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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 |
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* 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," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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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 |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
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* |
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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 |
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* documentation and/or other materials provided with the |
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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. |
| 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). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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+ |
* [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 __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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< |
namespace oopse { |
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> |
#include "primitives/Torsion.hpp" |
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> |
#include "primitives/Inversion.hpp" |
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> |
namespace OpenMD { |
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|
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void ForceManager::calcForces(bool needPotential, bool needStress) { |
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|
| 111 |
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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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+ |
Inversion* inversion; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::BondIterator bondIter;; |
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Molecule::BendIterator bendIter; |
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Molecule::TorsionIterator torsionIter; |
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+ |
Molecule::InversionIterator inversionIter; |
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RealType bondPotential = 0.0; |
| 122 |
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RealType bendPotential = 0.0; |
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RealType torsionPotential = 0.0; |
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+ |
RealType inversionPotential = 0.0; |
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|
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//calculate short range interactions |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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RealType angle; |
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bend->calcForce(angle); |
| 147 |
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RealType currBendPot = bend->getPotential(); |
| 148 |
+ |
|
| 149 |
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bendPotential += bend->getPotential(); |
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std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend); |
| 151 |
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if (i == bendDataSets.end()) { |
| 186 |
|
i->second.prev.potential); |
| 187 |
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} |
| 188 |
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} |
| 189 |
+ |
|
| 190 |
+ |
for (inversion = mol->beginInversion(inversionIter); |
| 191 |
+ |
inversion != NULL; |
| 192 |
+ |
inversion = mol->nextInversion(inversionIter)) { |
| 193 |
+ |
RealType angle; |
| 194 |
+ |
inversion->calcForce(angle); |
| 195 |
+ |
RealType currInversionPot = inversion->getPotential(); |
| 196 |
+ |
inversionPotential += inversion->getPotential(); |
| 197 |
+ |
std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion); |
| 198 |
+ |
if (i == inversionDataSets.end()) { |
| 199 |
+ |
InversionDataSet dataSet; |
| 200 |
+ |
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 201 |
+ |
dataSet.prev.potential = dataSet.curr.potential = currInversionPot; |
| 202 |
+ |
dataSet.deltaV = 0.0; |
| 203 |
+ |
inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet)); |
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+ |
}else { |
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+ |
i->second.prev.angle = i->second.curr.angle; |
| 206 |
+ |
i->second.prev.potential = i->second.curr.potential; |
| 207 |
+ |
i->second.curr.angle = angle; |
| 208 |
+ |
i->second.curr.potential = currInversionPot; |
| 209 |
+ |
i->second.deltaV = fabs(i->second.curr.potential - |
| 210 |
+ |
i->second.prev.potential); |
| 211 |
+ |
} |
| 212 |
+ |
} |
| 213 |
|
} |
| 214 |
|
|
| 215 |
|
RealType shortRangePotential = bondPotential + bendPotential + |
| 216 |
< |
torsionPotential; |
| 216 |
> |
torsionPotential + inversionPotential; |
| 217 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 218 |
|
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
| 219 |
|
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 220 |
|
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
| 221 |
|
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
| 222 |
+ |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 223 |
|
|
| 224 |
|
} |
| 225 |
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|
| 356 |
|
} |
| 357 |
|
} |
| 358 |
|
|
| 359 |
< |
} //end namespace oopse |
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> |
} //end namespace OpenMD |
