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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 |
< |
* |
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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). |
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*/ |
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|
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/** |
| 50 |
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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 __OOPSE_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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> |
lj_ = LJ::Instance(); |
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> |
lj_->setForceField(info_->getForceField()); |
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> |
|
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> |
gb_ = GB::Instance(); |
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> |
gb_->setForceField(info_->getForceField()); |
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> |
|
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> |
sticky_ = Sticky::Instance(); |
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> |
sticky_->setForceField(info_->getForceField()); |
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> |
|
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> |
eam_ = EAM::Instance(); |
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> |
eam_->setForceField(info_->getForceField()); |
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> |
} |
| 77 |
> |
|
| 78 |
> |
void ForceManager::calcForces() { |
| 79 |
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|
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if (!info_->isFortranInitialized()) { |
| 81 |
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info_->update(); |
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|
| 86 |
|
calcShortRangeInteraction(); |
| 87 |
|
|
| 88 |
< |
calcLongRangeInteraction(needPotential, needStress); |
| 88 |
> |
calcLongRangeInteraction(); |
| 89 |
|
|
| 90 |
< |
postCalculation(needStress); |
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> |
postCalculation(); |
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|
| 92 |
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} |
| 93 |
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|
| 161 |
|
RealType angle; |
| 162 |
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bend->calcForce(angle); |
| 163 |
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RealType currBendPot = bend->getPotential(); |
| 164 |
+ |
|
| 165 |
|
bendPotential += bend->getPotential(); |
| 166 |
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std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend); |
| 167 |
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if (i == bendDataSets.end()) { |
| 239 |
|
|
| 240 |
|
} |
| 241 |
|
|
| 242 |
< |
void ForceManager::calcLongRangeInteraction(bool needPotential, |
| 226 |
< |
bool needStress) { |
| 242 |
> |
void ForceManager::calcLongRangeInteraction() { |
| 243 |
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Snapshot* curSnapshot; |
| 244 |
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DataStorage* config; |
| 245 |
|
RealType* frc; |
| 292 |
|
RealType longRangePotential[LR_POT_TYPES]; |
| 293 |
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RealType lrPot = 0.0; |
| 294 |
|
Vector3d totalDipole; |
| 279 |
– |
short int passedCalcPot = needPotential; |
| 280 |
– |
short int passedCalcStress = needStress; |
| 295 |
|
int isError = 0; |
| 296 |
|
|
| 297 |
|
for (int i=0; i<LR_POT_TYPES;i++){ |
| 307 |
|
tau.getArrayPointer(), |
| 308 |
|
longRangePotential, |
| 309 |
|
particlePot, |
| 296 |
– |
&passedCalcPot, |
| 297 |
– |
&passedCalcStress, |
| 310 |
|
&isError ); |
| 311 |
|
|
| 312 |
|
if( isError ){ |
| 335 |
|
} |
| 336 |
|
|
| 337 |
|
|
| 338 |
< |
void ForceManager::postCalculation(bool needStress) { |
| 338 |
> |
void ForceManager::postCalculation() { |
| 339 |
|
SimInfo::MoleculeIterator mi; |
| 340 |
|
Molecule* mol; |
| 341 |
|
Molecule::RigidBodyIterator rbIter; |
| 348 |
|
mol = info_->nextMolecule(mi)) { |
| 349 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 350 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 351 |
< |
if (needStress) { |
| 352 |
< |
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 341 |
< |
tau += rbTau; |
| 342 |
< |
} else{ |
| 343 |
< |
rb->calcForcesAndTorques(); |
| 344 |
< |
} |
| 351 |
> |
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 352 |
> |
tau += rbTau; |
| 353 |
|
} |
| 354 |
|
} |
| 355 |
< |
|
| 348 |
< |
if (needStress) { |
| 355 |
> |
|
| 356 |
|
#ifdef IS_MPI |
| 357 |
< |
Mat3x3d tmpTau(tau); |
| 358 |
< |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 359 |
< |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 357 |
> |
Mat3x3d tmpTau(tau); |
| 358 |
> |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 359 |
> |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 360 |
|
#endif |
| 361 |
< |
curSnapshot->statData.setTau(tau); |
| 355 |
< |
} |
| 361 |
> |
curSnapshot->statData.setTau(tau); |
| 362 |
|
} |
| 363 |
|
|
| 364 |
< |
} //end namespace oopse |
| 364 |
> |
} //end namespace OpenMD |
