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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 |
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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 |
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< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* 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 |
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|
* 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 |
| 13 |
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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). |
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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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/** |
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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/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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|
| 85 |
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|
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// forces are zeroed here, before any are accumulated. |
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// NOTE: do not rezero the forces in Fortran. |
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< |
|
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> |
|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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atom->zeroForcesAndTorques(); |
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} |
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< |
|
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> |
|
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->zeroForcesAndTorques(); |
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} |
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+ |
|
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} |
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|
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// Zero out the stress tensor |
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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; |
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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); |
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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()) { |
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i->second.prev.potential); |
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} |
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} |
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+ |
|
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+ |
for (inversion = mol->beginInversion(inversionIter); |
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+ |
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; |
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+ |
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 201 |
+ |
dataSet.prev.potential = dataSet.curr.potential = currInversionPot; |
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+ |
dataSet.deltaV = 0.0; |
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+ |
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; |
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+ |
i->second.prev.potential = i->second.curr.potential; |
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+ |
i->second.curr.angle = angle; |
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+ |
i->second.curr.potential = currInversionPot; |
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+ |
i->second.deltaV = fabs(i->second.curr.potential - |
| 210 |
+ |
i->second.prev.potential); |
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+ |
} |
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+ |
} |
| 213 |
|
} |
| 214 |
|
|
| 215 |
|
RealType shortRangePotential = bondPotential + bendPotential + |
| 216 |
< |
torsionPotential; |
| 216 |
> |
torsionPotential + inversionPotential; |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 218 |
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curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
| 219 |
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curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 220 |
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curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
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curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
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+ |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 223 |
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|
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|
} |
| 225 |
|
|
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|
RealType* A; |
| 234 |
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RealType* electroFrame; |
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|
RealType* rc; |
| 236 |
+ |
RealType* particlePot; |
| 237 |
|
|
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|
//get current snapshot from SimInfo |
| 239 |
|
curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
trq = config->getArrayPointer(DataStorage::dslTorque); |
| 246 |
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A = config->getArrayPointer(DataStorage::dslAmat); |
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electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
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+ |
particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 249 |
|
|
| 250 |
|
//calculate the center of mass of cutoff group |
| 251 |
|
SimInfo::MoleculeIterator mi; |
| 285 |
|
longRangePotential[i]=0.0; //Initialize array |
| 286 |
|
} |
| 287 |
|
|
| 288 |
< |
doForceLoop( pos, |
| 289 |
< |
rc, |
| 290 |
< |
A, |
| 291 |
< |
electroFrame, |
| 292 |
< |
frc, |
| 293 |
< |
trq, |
| 294 |
< |
tau.getArrayPointer(), |
| 295 |
< |
longRangePotential, |
| 296 |
< |
&passedCalcPot, |
| 297 |
< |
&passedCalcStress, |
| 298 |
< |
&isError ); |
| 299 |
< |
|
| 288 |
> |
doForceLoop(pos, |
| 289 |
> |
rc, |
| 290 |
> |
A, |
| 291 |
> |
electroFrame, |
| 292 |
> |
frc, |
| 293 |
> |
trq, |
| 294 |
> |
tau.getArrayPointer(), |
| 295 |
> |
longRangePotential, |
| 296 |
> |
particlePot, |
| 297 |
> |
&passedCalcPot, |
| 298 |
> |
&passedCalcStress, |
| 299 |
> |
&isError ); |
| 300 |
> |
|
| 301 |
|
if( isError ){ |
| 302 |
|
sprintf( painCave.errMsg, |
| 303 |
|
"Error returned from the fortran force calculation.\n" ); |
| 356 |
|
} |
| 357 |
|
} |
| 358 |
|
|
| 359 |
< |
} //end namespace oopse |
| 359 |
> |
} //end namespace OpenMD |
