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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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< |
* 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 |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* 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 |
|
* |
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< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
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* 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. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
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+ |
* |
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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). |
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*/ |
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|
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/** |
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#include "brains/ForceManager.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "UseTheForce/doForces_interface.h" |
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#define __C |
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> |
#define __OPENMD_C |
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#include "UseTheForce/DarkSide/fInteractionMap.h" |
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#include "utils/simError.h" |
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#include "primitives/Bond.hpp" |
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#include "primitives/Bend.hpp" |
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#include "primitives/Torsion.hpp" |
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#include "primitives/Inversion.hpp" |
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namespace oopse { |
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|
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< |
void ForceManager::calcForces(bool needPotential, bool needStress) { |
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> |
namespace OpenMD { |
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> |
|
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> |
ForceManager::ForceManager(SimInfo * info) : info_(info), |
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> |
NBforcesInitialized_(false) { |
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> |
} |
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> |
|
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> |
void ForceManager::calcForces() { |
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|
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if (!info_->isFortranInitialized()) { |
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info_->update(); |
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|
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calcShortRangeInteraction(); |
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|
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calcLongRangeInteraction(needPotential, needStress); |
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> |
calcLongRangeInteraction(); |
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|
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< |
postCalculation(needStress); |
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> |
postCalculation(); |
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|
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} |
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|
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RealType angle; |
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bend->calcForce(angle); |
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RealType currBendPot = bend->getPotential(); |
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+ |
|
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bendPotential += bend->getPotential(); |
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std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend); |
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if (i == bendDataSets.end()) { |
| 228 |
|
|
| 229 |
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} |
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|
|
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< |
void ForceManager::calcLongRangeInteraction(bool needPotential, |
| 226 |
< |
bool needStress) { |
| 231 |
> |
void ForceManager::calcLongRangeInteraction() { |
| 232 |
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Snapshot* curSnapshot; |
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DataStorage* config; |
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RealType* frc; |
| 280 |
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//initialize data before passing to fortran |
| 281 |
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RealType longRangePotential[LR_POT_TYPES]; |
| 282 |
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RealType lrPot = 0.0; |
| 278 |
– |
Vector3d totalDipole; |
| 279 |
– |
short int passedCalcPot = needPotential; |
| 280 |
– |
short int passedCalcStress = needStress; |
| 283 |
|
int isError = 0; |
| 284 |
|
|
| 285 |
|
for (int i=0; i<LR_POT_TYPES;i++){ |
| 295 |
|
tau.getArrayPointer(), |
| 296 |
|
longRangePotential, |
| 297 |
|
particlePot, |
| 296 |
– |
&passedCalcPot, |
| 297 |
– |
&passedCalcStress, |
| 298 |
|
&isError ); |
| 299 |
|
|
| 300 |
|
if( isError ){ |
| 306 |
|
for (int i=0; i<LR_POT_TYPES;i++){ |
| 307 |
|
lrPot += longRangePotential[i]; //Quick hack |
| 308 |
|
} |
| 309 |
< |
|
| 310 |
< |
// grab the simulation box dipole moment if specified |
| 311 |
< |
if (info_->getCalcBoxDipole()){ |
| 312 |
< |
getAccumulatedBoxDipole(totalDipole.getArrayPointer()); |
| 313 |
< |
|
| 314 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0); |
| 315 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
| 316 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
| 317 |
< |
} |
| 318 |
< |
|
| 309 |
> |
|
| 310 |
|
//store the tau and long range potential |
| 311 |
|
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 312 |
|
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT]; |
| 314 |
|
} |
| 315 |
|
|
| 316 |
|
|
| 317 |
< |
void ForceManager::postCalculation(bool needStress) { |
| 317 |
> |
void ForceManager::postCalculation() { |
| 318 |
|
SimInfo::MoleculeIterator mi; |
| 319 |
|
Molecule* mol; |
| 320 |
|
Molecule::RigidBodyIterator rbIter; |
| 327 |
|
mol = info_->nextMolecule(mi)) { |
| 328 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 329 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 330 |
< |
if (needStress) { |
| 331 |
< |
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 341 |
< |
tau += rbTau; |
| 342 |
< |
} else{ |
| 343 |
< |
rb->calcForcesAndTorques(); |
| 344 |
< |
} |
| 330 |
> |
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 331 |
> |
tau += rbTau; |
| 332 |
|
} |
| 333 |
|
} |
| 334 |
< |
|
| 348 |
< |
if (needStress) { |
| 334 |
> |
|
| 335 |
|
#ifdef IS_MPI |
| 336 |
< |
Mat3x3d tmpTau(tau); |
| 337 |
< |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 338 |
< |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 336 |
> |
Mat3x3d tmpTau(tau); |
| 337 |
> |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 338 |
> |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 339 |
|
#endif |
| 340 |
< |
curSnapshot->statData.setTau(tau); |
| 355 |
< |
} |
| 340 |
> |
curSnapshot->statData.setTau(tau); |
| 341 |
|
} |
| 342 |
|
|
| 343 |
< |
} //end namespace oopse |
| 343 |
> |
} //end namespace OpenMD |
