n" | 
| 207 | > | "\tOOPSE found more than one axis in this rigid body with a vanishing \n" | 
| 208 | > | "\tmoment of inertia.  This can happen in one of three ways:\n" | 
| 209 | > | "\t 1) Only one atom was specified, or \n" | 
| 210 | > | "\t 2) All atoms were specified at the same location, or\n" | 
| 211 | > | "\t 3) The programmers did something stupid.\n" | 
| 212 | > | "\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n" | 
| 213 | > | ); | 
| 214 | > | painCave.isFatal = 1; | 
| 215 | > | simError(); | 
| 216 |  | } | 
| 217 |  |  | 
| 218 | < | } | 
| 218 | > | } | 
| 219 |  |  | 
| 220 | < | void  RigidBody::calcForcesAndTorques() { | 
| 220 | > | void  RigidBody::calcForcesAndTorques() { | 
| 221 |  | Vector3d afrc; | 
| 222 |  | Vector3d atrq; | 
| 223 |  | Vector3d apos; | 
| 227 |  | Vector3d pos = this->getPos(); | 
| 228 |  | for (int i = 0; i < atoms_.size(); i++) { | 
| 229 |  |  | 
| 230 | < | afrc = atoms_[i]->getFrc(); | 
| 231 | < | apos = atoms_[i]->getPos(); | 
| 232 | < | rpos = apos - pos; | 
| 230 | > | afrc = atoms_[i]->getFrc(); | 
| 231 | > | apos = atoms_[i]->getPos(); | 
| 232 | > | rpos = apos - pos; | 
| 233 |  |  | 
| 234 | < | frc += afrc; | 
| 234 | > | frc += afrc; | 
| 235 |  |  | 
| 236 | < | trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; | 
| 237 | < | trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; | 
| 238 | < | trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; | 
| 236 | > | trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; | 
| 237 | > | trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; | 
| 238 | > | trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; | 
| 239 |  |  | 
| 240 | < | // If the atom has a torque associated with it, then we also need to | 
| 241 | < | // migrate the torques onto the center of mass: | 
| 240 | > | // If the atom has a torque associated with it, then we also need to | 
| 241 | > | // migrate the torques onto the center of mass: | 
| 242 |  |  | 
| 243 | < | if (atoms_[i]->isDirectional()) { | 
| 244 | < | atrq = atoms_[i]->getTrq(); | 
| 245 | < | trq += atrq; | 
| 246 | < | } | 
| 243 | > | if (atoms_[i]->isDirectional()) { | 
| 244 | > | atrq = atoms_[i]->getTrq(); | 
| 245 | > | trq += atrq; | 
| 246 | > | } | 
| 247 |  |  | 
| 248 |  | } | 
| 249 |  |  | 
| 250 |  | setFrc(frc); | 
| 251 |  | setTrq(trq); | 
| 252 |  |  | 
| 253 | < | } | 
| 253 | > | } | 
| 254 |  |  | 
| 255 | < | void  RigidBody::updateAtoms() { | 
| 255 | > | void  RigidBody::updateAtoms() { | 
| 256 |  | unsigned int i; | 
| 257 |  | Vector3d ref; | 
| 258 |  | Vector3d apos; | 
| 262 |  |  | 
| 263 |  | for (i = 0; i < atoms_.size(); i++) { | 
| 264 |  |  | 
| 265 | < | ref = body2Lab(refCoords_[i]); | 
| 265 | > | ref = body2Lab(refCoords_[i]); | 
| 266 |  |  | 
| 267 | < | apos = pos + ref; | 
| 267 | > | apos = pos + ref; | 
| 268 |  |  | 
| 269 | < | atoms_[i]->setPos(apos); | 
| 269 | > | atoms_[i]->setPos(apos); | 
| 270 |  |  | 
| 271 | < | if (atoms_[i]->isDirectional()) { | 
| 271 | > | if (atoms_[i]->isDirectional()) { | 
| 272 |  |  | 
| 273 | < | dAtom = (DirectionalAtom *) atoms_[i]; | 
| 274 | < | dAtom->setA(a * refOrients_[i]); | 
| 275 | < | //dAtom->rotateBy( A ); | 
| 278 | < | } | 
| 273 | > | dAtom = (DirectionalAtom *) atoms_[i]; | 
| 274 | > | dAtom->setA(refOrients_[i] * a); | 
| 275 | > | } | 
| 276 |  |  | 
| 277 |  | } | 
| 278 |  |  | 
| 279 | < | } | 
| 279 | > | } | 
| 280 |  |  | 
| 281 |  |  | 
| 282 | < | void  RigidBody::updateAtoms(int frame) { | 
| 282 | > | void  RigidBody::updateAtoms(int frame) { | 
| 283 |  | unsigned int i; | 
| 284 |  | Vector3d ref; | 
| 285 |  | Vector3d apos; | 
| 289 |  |  | 
| 290 |  | for (i = 0; i < atoms_.size(); i++) { | 
| 291 |  |  | 
| 292 | < | ref = body2Lab(refCoords_[i], frame); | 
| 292 | > | ref = body2Lab(refCoords_[i], frame); | 
| 293 |  |  | 
| 294 | < | apos = pos + ref; | 
| 294 | > | apos = pos + ref; | 
| 295 |  |  | 
| 296 | < | atoms_[i]->setPos(apos, frame); | 
| 296 | > | atoms_[i]->setPos(apos, frame); | 
| 297 |  |  | 
| 298 | < | if (atoms_[i]->isDirectional()) { | 
| 298 | > | if (atoms_[i]->isDirectional()) { | 
| 299 |  |  | 
| 300 | < | dAtom = (DirectionalAtom *) atoms_[i]; | 
| 301 | < | dAtom->setA(a * refOrients_[i], frame); | 
| 302 | < | } | 
| 300 | > | dAtom = (DirectionalAtom *) atoms_[i]; | 
| 301 | > | dAtom->setA(refOrients_[i] * a, frame); | 
| 302 | > | } | 
| 303 |  |  | 
| 304 |  | } | 
| 305 |  |  | 
| 306 | < | } | 
| 306 | > | } | 
| 307 |  |  | 
| 308 | < | void RigidBody::updateAtomVel() { | 
| 308 | > | void RigidBody::updateAtomVel() { | 
| 309 |  | Mat3x3d skewMat;; | 
| 310 |  |  | 
| 311 |  | Vector3d ji = getJ(); | 
| 329 |  |  | 
| 330 |  | Vector3d velRot; | 
| 331 |  | for (int i =0 ; i < refCoords_.size(); ++i) { | 
| 332 | < | atoms_[i]->setVel(rbVel + mat * refCoords_[i]); | 
| 332 | > | atoms_[i]->setVel(rbVel + mat * refCoords_[i]); | 
| 333 |  | } | 
| 334 |  |  | 
| 335 | < | } | 
| 335 | > | } | 
| 336 |  |  | 
| 337 | < | void RigidBody::updateAtomVel(int frame) { | 
| 337 | > | void RigidBody::updateAtomVel(int frame) { | 
| 338 |  | Mat3x3d skewMat;; | 
| 339 |  |  | 
| 340 |  | Vector3d ji = getJ(frame); | 
| 358 |  |  | 
| 359 |  | Vector3d velRot; | 
| 360 |  | for (int i =0 ; i < refCoords_.size(); ++i) { | 
| 361 | < | atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame); | 
| 361 | > | atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame); | 
| 362 |  | } | 
| 363 |  |  | 
| 364 | < | } | 
| 364 | > | } | 
| 365 |  |  | 
| 366 |  |  | 
| 367 |  |  | 
| 368 | < | bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) { | 
| 368 | > | bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) { | 
| 369 |  | if (index < atoms_.size()) { | 
| 370 |  |  | 
| 371 | < | Vector3d ref = body2Lab(refCoords_[index]); | 
| 372 | < | pos = getPos() + ref; | 
| 373 | < | return true; | 
| 371 | > | Vector3d ref = body2Lab(refCoords_[index]); | 
| 372 | > | pos = getPos() + ref; | 
| 373 | > | return true; | 
| 374 |  | } else { | 
| 375 | < | std::cerr << index << " is an invalid index, current rigid body contains " | 
| 376 | < | << atoms_.size() << "atoms" << std::endl; | 
| 377 | < | return false; | 
| 375 | > | std::cerr << index << " is an invalid index, current rigid body contains " | 
| 376 | > | << atoms_.size() << "atoms" << std::endl; | 
| 377 | > | return false; | 
| 378 |  | } | 
| 379 | < | } | 
| 379 | > | } | 
| 380 |  |  | 
| 381 | < | bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) { | 
| 381 | > | bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) { | 
| 382 |  | std::vector<Atom*>::iterator i; | 
| 383 |  | i = std::find(atoms_.begin(), atoms_.end(), atom); | 
| 384 |  | if (i != atoms_.end()) { | 
| 385 | < | //RigidBody class makes sure refCoords_ and atoms_ match each other | 
| 386 | < | Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]); | 
| 387 | < | pos = getPos() + ref; | 
| 388 | < | return true; | 
| 385 | > | //RigidBody class makes sure refCoords_ and atoms_ match each other | 
| 386 | > | Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]); | 
| 387 | > | pos = getPos() + ref; | 
| 388 | > | return true; | 
| 389 |  | } else { | 
| 390 | < | std::cerr << "Atom " << atom->getGlobalIndex() | 
| 391 | < | <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; | 
| 392 | < | return false; | 
| 390 | > | std::cerr << "Atom " << atom->getGlobalIndex() | 
| 391 | > | <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; | 
| 392 | > | return false; | 
| 393 |  | } | 
| 394 | < | } | 
| 395 | < | bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) { | 
| 394 | > | } | 
| 395 | > | bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) { | 
| 396 |  |  | 
| 397 |  | //velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$ | 
| 398 |  |  | 
| 399 |  | if (index < atoms_.size()) { | 
| 400 |  |  | 
| 401 | < | Vector3d velRot; | 
| 402 | < | Mat3x3d skewMat;; | 
| 403 | < | Vector3d ref = refCoords_[index]; | 
| 404 | < | Vector3d ji = getJ(); | 
| 405 | < | Mat3x3d I =  getI(); | 
| 401 | > | Vector3d velRot; | 
| 402 | > | Mat3x3d skewMat;; | 
| 403 | > | Vector3d ref = refCoords_[index]; | 
| 404 | > | Vector3d ji = getJ(); | 
| 405 | > | Mat3x3d I =  getI(); | 
| 406 |  |  | 
| 407 | < | skewMat(0, 0) =0; | 
| 408 | < | skewMat(0, 1) = ji[2] /I(2, 2); | 
| 409 | < | skewMat(0, 2) = -ji[1] /I(1, 1); | 
| 407 | > | skewMat(0, 0) =0; | 
| 408 | > | skewMat(0, 1) = ji[2] /I(2, 2); | 
| 409 | > | skewMat(0, 2) = -ji[1] /I(1, 1); | 
| 410 |  |  | 
| 411 | < | skewMat(1, 0) = -ji[2] /I(2, 2); | 
| 412 | < | skewMat(1, 1) = 0; | 
| 413 | < | skewMat(1, 2) = ji[0]/I(0, 0); | 
| 411 | > | skewMat(1, 0) = -ji[2] /I(2, 2); | 
| 412 | > | skewMat(1, 1) = 0; | 
| 413 | > | skewMat(1, 2) = ji[0]/I(0, 0); | 
| 414 |  |  | 
| 415 | < | skewMat(2, 0) =ji[1] /I(1, 1); | 
| 416 | < | skewMat(2, 1) = -ji[0]/I(0, 0); | 
| 417 | < | skewMat(2, 2) = 0; | 
| 415 | > | skewMat(2, 0) =ji[1] /I(1, 1); | 
| 416 | > | skewMat(2, 1) = -ji[0]/I(0, 0); | 
| 417 | > | skewMat(2, 2) = 0; | 
| 418 |  |  | 
| 419 | < | velRot = (getA() * skewMat).transpose() * ref; | 
| 419 | > | velRot = (getA() * skewMat).transpose() * ref; | 
| 420 |  |  | 
| 421 | < | vel =getVel() + velRot; | 
| 422 | < | return true; | 
| 421 | > | vel =getVel() + velRot; | 
| 422 | > | return true; | 
| 423 |  |  | 
| 424 |  | } else { | 
| 425 | < | std::cerr << index << " is an invalid index, current rigid body contains " | 
| 426 | < | << atoms_.size() << "atoms" << std::endl; | 
| 427 | < | return false; | 
| 425 | > | std::cerr << index << " is an invalid index, current rigid body contains " | 
| 426 | > | << atoms_.size() << "atoms" << std::endl; | 
| 427 | > | return false; | 
| 428 |  | } | 
| 429 | < | } | 
| 429 | > | } | 
| 430 |  |  | 
| 431 | < | bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) { | 
| 431 | > | bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) { | 
| 432 |  |  | 
| 433 |  | std::vector<Atom*>::iterator i; | 
| 434 |  | i = std::find(atoms_.begin(), atoms_.end(), atom); | 
| 435 |  | if (i != atoms_.end()) { | 
| 436 | < | return getAtomVel(vel, i - atoms_.begin()); | 
| 436 | > | return getAtomVel(vel, i - atoms_.begin()); | 
| 437 |  | } else { | 
| 438 | < | std::cerr << "Atom " << atom->getGlobalIndex() | 
| 439 | < | <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; | 
| 440 | < | return false; | 
| 438 | > | std::cerr << "Atom " << atom->getGlobalIndex() | 
| 439 | > | <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; | 
| 440 | > | return false; | 
| 441 |  | } | 
| 442 | < | } | 
| 442 | > | } | 
| 443 |  |  | 
| 444 | < | bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) { | 
| 444 | > | bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) { | 
| 445 |  | if (index < atoms_.size()) { | 
| 446 |  |  | 
| 447 | < | coor = refCoords_[index]; | 
| 448 | < | return true; | 
| 447 | > | coor = refCoords_[index]; | 
| 448 | > | return true; | 
| 449 |  | } else { | 
| 450 | < | std::cerr << index << " is an invalid index, current rigid body contains " | 
| 451 | < | << atoms_.size() << "atoms" << std::endl; | 
| 452 | < | return false; | 
| 450 | > | std::cerr << index << " is an invalid index, current rigid body contains " | 
| 451 | > | << atoms_.size() << "atoms" << std::endl; | 
| 452 | > | return false; | 
| 453 |  | } | 
| 454 |  |  | 
| 455 | < | } | 
| 455 | > | } | 
| 456 |  |  | 
| 457 | < | bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) { | 
| 457 | > | bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) { | 
| 458 |  | std::vector<Atom*>::iterator i; | 
| 459 |  | i = std::find(atoms_.begin(), atoms_.end(), atom); | 
| 460 |  | if (i != atoms_.end()) { | 
| 461 | < | //RigidBody class makes sure refCoords_ and atoms_ match each other | 
| 462 | < | coor = refCoords_[i - atoms_.begin()]; | 
| 463 | < | return true; | 
| 461 | > | //RigidBody class makes sure refCoords_ and atoms_ match each other | 
| 462 | > | coor = refCoords_[i - atoms_.begin()]; | 
| 463 | > | return true; | 
| 464 |  | } else { | 
| 465 | < | std::cerr << "Atom " << atom->getGlobalIndex() | 
| 466 | < | <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; | 
| 467 | < | return false; | 
| 465 | > | std::cerr << "Atom " << atom->getGlobalIndex() | 
| 466 | > | <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; | 
| 467 | > | return false; | 
| 468 |  | } | 
| 469 |  |  | 
| 470 | < | } | 
| 470 | > | } | 
| 471 |  |  | 
| 472 |  |  | 
| 473 | < | void RigidBody::addAtom(Atom* at, AtomStamp* ats) { | 
| 473 | > | void RigidBody::addAtom(Atom* at, AtomStamp* ats) { | 
| 474 |  |  | 
| 475 | < | Vector3d coords; | 
| 476 | < | Vector3d euler; | 
| 475 | > | Vector3d coords; | 
| 476 | > | Vector3d euler; | 
| 477 |  |  | 
| 478 |  |  | 
| 479 | < | atoms_.push_back(at); | 
| 479 | > | atoms_.push_back(at); | 
| 480 |  |  | 
| 481 | < | if( !ats->havePosition() ){ | 
| 482 | < | sprintf( painCave.errMsg, | 
| 483 | < | "RigidBody error.\n" | 
| 484 | < | "\tAtom %s does not have a position specified.\n" | 
| 485 | < | "\tThis means RigidBody cannot set up reference coordinates.\n", | 
| 486 | < | ats->getType() ); | 
| 487 | < | painCave.isFatal = 1; | 
| 488 | < | simError(); | 
| 489 | < | } | 
| 481 | > | if( !ats->havePosition() ){ | 
| 482 | > | sprintf( painCave.errMsg, | 
| 483 | > | "RigidBody error.\n" | 
| 484 | > | "\tAtom %s does not have a position specified.\n" | 
| 485 | > | "\tThis means RigidBody cannot set up reference coordinates.\n", | 
| 486 | > | ats->getType() ); | 
| 487 | > | painCave.isFatal = 1; | 
| 488 | > | simError(); | 
| 489 | > | } | 
| 490 |  |  | 
| 491 | < | coords[0] = ats->getPosX(); | 
| 492 | < | coords[1] = ats->getPosY(); | 
| 493 | < | coords[2] = ats->getPosZ(); | 
| 491 | > | coords[0] = ats->getPosX(); | 
| 492 | > | coords[1] = ats->getPosY(); | 
| 493 | > | coords[2] = ats->getPosZ(); | 
| 494 |  |  | 
| 495 | < | refCoords_.push_back(coords); | 
| 495 | > | refCoords_.push_back(coords); | 
| 496 |  |  | 
| 497 | < | RotMat3x3d identMat = RotMat3x3d::identity(); | 
| 497 | > | RotMat3x3d identMat = RotMat3x3d::identity(); | 
| 498 |  |  | 
| 499 | < | if (at->isDirectional()) { | 
| 499 | > | if (at->isDirectional()) { | 
| 500 |  |  | 
| 501 | < | if( !ats->haveOrientation() ){ | 
| 502 | < | sprintf( painCave.errMsg, | 
| 503 | < | "RigidBody error.\n" | 
| 504 | < | "\tAtom %s does not have an orientation specified.\n" | 
| 505 | < | "\tThis means RigidBody cannot set up reference orientations.\n", | 
| 506 | < | ats->getType() ); | 
| 507 | < | painCave.isFatal = 1; | 
| 508 | < | simError(); | 
| 509 | < | } | 
| 501 | > | if( !ats->haveOrientation() ){ | 
| 502 | > | sprintf( painCave.errMsg, | 
| 503 | > | "RigidBody error.\n" | 
| 504 | > | "\tAtom %s does not have an orientation specified.\n" | 
| 505 | > | "\tThis means RigidBody cannot set up reference orientations.\n", | 
| 506 | > | ats->getType() ); | 
| 507 | > | painCave.isFatal = 1; | 
| 508 | > | simError(); | 
| 509 | > | } | 
| 510 |  |  | 
| 511 | < | euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0; | 
| 512 | < | euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0; | 
| 513 | < | euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0; | 
| 511 | > | euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0; | 
| 512 | > | euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0; | 
| 513 | > | euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0; | 
| 514 |  |  | 
| 515 | < | RotMat3x3d Atmp(euler); | 
| 516 | < | refOrients_.push_back(Atmp); | 
| 515 | > | RotMat3x3d Atmp(euler); | 
| 516 | > | refOrients_.push_back(Atmp); | 
| 517 |  |  | 
| 518 | < | }else { | 
| 519 | < | refOrients_.push_back(identMat); | 
| 520 | < | } | 
| 518 | > | }else { | 
| 519 | > | refOrients_.push_back(identMat); | 
| 520 | > | } | 
| 521 |  |  | 
| 522 |  |  | 
| 523 | < | } | 
| 523 | > | } | 
| 524 |  |  | 
| 525 |  | } | 
| 526 |  |  |