| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
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|
#include <algorithm> |
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|
#include <math.h> |
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#include "primitives/RigidBody.hpp" |
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#include "utils/simError.h" |
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#include "utils/NumericConstant.hpp" |
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), |
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inertiaTensor_(0.0){ |
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void RigidBody::setPrevA(const RotMat3x3d& a) { |
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((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
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|
| 56 |
< |
for (int i =0 ; i < atoms_.size(); ++i){ |
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> |
for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
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|
if (atoms_[i]->isDirectional()) { |
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atoms_[i]->setPrevA(refOrients_[i].transpose() * a); |
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} |
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void RigidBody::setA(const RotMat3x3d& a) { |
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((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
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|
| 68 |
< |
for (int i =0 ; i < atoms_.size(); ++i){ |
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> |
for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
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|
if (atoms_[i]->isDirectional()) { |
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atoms_[i]->setA(refOrients_[i].transpose() * a); |
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} |
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|
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void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) { |
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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
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< |
|
| 78 |
< |
//((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
| 78 |
< |
|
| 79 |
< |
for (int i =0 ; i < atoms_.size(); ++i){ |
| 77 |
> |
|
| 78 |
> |
for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
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|
if (atoms_[i]->isDirectional()) { |
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atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo); |
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} |
| 92 |
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Vector3d force; |
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Vector3d torque; |
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Vector3d myEuler; |
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< |
RealType phi, theta, psi; |
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> |
RealType phi, theta; |
| 96 |
> |
// RealType psi; |
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|
RealType cphi, sphi, ctheta, stheta; |
| 98 |
|
Vector3d ephi; |
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Vector3d etheta; |
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|
|
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|
phi = myEuler[0]; |
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|
theta = myEuler[1]; |
| 108 |
< |
psi = myEuler[2]; |
| 108 |
> |
// psi = myEuler[2]; |
| 109 |
|
|
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|
cphi = cos(phi); |
| 111 |
|
sphi = sin(phi); |
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ephi[1] = 0.0; |
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ephi[2] = 1.0; |
| 120 |
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|
| 121 |
< |
etheta[0] = -sphi; |
| 122 |
< |
etheta[1] = cphi; |
| 121 |
> |
//etheta[0] = -sphi; |
| 122 |
> |
//etheta[1] = cphi; |
| 123 |
> |
//etheta[2] = 0.0; |
| 124 |
> |
|
| 125 |
> |
etheta[0] = cphi; |
| 126 |
> |
etheta[1] = sphi; |
| 127 |
|
etheta[2] = 0.0; |
| 128 |
|
|
| 129 |
|
epsi[0] = stheta * cphi; |
| 197 |
|
|
| 198 |
|
int nLinearAxis = 0; |
| 199 |
|
for (int i = 0; i < 3; i++) { |
| 200 |
< |
if (fabs(evals[i]) < oopse::epsilon) { |
| 200 |
> |
if (fabs(evals[i]) < OpenMD::epsilon) { |
| 201 |
|
linear_ = true; |
| 202 |
|
linearAxis_ = i; |
| 203 |
|
++ nLinearAxis; |
| 207 |
|
if (nLinearAxis > 1) { |
| 208 |
|
sprintf( painCave.errMsg, |
| 209 |
|
"RigidBody error.\n" |
| 210 |
< |
"\tOOPSE found more than one axis in this rigid body with a vanishing \n" |
| 210 |
> |
"\tOpenMD found more than one axis in this rigid body with a vanishing \n" |
| 211 |
|
"\tmoment of inertia. This can happen in one of three ways:\n" |
| 212 |
|
"\t 1) Only one atom was specified, or \n" |
| 213 |
|
"\t 2) All atoms were specified at the same location, or\n" |
| 226 |
|
Vector3d apos; |
| 227 |
|
Vector3d rpos; |
| 228 |
|
Vector3d frc(0.0); |
| 229 |
< |
Vector3d trq(0.0); |
| 229 |
> |
Vector3d trq(0.0); |
| 230 |
> |
Vector3d ef(0.0); |
| 231 |
|
Vector3d pos = this->getPos(); |
| 232 |
< |
for (int i = 0; i < atoms_.size(); i++) { |
| 232 |
> |
AtomType* atype; |
| 233 |
> |
int eCount = 0; |
| 234 |
> |
|
| 235 |
> |
int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout(); |
| 236 |
> |
|
| 237 |
> |
for (unsigned int i = 0; i < atoms_.size(); i++) { |
| 238 |
|
|
| 239 |
+ |
atype = atoms_[i]->getAtomType(); |
| 240 |
+ |
|
| 241 |
|
afrc = atoms_[i]->getFrc(); |
| 242 |
|
apos = atoms_[i]->getPos(); |
| 243 |
|
rpos = apos - pos; |
| 254 |
|
if (atoms_[i]->isDirectional()) { |
| 255 |
|
atrq = atoms_[i]->getTrq(); |
| 256 |
|
trq += atrq; |
| 257 |
< |
} |
| 257 |
> |
} |
| 258 |
> |
|
| 259 |
> |
if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) { |
| 260 |
> |
ef += atoms_[i]->getElectricField(); |
| 261 |
> |
eCount++; |
| 262 |
> |
} |
| 263 |
|
} |
| 264 |
|
addFrc(frc); |
| 265 |
|
addTrq(trq); |
| 266 |
+ |
|
| 267 |
+ |
if (sl & DataStorage::dslElectricField) { |
| 268 |
+ |
ef /= eCount; |
| 269 |
+ |
setElectricField(ef); |
| 270 |
+ |
} |
| 271 |
+ |
|
| 272 |
|
} |
| 273 |
|
|
| 274 |
|
Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() { |
| 278 |
|
Vector3d rpos; |
| 279 |
|
Vector3d dfrc; |
| 280 |
|
Vector3d frc(0.0); |
| 281 |
< |
Vector3d trq(0.0); |
| 281 |
> |
Vector3d trq(0.0); |
| 282 |
> |
Vector3d ef(0.0); |
| 283 |
> |
AtomType* atype; |
| 284 |
> |
int eCount = 0; |
| 285 |
> |
|
| 286 |
|
Vector3d pos = this->getPos(); |
| 287 |
|
Mat3x3d tau_(0.0); |
| 288 |
|
|
| 289 |
< |
for (int i = 0; i < atoms_.size(); i++) { |
| 289 |
> |
int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout(); |
| 290 |
> |
|
| 291 |
> |
for (unsigned int i = 0; i < atoms_.size(); i++) { |
| 292 |
|
|
| 293 |
+ |
atype = atoms_[i]->getAtomType(); |
| 294 |
+ |
|
| 295 |
|
afrc = atoms_[i]->getFrc(); |
| 296 |
|
apos = atoms_[i]->getPos(); |
| 297 |
|
rpos = apos - pos; |
| 309 |
|
atrq = atoms_[i]->getTrq(); |
| 310 |
|
trq += atrq; |
| 311 |
|
} |
| 312 |
+ |
|
| 313 |
+ |
if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) { |
| 314 |
+ |
ef += atoms_[i]->getElectricField(); |
| 315 |
+ |
eCount++; |
| 316 |
+ |
} |
| 317 |
|
|
| 318 |
|
tau_(0,0) -= rpos[0]*afrc[0]; |
| 319 |
|
tau_(0,1) -= rpos[0]*afrc[1]; |
| 328 |
|
} |
| 329 |
|
addFrc(frc); |
| 330 |
|
addTrq(trq); |
| 331 |
+ |
|
| 332 |
+ |
if (sl & DataStorage::dslElectricField) { |
| 333 |
+ |
ef /= eCount; |
| 334 |
+ |
setElectricField(ef); |
| 335 |
+ |
} |
| 336 |
+ |
|
| 337 |
|
return tau_; |
| 338 |
|
} |
| 339 |
|
|
| 355 |
|
|
| 356 |
|
if (atoms_[i]->isDirectional()) { |
| 357 |
|
|
| 358 |
< |
dAtom = (DirectionalAtom *) atoms_[i]; |
| 358 |
> |
dAtom = dynamic_cast<DirectionalAtom *>(atoms_[i]); |
| 359 |
|
dAtom->setA(refOrients_[i].transpose() * a); |
| 360 |
|
} |
| 361 |
|
|
| 382 |
|
|
| 383 |
|
if (atoms_[i]->isDirectional()) { |
| 384 |
|
|
| 385 |
< |
dAtom = (DirectionalAtom *) atoms_[i]; |
| 385 |
> |
dAtom = dynamic_cast<DirectionalAtom *>(atoms_[i]); |
| 386 |
|
dAtom->setA(refOrients_[i].transpose() * a, frame); |
| 387 |
|
} |
| 388 |
|
|
| 413 |
|
|
| 414 |
|
|
| 415 |
|
Vector3d velRot; |
| 416 |
< |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 416 |
> |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 417 |
|
atoms_[i]->setVel(rbVel + mat * refCoords_[i]); |
| 418 |
|
} |
| 419 |
|
|
| 442 |
|
|
| 443 |
|
|
| 444 |
|
Vector3d velRot; |
| 445 |
< |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 445 |
> |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 446 |
|
atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame); |
| 447 |
|
} |
| 448 |
|
|
