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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 |
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* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
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< |
* 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 |
< |
* |
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< |
* 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 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
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|
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|
#include <math.h> |
| 49 |
|
#include "brains/Thermo.hpp" |
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|
#include "primitives/Molecule.hpp" |
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|
#include "utils/simError.h" |
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< |
#include "utils/OOPSEConstant.hpp" |
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> |
#include "utils/PhysicalConstants.hpp" |
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|
|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
| 56 |
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RealType Thermo::getKinetic() { |
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SimInfo::MoleculeIterator miter; |
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|
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#endif //is_mpi |
| 105 |
|
|
| 106 |
< |
kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert; |
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> |
kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert; |
| 107 |
|
|
| 108 |
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return kinetic; |
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} |
| 139 |
|
|
| 140 |
|
RealType Thermo::getTemperature() { |
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|
|
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< |
RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb ); |
| 142 |
> |
RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb ); |
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|
return temperature; |
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|
} |
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|
|
| 158 |
|
|
| 159 |
|
tensor = getPressureTensor(); |
| 160 |
|
|
| 161 |
< |
pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0; |
| 161 |
> |
pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0; |
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|
|
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return pressure; |
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} |
| 173 |
|
|
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|
tensor = getPressureTensor(); |
| 175 |
|
|
| 176 |
< |
pressure = OOPSEConstant::pressureConvert * tensor(direction, direction); |
| 176 |
> |
pressure = PhysicalConstants::pressureConvert * tensor(direction, direction); |
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|
|
| 178 |
|
return pressure; |
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} |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Mat3x3d tau = curSnapshot->statData.getTau(); |
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|
|
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< |
pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume; |
| 213 |
> |
pressureTensor = (p_global + PhysicalConstants::energyConvert* tau)/volume; |
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|
|
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|
return pressureTensor; |
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} |
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stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1); |
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|
stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2); |
| 240 |
|
|
| 241 |
+ |
// grab the simulation box dipole moment if specified |
| 242 |
+ |
if (info_->getCalcBoxDipole()){ |
| 243 |
+ |
Vector3d totalDipole = getBoxDipole(); |
| 244 |
+ |
stat[Stats::BOX_DIPOLE_X] = totalDipole(0); |
| 245 |
+ |
stat[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
| 246 |
+ |
stat[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
| 247 |
+ |
} |
| 248 |
|
|
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|
Globals* simParams = info_->getSimParams(); |
| 250 |
|
|
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|
Vector3d pos1, pos2, rab; |
| 257 |
|
|
| 258 |
|
#ifdef IS_MPI |
| 259 |
+ |
std::cerr << "tap = " << tap.first << " " << tap.second << std::endl; |
| 260 |
|
|
| 261 |
|
int mol1 = info_->getGlobalMolMembership(tap.first); |
| 262 |
|
int mol2 = info_->getGlobalMolMembership(tap.second); |
| 263 |
< |
|
| 263 |
> |
std::cerr << "mols = " << mol1 << " " << mol2 << std::endl; |
| 264 |
> |
|
| 265 |
|
int proc1 = info_->getMolToProc(mol1); |
| 266 |
|
int proc2 = info_->getMolToProc(mol2); |
| 267 |
|
|
| 268 |
+ |
std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl; |
| 269 |
+ |
|
| 270 |
|
RealType data[3]; |
| 271 |
|
if (proc1 == worldRank) { |
| 272 |
|
StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first); |
| 273 |
+ |
std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl; |
| 274 |
|
pos1 = sd1->getPos(); |
| 275 |
|
data[0] = pos1.x(); |
| 276 |
|
data[1] = pos1.y(); |
| 284 |
|
|
| 285 |
|
if (proc2 == worldRank) { |
| 286 |
|
StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second); |
| 287 |
+ |
std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl; |
| 288 |
|
pos2 = sd2->getPos(); |
| 289 |
|
data[0] = pos2.x(); |
| 290 |
|
data[1] = pos2.y(); |
| 311 |
|
|
| 312 |
|
} |
| 313 |
|
|
| 314 |
< |
} //end namespace oopse |
| 314 |
> |
|
| 315 |
> |
Vector3d Thermo::getBoxDipole() { |
| 316 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 317 |
> |
SimInfo::MoleculeIterator miter; |
| 318 |
> |
std::vector<Atom*>::iterator aiter; |
| 319 |
> |
Molecule* mol; |
| 320 |
> |
Atom* atom; |
| 321 |
> |
RealType charge; |
| 322 |
> |
RealType moment(0.0); |
| 323 |
> |
Vector3d ri(0.0); |
| 324 |
> |
Vector3d dipoleVector(0.0); |
| 325 |
> |
Vector3d nPos(0.0); |
| 326 |
> |
Vector3d pPos(0.0); |
| 327 |
> |
RealType nChg(0.0); |
| 328 |
> |
RealType pChg(0.0); |
| 329 |
> |
int nCount = 0; |
| 330 |
> |
int pCount = 0; |
| 331 |
> |
|
| 332 |
> |
RealType chargeToC = 1.60217733e-19; |
| 333 |
> |
RealType angstromToM = 1.0e-10; |
| 334 |
> |
RealType debyeToCm = 3.33564095198e-30; |
| 335 |
> |
|
| 336 |
> |
for (mol = info_->beginMolecule(miter); mol != NULL; |
| 337 |
> |
mol = info_->nextMolecule(miter)) { |
| 338 |
> |
|
| 339 |
> |
for (atom = mol->beginAtom(aiter); atom != NULL; |
| 340 |
> |
atom = mol->nextAtom(aiter)) { |
| 341 |
> |
|
| 342 |
> |
if (atom->isCharge() ) { |
| 343 |
> |
charge = 0.0; |
| 344 |
> |
GenericData* data = atom->getAtomType()->getPropertyByName("Charge"); |
| 345 |
> |
if (data != NULL) { |
| 346 |
> |
|
| 347 |
> |
charge = (dynamic_cast<DoubleGenericData*>(data))->getData(); |
| 348 |
> |
charge *= chargeToC; |
| 349 |
> |
|
| 350 |
> |
ri = atom->getPos(); |
| 351 |
> |
currSnapshot->wrapVector(ri); |
| 352 |
> |
ri *= angstromToM; |
| 353 |
> |
|
| 354 |
> |
if (charge < 0.0) { |
| 355 |
> |
nPos += ri; |
| 356 |
> |
nChg -= charge; |
| 357 |
> |
nCount++; |
| 358 |
> |
} else if (charge > 0.0) { |
| 359 |
> |
pPos += ri; |
| 360 |
> |
pChg += charge; |
| 361 |
> |
pCount++; |
| 362 |
> |
} |
| 363 |
> |
} |
| 364 |
> |
} |
| 365 |
> |
|
| 366 |
> |
if (atom->isDipole() ) { |
| 367 |
> |
Vector3d u_i = atom->getElectroFrame().getColumn(2); |
| 368 |
> |
GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole"); |
| 369 |
> |
if (data != NULL) { |
| 370 |
> |
moment = (dynamic_cast<DoubleGenericData*>(data))->getData(); |
| 371 |
> |
|
| 372 |
> |
moment *= debyeToCm; |
| 373 |
> |
dipoleVector += u_i * moment; |
| 374 |
> |
} |
| 375 |
> |
} |
| 376 |
> |
} |
| 377 |
> |
} |
| 378 |
> |
|
| 379 |
> |
|
| 380 |
> |
#ifdef IS_MPI |
| 381 |
> |
RealType pChg_global, nChg_global; |
| 382 |
> |
int pCount_global, nCount_global; |
| 383 |
> |
Vector3d pPos_global, nPos_global, dipVec_global; |
| 384 |
> |
|
| 385 |
> |
MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM, |
| 386 |
> |
MPI_COMM_WORLD); |
| 387 |
> |
pChg = pChg_global; |
| 388 |
> |
MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM, |
| 389 |
> |
MPI_COMM_WORLD); |
| 390 |
> |
nChg = nChg_global; |
| 391 |
> |
MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM, |
| 392 |
> |
MPI_COMM_WORLD); |
| 393 |
> |
pCount = pCount_global; |
| 394 |
> |
MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM, |
| 395 |
> |
MPI_COMM_WORLD); |
| 396 |
> |
nCount = nCount_global; |
| 397 |
> |
MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3, |
| 398 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 399 |
> |
pPos = pPos_global; |
| 400 |
> |
MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3, |
| 401 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 402 |
> |
nPos = nPos_global; |
| 403 |
> |
MPI_Allreduce(dipoleVector.getArrayPointer(), |
| 404 |
> |
dipVec_global.getArrayPointer(), 3, |
| 405 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 406 |
> |
dipoleVector = dipVec_global; |
| 407 |
> |
#endif //is_mpi |
| 408 |
> |
|
| 409 |
> |
// first load the accumulated dipole moment (if dipoles were present) |
| 410 |
> |
Vector3d boxDipole = dipoleVector; |
| 411 |
> |
// now include the dipole moment due to charges |
| 412 |
> |
// use the lesser of the positive and negative charge totals |
| 413 |
> |
RealType chg_value = nChg <= pChg ? nChg : pChg; |
| 414 |
> |
|
| 415 |
> |
// find the average positions |
| 416 |
> |
if (pCount > 0 && nCount > 0 ) { |
| 417 |
> |
pPos /= pCount; |
| 418 |
> |
nPos /= nCount; |
| 419 |
> |
} |
| 420 |
> |
|
| 421 |
> |
// dipole is from the negative to the positive (physics notation) |
| 422 |
> |
boxDipole += (pPos - nPos) * chg_value; |
| 423 |
> |
|
| 424 |
> |
return boxDipole; |
| 425 |
> |
} |
| 426 |
> |
} //end namespace OpenMD |
