| 302 |
|
/**@todo need refactorying*/ |
| 303 |
|
//Conserved Quantity is set by integrator and time is set by setTime |
| 304 |
|
|
| 305 |
+ |
} |
| 306 |
+ |
|
| 307 |
+ |
|
| 308 |
+ |
|
| 309 |
+ |
Vector3d Thermo::getBoxDipole() { |
| 310 |
+ |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 311 |
+ |
SimInfo::MoleculeIterator miter; |
| 312 |
+ |
std::vector<Atom*>::iterator aiter; |
| 313 |
+ |
Molecule* mol; |
| 314 |
+ |
Atom* atom; |
| 315 |
+ |
RealType charge; |
| 316 |
+ |
RealType moment(0.0); |
| 317 |
+ |
Vector3d ri(0.0); |
| 318 |
+ |
Vector3d dipoleVector(0.0); |
| 319 |
+ |
Vector3d nPos(0.0); |
| 320 |
+ |
Vector3d pPos(0.0); |
| 321 |
+ |
RealType nChg(0.0); |
| 322 |
+ |
RealType pChg(0.0); |
| 323 |
+ |
int nCount = 0; |
| 324 |
+ |
int pCount = 0; |
| 325 |
+ |
|
| 326 |
+ |
RealType chargeToC = 1.60217733e-19; |
| 327 |
+ |
RealType angstromToM = 1.0e-10; RealType debyeToCm = 3.33564095198e-30; |
| 328 |
+ |
|
| 329 |
+ |
for (mol = info_->beginMolecule(miter); mol != NULL; |
| 330 |
+ |
mol = info_->nextMolecule(miter)) { |
| 331 |
+ |
|
| 332 |
+ |
for (atom = mol->beginAtom(aiter); atom != NULL; |
| 333 |
+ |
atom = mol->nextAtom(aiter)) { |
| 334 |
+ |
|
| 335 |
+ |
if (atom->isCharge() ) { |
| 336 |
+ |
charge = 0.0; |
| 337 |
+ |
GenericData* data = atom->getAtomType()->getPropertyByName("Charge"); |
| 338 |
+ |
if (data != NULL) { |
| 339 |
+ |
|
| 340 |
+ |
charge = (dynamic_cast<DoubleGenericData*>(data))->getData(); |
| 341 |
+ |
charge *= chargeToC; |
| 342 |
+ |
|
| 343 |
+ |
ri = atom->getPos(); |
| 344 |
+ |
currSnapshot->wrapVector(ri); |
| 345 |
+ |
ri *= angstromToM; |
| 346 |
+ |
|
| 347 |
+ |
if (charge < 0.0) { |
| 348 |
+ |
nPos += ri; |
| 349 |
+ |
nChg -= charge; |
| 350 |
+ |
nCount++; |
| 351 |
+ |
} else if (charge > 0.0) { |
| 352 |
+ |
pPos += ri; |
| 353 |
+ |
pChg += charge; |
| 354 |
+ |
pCount++; |
| 355 |
+ |
} |
| 356 |
+ |
} |
| 357 |
+ |
} |
| 358 |
+ |
|
| 359 |
+ |
if (atom->isDipole() ) { |
| 360 |
+ |
Vector3d u_i = atom->getElectroFrame().getColumn(2); |
| 361 |
+ |
GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole"); |
| 362 |
+ |
if (data != NULL) { |
| 363 |
+ |
moment = (dynamic_cast<DoubleGenericData*>(data))->getData(); |
| 364 |
+ |
|
| 365 |
+ |
moment *= debyeToCm; |
| 366 |
+ |
dipoleVector += u_i * moment; |
| 367 |
+ |
} |
| 368 |
+ |
} |
| 369 |
+ |
} |
| 370 |
+ |
} |
| 371 |
+ |
|
| 372 |
+ |
|
| 373 |
+ |
#ifdef IS_MPI |
| 374 |
+ |
RealType pChg_global, nChg_global; |
| 375 |
+ |
int pCount_global, nCount_global; |
| 376 |
+ |
Vector3d pPos_global, nPos_global, dipVec_global; |
| 377 |
+ |
|
| 378 |
+ |
MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM, |
| 379 |
+ |
MPI_COMM_WORLD); |
| 380 |
+ |
pChg = pChg_global; |
| 381 |
+ |
MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM, |
| 382 |
+ |
MPI_COMM_WORLD); |
| 383 |
+ |
nChg = nChg_global; |
| 384 |
+ |
MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM, |
| 385 |
+ |
MPI_COMM_WORLD); |
| 386 |
+ |
pCount = pCount_global; |
| 387 |
+ |
MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM, |
| 388 |
+ |
MPI_COMM_WORLD); |
| 389 |
+ |
nCount = nCount_global; |
| 390 |
+ |
MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3, |
| 391 |
+ |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 392 |
+ |
pPos = pPos_global; |
| 393 |
+ |
MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3, |
| 394 |
+ |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 395 |
+ |
nPos = nPos_global; |
| 396 |
+ |
MPI_Allreduce(dipoleVector.getArrayPointer(), |
| 397 |
+ |
dipVec_global.getArrayPointer(), 3, |
| 398 |
+ |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 399 |
+ |
dipoleVector = dipVec_global; |
| 400 |
+ |
#endif //is_mpi |
| 401 |
+ |
|
| 402 |
+ |
// first load the accumulated dipole moment (if dipoles were present) |
| 403 |
+ |
Vector3d boxDipole = dipoleVector; |
| 404 |
+ |
// now include the dipole moment due to charges |
| 405 |
+ |
// use the lesser of the positive and negative charge totals |
| 406 |
+ |
RealType chg_value = nChg <= pChg ? nChg : pChg; |
| 407 |
+ |
|
| 408 |
+ |
// find the average positions |
| 409 |
+ |
if (pCount > 0 && nCount > 0 ) { |
| 410 |
+ |
pPos /= pCount; |
| 411 |
+ |
nPos /= nCount; |
| 412 |
+ |
} |
| 413 |
+ |
|
| 414 |
+ |
// dipole is from the negative to the positive (physics notation) |
| 415 |
+ |
boxDipole += (pPos - nPos) * chg_value; |
| 416 |
+ |
|
| 417 |
+ |
return boxDipole; |
| 418 |
|
} |
| 419 |
|
|
| 420 |
+ |
|
| 421 |
|
} //end namespace OpenMD |
