| 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, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include <math.h> |
| 49 |
|
#include "brains/Thermo.hpp" |
| 50 |
|
#include "primitives/Molecule.hpp" |
| 51 |
|
#include "utils/simError.h" |
| 52 |
< |
#include "utils/OOPSEConstant.hpp" |
| 52 |
> |
#include "utils/PhysicalConstants.hpp" |
| 53 |
|
|
| 54 |
< |
namespace oopse { |
| 54 |
> |
namespace OpenMD { |
| 55 |
|
|
| 56 |
|
RealType Thermo::getKinetic() { |
| 57 |
|
SimInfo::MoleculeIterator miter; |
| 64 |
|
int i; |
| 65 |
|
int j; |
| 66 |
|
int k; |
| 67 |
+ |
RealType mass; |
| 68 |
|
RealType kinetic = 0.0; |
| 69 |
|
RealType kinetic_global = 0.0; |
| 70 |
|
|
| 72 |
|
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
| 73 |
|
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 74 |
|
|
| 75 |
< |
RealType mass = integrableObject->getMass(); |
| 76 |
< |
Vector3d vel = integrableObject->getVel(); |
| 75 |
> |
mass = integrableObject->getMass(); |
| 76 |
> |
vel = integrableObject->getVel(); |
| 77 |
|
|
| 78 |
|
kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
| 79 |
|
|
| 103 |
|
|
| 104 |
|
#endif //is_mpi |
| 105 |
|
|
| 106 |
< |
kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert; |
| 106 |
> |
kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert; |
| 107 |
|
|
| 108 |
|
return kinetic; |
| 109 |
|
} |
| 139 |
|
|
| 140 |
|
RealType Thermo::getTemperature() { |
| 141 |
|
|
| 142 |
< |
RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb ); |
| 142 |
> |
RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb ); |
| 143 |
|
return temperature; |
| 144 |
|
} |
| 145 |
|
|
| 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; |
| 162 |
|
|
| 163 |
|
return pressure; |
| 164 |
|
} |
| 173 |
|
|
| 174 |
|
tensor = getPressureTensor(); |
| 175 |
|
|
| 176 |
< |
pressure = OOPSEConstant::pressureConvert * tensor(direction, direction); |
| 176 |
> |
pressure = PhysicalConstants::pressureConvert * tensor(direction, direction); |
| 177 |
|
|
| 178 |
|
return pressure; |
| 179 |
|
} |
| 180 |
|
|
| 180 |
– |
|
| 181 |
– |
|
| 181 |
|
Mat3x3d Thermo::getPressureTensor() { |
| 182 |
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// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 183 |
|
// routine derived via viral theorem description in: |
| 210 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 211 |
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Mat3x3d tau = curSnapshot->statData.getTau(); |
| 212 |
|
|
| 213 |
< |
pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume; |
| 214 |
< |
|
| 213 |
> |
pressureTensor = (p_global + PhysicalConstants::energyConvert* tau)/volume; |
| 214 |
> |
|
| 215 |
|
return pressureTensor; |
| 216 |
|
} |
| 217 |
|
|
| 218 |
+ |
|
| 219 |
|
void Thermo::saveStat(){ |
| 220 |
|
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 221 |
|
Stats& stat = currSnapshot->statData; |
| 228 |
|
stat[Stats::VOLUME] = getVolume(); |
| 229 |
|
|
| 230 |
|
Mat3x3d tensor =getPressureTensor(); |
| 231 |
< |
stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0); |
| 232 |
< |
stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1); |
| 233 |
< |
stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2); |
| 231 |
> |
stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0); |
| 232 |
> |
stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1); |
| 233 |
> |
stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2); |
| 234 |
> |
stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0); |
| 235 |
> |
stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1); |
| 236 |
> |
stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2); |
| 237 |
> |
stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0); |
| 238 |
> |
stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1); |
| 239 |
> |
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 |
|
|
| 249 |
+ |
Globals* simParams = info_->getSimParams(); |
| 250 |
+ |
|
| 251 |
+ |
if (simParams->haveTaggedAtomPair() && |
| 252 |
+ |
simParams->havePrintTaggedPairDistance()) { |
| 253 |
+ |
if ( simParams->getPrintTaggedPairDistance()) { |
| 254 |
+ |
|
| 255 |
+ |
std::pair<int, int> tap = simParams->getTaggedAtomPair(); |
| 256 |
+ |
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 |
+ |
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(); |
| 277 |
+ |
data[2] = pos1.z(); |
| 278 |
+ |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 279 |
+ |
} else { |
| 280 |
+ |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 281 |
+ |
pos1 = Vector3d(data); |
| 282 |
+ |
} |
| 283 |
+ |
|
| 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(); |
| 291 |
+ |
data[2] = pos2.z(); |
| 292 |
+ |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 293 |
+ |
} else { |
| 294 |
+ |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 295 |
+ |
pos2 = Vector3d(data); |
| 296 |
+ |
} |
| 297 |
+ |
#else |
| 298 |
+ |
StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first); |
| 299 |
+ |
StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second); |
| 300 |
+ |
pos1 = at1->getPos(); |
| 301 |
+ |
pos2 = at2->getPos(); |
| 302 |
+ |
#endif |
| 303 |
+ |
rab = pos2 - pos1; |
| 304 |
+ |
currSnapshot->wrapVector(rab); |
| 305 |
+ |
stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length(); |
| 306 |
+ |
} |
| 307 |
+ |
} |
| 308 |
+ |
|
| 309 |
|
/**@todo need refactorying*/ |
| 310 |
|
//Conserved Quantity is set by integrator and time is set by setTime |
| 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 |
