| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 36 |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
#include <algorithm> |
| 43 |
#include <math.h> |
| 44 |
#include "primitives/RigidBody.hpp" |
| 45 |
#include "utils/simError.h" |
| 46 |
#include "utils/NumericConstant.hpp" |
| 47 |
namespace OpenMD { |
| 48 |
|
| 49 |
RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), |
| 50 |
inertiaTensor_(0.0){ |
| 51 |
} |
| 52 |
|
| 53 |
void RigidBody::setPrevA(const RotMat3x3d& a) { |
| 54 |
((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
| 55 |
|
| 56 |
for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
| 57 |
if (atoms_[i]->isDirectional()) { |
| 58 |
atoms_[i]->setPrevA(refOrients_[i].transpose() * a); |
| 59 |
} |
| 60 |
} |
| 61 |
|
| 62 |
} |
| 63 |
|
| 64 |
|
| 65 |
void RigidBody::setA(const RotMat3x3d& a) { |
| 66 |
((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
| 67 |
|
| 68 |
for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
| 69 |
if (atoms_[i]->isDirectional()) { |
| 70 |
atoms_[i]->setA(refOrients_[i].transpose() * a); |
| 71 |
} |
| 72 |
} |
| 73 |
} |
| 74 |
|
| 75 |
void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) { |
| 76 |
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
| 77 |
|
| 78 |
for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
| 79 |
if (atoms_[i]->isDirectional()) { |
| 80 |
atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo); |
| 81 |
} |
| 82 |
} |
| 83 |
|
| 84 |
} |
| 85 |
|
| 86 |
Mat3x3d RigidBody::getI() { |
| 87 |
return inertiaTensor_; |
| 88 |
} |
| 89 |
|
| 90 |
std::vector<RealType> RigidBody::getGrad() { |
| 91 |
std::vector<RealType> grad(6, 0.0); |
| 92 |
Vector3d force; |
| 93 |
Vector3d torque; |
| 94 |
Vector3d myEuler; |
| 95 |
RealType phi, theta, psi; |
| 96 |
RealType cphi, sphi, ctheta, stheta; |
| 97 |
Vector3d ephi; |
| 98 |
Vector3d etheta; |
| 99 |
Vector3d epsi; |
| 100 |
|
| 101 |
force = getFrc(); |
| 102 |
torque =getTrq(); |
| 103 |
myEuler = getA().toEulerAngles(); |
| 104 |
|
| 105 |
phi = myEuler[0]; |
| 106 |
theta = myEuler[1]; |
| 107 |
psi = myEuler[2]; |
| 108 |
|
| 109 |
cphi = cos(phi); |
| 110 |
sphi = sin(phi); |
| 111 |
ctheta = cos(theta); |
| 112 |
stheta = sin(theta); |
| 113 |
|
| 114 |
// get unit vectors along the phi, theta and psi rotation axes |
| 115 |
|
| 116 |
ephi[0] = 0.0; |
| 117 |
ephi[1] = 0.0; |
| 118 |
ephi[2] = 1.0; |
| 119 |
|
| 120 |
//etheta[0] = -sphi; |
| 121 |
//etheta[1] = cphi; |
| 122 |
//etheta[2] = 0.0; |
| 123 |
|
| 124 |
etheta[0] = cphi; |
| 125 |
etheta[1] = sphi; |
| 126 |
etheta[2] = 0.0; |
| 127 |
|
| 128 |
epsi[0] = stheta * cphi; |
| 129 |
epsi[1] = stheta * sphi; |
| 130 |
epsi[2] = ctheta; |
| 131 |
|
| 132 |
//gradient is equal to -force |
| 133 |
for (int j = 0 ; j<3; j++) |
| 134 |
grad[j] = -force[j]; |
| 135 |
|
| 136 |
for (int j = 0; j < 3; j++ ) { |
| 137 |
|
| 138 |
grad[3] += torque[j]*ephi[j]; |
| 139 |
grad[4] += torque[j]*etheta[j]; |
| 140 |
grad[5] += torque[j]*epsi[j]; |
| 141 |
|
| 142 |
} |
| 143 |
|
| 144 |
return grad; |
| 145 |
} |
| 146 |
|
| 147 |
void RigidBody::accept(BaseVisitor* v) { |
| 148 |
v->visit(this); |
| 149 |
} |
| 150 |
|
| 151 |
/**@todo need modification */ |
| 152 |
void RigidBody::calcRefCoords() { |
| 153 |
RealType mtmp; |
| 154 |
Vector3d refCOM(0.0); |
| 155 |
mass_ = 0.0; |
| 156 |
for (std::size_t i = 0; i < atoms_.size(); ++i) { |
| 157 |
mtmp = atoms_[i]->getMass(); |
| 158 |
mass_ += mtmp; |
| 159 |
refCOM += refCoords_[i]*mtmp; |
| 160 |
} |
| 161 |
refCOM /= mass_; |
| 162 |
|
| 163 |
// Next, move the origin of the reference coordinate system to the COM: |
| 164 |
for (std::size_t i = 0; i < atoms_.size(); ++i) { |
| 165 |
refCoords_[i] -= refCOM; |
| 166 |
} |
| 167 |
|
| 168 |
// Moment of Inertia calculation |
| 169 |
Mat3x3d Itmp(0.0); |
| 170 |
for (std::size_t i = 0; i < atoms_.size(); i++) { |
| 171 |
Mat3x3d IAtom(0.0); |
| 172 |
mtmp = atoms_[i]->getMass(); |
| 173 |
IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp; |
| 174 |
RealType r2 = refCoords_[i].lengthSquare(); |
| 175 |
IAtom(0, 0) += mtmp * r2; |
| 176 |
IAtom(1, 1) += mtmp * r2; |
| 177 |
IAtom(2, 2) += mtmp * r2; |
| 178 |
Itmp += IAtom; |
| 179 |
|
| 180 |
//project the inertial moment of directional atoms into this rigid body |
| 181 |
if (atoms_[i]->isDirectional()) { |
| 182 |
Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i]; |
| 183 |
} |
| 184 |
} |
| 185 |
|
| 186 |
// std::cout << Itmp << std::endl; |
| 187 |
|
| 188 |
//diagonalize |
| 189 |
Vector3d evals; |
| 190 |
Mat3x3d::diagonalize(Itmp, evals, sU_); |
| 191 |
|
| 192 |
// zero out I and then fill the diagonals with the moments of inertia: |
| 193 |
inertiaTensor_(0, 0) = evals[0]; |
| 194 |
inertiaTensor_(1, 1) = evals[1]; |
| 195 |
inertiaTensor_(2, 2) = evals[2]; |
| 196 |
|
| 197 |
int nLinearAxis = 0; |
| 198 |
for (int i = 0; i < 3; i++) { |
| 199 |
if (fabs(evals[i]) < OpenMD::epsilon) { |
| 200 |
linear_ = true; |
| 201 |
linearAxis_ = i; |
| 202 |
++ nLinearAxis; |
| 203 |
} |
| 204 |
} |
| 205 |
|
| 206 |
if (nLinearAxis > 1) { |
| 207 |
sprintf( painCave.errMsg, |
| 208 |
"RigidBody error.\n" |
| 209 |
"\tOpenMD found more than one axis in this rigid body with a vanishing \n" |
| 210 |
"\tmoment of inertia. This can happen in one of three ways:\n" |
| 211 |
"\t 1) Only one atom was specified, or \n" |
| 212 |
"\t 2) All atoms were specified at the same location, or\n" |
| 213 |
"\t 3) The programmers did something stupid.\n" |
| 214 |
"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n" |
| 215 |
); |
| 216 |
painCave.isFatal = 1; |
| 217 |
simError(); |
| 218 |
} |
| 219 |
|
| 220 |
} |
| 221 |
|
| 222 |
void RigidBody::calcForcesAndTorques() { |
| 223 |
Vector3d afrc; |
| 224 |
Vector3d atrq; |
| 225 |
Vector3d apos; |
| 226 |
Vector3d rpos; |
| 227 |
Vector3d frc(0.0); |
| 228 |
Vector3d trq(0.0); |
| 229 |
Vector3d pos = this->getPos(); |
| 230 |
for (unsigned int i = 0; i < atoms_.size(); i++) { |
| 231 |
|
| 232 |
afrc = atoms_[i]->getFrc(); |
| 233 |
apos = atoms_[i]->getPos(); |
| 234 |
rpos = apos - pos; |
| 235 |
|
| 236 |
frc += afrc; |
| 237 |
|
| 238 |
trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
| 239 |
trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
| 240 |
trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
| 241 |
|
| 242 |
// If the atom has a torque associated with it, then we also need to |
| 243 |
// migrate the torques onto the center of mass: |
| 244 |
|
| 245 |
if (atoms_[i]->isDirectional()) { |
| 246 |
atrq = atoms_[i]->getTrq(); |
| 247 |
trq += atrq; |
| 248 |
} |
| 249 |
} |
| 250 |
addFrc(frc); |
| 251 |
addTrq(trq); |
| 252 |
} |
| 253 |
|
| 254 |
Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() { |
| 255 |
Vector3d afrc; |
| 256 |
Vector3d atrq; |
| 257 |
Vector3d apos; |
| 258 |
Vector3d rpos; |
| 259 |
Vector3d dfrc; |
| 260 |
Vector3d frc(0.0); |
| 261 |
Vector3d trq(0.0); |
| 262 |
Vector3d pos = this->getPos(); |
| 263 |
Mat3x3d tau_(0.0); |
| 264 |
|
| 265 |
for (unsigned int i = 0; i < atoms_.size(); i++) { |
| 266 |
|
| 267 |
afrc = atoms_[i]->getFrc(); |
| 268 |
apos = atoms_[i]->getPos(); |
| 269 |
rpos = apos - pos; |
| 270 |
|
| 271 |
frc += afrc; |
| 272 |
|
| 273 |
trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
| 274 |
trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
| 275 |
trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
| 276 |
|
| 277 |
// If the atom has a torque associated with it, then we also need to |
| 278 |
// migrate the torques onto the center of mass: |
| 279 |
|
| 280 |
if (atoms_[i]->isDirectional()) { |
| 281 |
atrq = atoms_[i]->getTrq(); |
| 282 |
trq += atrq; |
| 283 |
} |
| 284 |
|
| 285 |
tau_(0,0) -= rpos[0]*afrc[0]; |
| 286 |
tau_(0,1) -= rpos[0]*afrc[1]; |
| 287 |
tau_(0,2) -= rpos[0]*afrc[2]; |
| 288 |
tau_(1,0) -= rpos[1]*afrc[0]; |
| 289 |
tau_(1,1) -= rpos[1]*afrc[1]; |
| 290 |
tau_(1,2) -= rpos[1]*afrc[2]; |
| 291 |
tau_(2,0) -= rpos[2]*afrc[0]; |
| 292 |
tau_(2,1) -= rpos[2]*afrc[1]; |
| 293 |
tau_(2,2) -= rpos[2]*afrc[2]; |
| 294 |
|
| 295 |
} |
| 296 |
addFrc(frc); |
| 297 |
addTrq(trq); |
| 298 |
return tau_; |
| 299 |
} |
| 300 |
|
| 301 |
void RigidBody::updateAtoms() { |
| 302 |
unsigned int i; |
| 303 |
Vector3d ref; |
| 304 |
Vector3d apos; |
| 305 |
DirectionalAtom* dAtom; |
| 306 |
Vector3d pos = getPos(); |
| 307 |
RotMat3x3d a = getA(); |
| 308 |
|
| 309 |
for (i = 0; i < atoms_.size(); i++) { |
| 310 |
|
| 311 |
ref = body2Lab(refCoords_[i]); |
| 312 |
|
| 313 |
apos = pos + ref; |
| 314 |
|
| 315 |
atoms_[i]->setPos(apos); |
| 316 |
|
| 317 |
if (atoms_[i]->isDirectional()) { |
| 318 |
|
| 319 |
dAtom = (DirectionalAtom *) atoms_[i]; |
| 320 |
dAtom->setA(refOrients_[i].transpose() * a); |
| 321 |
} |
| 322 |
|
| 323 |
} |
| 324 |
|
| 325 |
} |
| 326 |
|
| 327 |
|
| 328 |
void RigidBody::updateAtoms(int frame) { |
| 329 |
unsigned int i; |
| 330 |
Vector3d ref; |
| 331 |
Vector3d apos; |
| 332 |
DirectionalAtom* dAtom; |
| 333 |
Vector3d pos = getPos(frame); |
| 334 |
RotMat3x3d a = getA(frame); |
| 335 |
|
| 336 |
for (i = 0; i < atoms_.size(); i++) { |
| 337 |
|
| 338 |
ref = body2Lab(refCoords_[i], frame); |
| 339 |
|
| 340 |
apos = pos + ref; |
| 341 |
|
| 342 |
atoms_[i]->setPos(apos, frame); |
| 343 |
|
| 344 |
if (atoms_[i]->isDirectional()) { |
| 345 |
|
| 346 |
dAtom = (DirectionalAtom *) atoms_[i]; |
| 347 |
dAtom->setA(refOrients_[i].transpose() * a, frame); |
| 348 |
} |
| 349 |
|
| 350 |
} |
| 351 |
|
| 352 |
} |
| 353 |
|
| 354 |
void RigidBody::updateAtomVel() { |
| 355 |
Mat3x3d skewMat;; |
| 356 |
|
| 357 |
Vector3d ji = getJ(); |
| 358 |
Mat3x3d I = getI(); |
| 359 |
|
| 360 |
skewMat(0, 0) =0; |
| 361 |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 362 |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 363 |
|
| 364 |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 365 |
skewMat(1, 1) = 0; |
| 366 |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 367 |
|
| 368 |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 369 |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 370 |
skewMat(2, 2) = 0; |
| 371 |
|
| 372 |
Mat3x3d mat = (getA() * skewMat).transpose(); |
| 373 |
Vector3d rbVel = getVel(); |
| 374 |
|
| 375 |
|
| 376 |
Vector3d velRot; |
| 377 |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 378 |
atoms_[i]->setVel(rbVel + mat * refCoords_[i]); |
| 379 |
} |
| 380 |
|
| 381 |
} |
| 382 |
|
| 383 |
void RigidBody::updateAtomVel(int frame) { |
| 384 |
Mat3x3d skewMat;; |
| 385 |
|
| 386 |
Vector3d ji = getJ(frame); |
| 387 |
Mat3x3d I = getI(); |
| 388 |
|
| 389 |
skewMat(0, 0) =0; |
| 390 |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 391 |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 392 |
|
| 393 |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 394 |
skewMat(1, 1) = 0; |
| 395 |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 396 |
|
| 397 |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 398 |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 399 |
skewMat(2, 2) = 0; |
| 400 |
|
| 401 |
Mat3x3d mat = (getA(frame) * skewMat).transpose(); |
| 402 |
Vector3d rbVel = getVel(frame); |
| 403 |
|
| 404 |
|
| 405 |
Vector3d velRot; |
| 406 |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 407 |
atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame); |
| 408 |
} |
| 409 |
|
| 410 |
} |
| 411 |
|
| 412 |
|
| 413 |
|
| 414 |
bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) { |
| 415 |
if (index < atoms_.size()) { |
| 416 |
|
| 417 |
Vector3d ref = body2Lab(refCoords_[index]); |
| 418 |
pos = getPos() + ref; |
| 419 |
return true; |
| 420 |
} else { |
| 421 |
std::cerr << index << " is an invalid index, current rigid body contains " |
| 422 |
<< atoms_.size() << "atoms" << std::endl; |
| 423 |
return false; |
| 424 |
} |
| 425 |
} |
| 426 |
|
| 427 |
bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) { |
| 428 |
std::vector<Atom*>::iterator i; |
| 429 |
i = std::find(atoms_.begin(), atoms_.end(), atom); |
| 430 |
if (i != atoms_.end()) { |
| 431 |
//RigidBody class makes sure refCoords_ and atoms_ match each other |
| 432 |
Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]); |
| 433 |
pos = getPos() + ref; |
| 434 |
return true; |
| 435 |
} else { |
| 436 |
std::cerr << "Atom " << atom->getGlobalIndex() |
| 437 |
<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
| 438 |
return false; |
| 439 |
} |
| 440 |
} |
| 441 |
bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) { |
| 442 |
|
| 443 |
//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$ |
| 444 |
|
| 445 |
if (index < atoms_.size()) { |
| 446 |
|
| 447 |
Vector3d velRot; |
| 448 |
Mat3x3d skewMat;; |
| 449 |
Vector3d ref = refCoords_[index]; |
| 450 |
Vector3d ji = getJ(); |
| 451 |
Mat3x3d I = getI(); |
| 452 |
|
| 453 |
skewMat(0, 0) =0; |
| 454 |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 455 |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 456 |
|
| 457 |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 458 |
skewMat(1, 1) = 0; |
| 459 |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 460 |
|
| 461 |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 462 |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 463 |
skewMat(2, 2) = 0; |
| 464 |
|
| 465 |
velRot = (getA() * skewMat).transpose() * ref; |
| 466 |
|
| 467 |
vel =getVel() + velRot; |
| 468 |
return true; |
| 469 |
|
| 470 |
} else { |
| 471 |
std::cerr << index << " is an invalid index, current rigid body contains " |
| 472 |
<< atoms_.size() << "atoms" << std::endl; |
| 473 |
return false; |
| 474 |
} |
| 475 |
} |
| 476 |
|
| 477 |
bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) { |
| 478 |
|
| 479 |
std::vector<Atom*>::iterator i; |
| 480 |
i = std::find(atoms_.begin(), atoms_.end(), atom); |
| 481 |
if (i != atoms_.end()) { |
| 482 |
return getAtomVel(vel, i - atoms_.begin()); |
| 483 |
} else { |
| 484 |
std::cerr << "Atom " << atom->getGlobalIndex() |
| 485 |
<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
| 486 |
return false; |
| 487 |
} |
| 488 |
} |
| 489 |
|
| 490 |
bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) { |
| 491 |
if (index < atoms_.size()) { |
| 492 |
|
| 493 |
coor = refCoords_[index]; |
| 494 |
return true; |
| 495 |
} else { |
| 496 |
std::cerr << index << " is an invalid index, current rigid body contains " |
| 497 |
<< atoms_.size() << "atoms" << std::endl; |
| 498 |
return false; |
| 499 |
} |
| 500 |
|
| 501 |
} |
| 502 |
|
| 503 |
bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) { |
| 504 |
std::vector<Atom*>::iterator i; |
| 505 |
i = std::find(atoms_.begin(), atoms_.end(), atom); |
| 506 |
if (i != atoms_.end()) { |
| 507 |
//RigidBody class makes sure refCoords_ and atoms_ match each other |
| 508 |
coor = refCoords_[i - atoms_.begin()]; |
| 509 |
return true; |
| 510 |
} else { |
| 511 |
std::cerr << "Atom " << atom->getGlobalIndex() |
| 512 |
<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
| 513 |
return false; |
| 514 |
} |
| 515 |
|
| 516 |
} |
| 517 |
|
| 518 |
|
| 519 |
void RigidBody::addAtom(Atom* at, AtomStamp* ats) { |
| 520 |
|
| 521 |
Vector3d coords; |
| 522 |
Vector3d euler; |
| 523 |
|
| 524 |
|
| 525 |
atoms_.push_back(at); |
| 526 |
|
| 527 |
if( !ats->havePosition() ){ |
| 528 |
sprintf( painCave.errMsg, |
| 529 |
"RigidBody error.\n" |
| 530 |
"\tAtom %s does not have a position specified.\n" |
| 531 |
"\tThis means RigidBody cannot set up reference coordinates.\n", |
| 532 |
ats->getType().c_str() ); |
| 533 |
painCave.isFatal = 1; |
| 534 |
simError(); |
| 535 |
} |
| 536 |
|
| 537 |
coords[0] = ats->getPosX(); |
| 538 |
coords[1] = ats->getPosY(); |
| 539 |
coords[2] = ats->getPosZ(); |
| 540 |
|
| 541 |
refCoords_.push_back(coords); |
| 542 |
|
| 543 |
RotMat3x3d identMat = RotMat3x3d::identity(); |
| 544 |
|
| 545 |
if (at->isDirectional()) { |
| 546 |
|
| 547 |
if( !ats->haveOrientation() ){ |
| 548 |
sprintf( painCave.errMsg, |
| 549 |
"RigidBody error.\n" |
| 550 |
"\tAtom %s does not have an orientation specified.\n" |
| 551 |
"\tThis means RigidBody cannot set up reference orientations.\n", |
| 552 |
ats->getType().c_str() ); |
| 553 |
painCave.isFatal = 1; |
| 554 |
simError(); |
| 555 |
} |
| 556 |
|
| 557 |
euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0; |
| 558 |
euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0; |
| 559 |
euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0; |
| 560 |
|
| 561 |
RotMat3x3d Atmp(euler); |
| 562 |
refOrients_.push_back(Atmp); |
| 563 |
|
| 564 |
}else { |
| 565 |
refOrients_.push_back(identMat); |
| 566 |
} |
| 567 |
|
| 568 |
|
| 569 |
} |
| 570 |
|
| 571 |
} |
| 572 |
|
