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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 |
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* 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 |
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* 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 |
| 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. |
| 28 |
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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). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "integrators/NVT.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/PhysicalConstants.hpp" |
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|
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namespace oopse { |
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namespace OpenMD { |
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|
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NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) { |
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|
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if (!simParams->haveTargetTemp()) { |
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sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n"); |
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painCave.isFatal = 1; |
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painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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simError(); |
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} else { |
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targetTemp_ = simParams->getTargetTemp(); |
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} |
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|
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// We must set tauThermostat_. |
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// We must set tauThermostat. |
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|
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if (!simParams->haveTauThermostat()) { |
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sprintf(painCave.errMsg, "If you use the constant temperature\n" |
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"\tintegrator, you must set tauThermostat_.\n"); |
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"\tintegrator, you must set tauThermostat.\n"); |
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|
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painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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StuntDouble* integrableObject; |
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Vector3d Tb; |
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Vector3d ji; |
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double mass; |
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> |
RealType mass; |
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Vector3d vel; |
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Vector3d pos; |
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Vector3d frc; |
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|
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< |
double chi = currentSnapshot_->getChi(); |
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< |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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> |
RealType chi = currentSnapshot_->getChi(); |
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> |
RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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|
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// We need the temperature at time = t for the chi update below: |
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|
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< |
double instTemp = thermo.getTemperature(); |
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> |
RealType instTemp = thermo.getTemperature(); |
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|
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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mass = integrableObject->getMass(); |
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|
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// velocity half step (use chi from previous step here): |
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< |
//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi); |
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vel += dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel; |
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> |
//vel[j] += dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - vel[j]*chi); |
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> |
vel += dt2 *PhysicalConstants::energyConvert/mass*frc - dt2*chi*vel; |
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|
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// position whole step |
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//pos[j] += dt * vel[j]; |
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|
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ji = integrableObject->getJ(); |
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|
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< |
//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi); |
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< |
ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *ji; |
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> |
//ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi); |
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> |
ji += dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *ji; |
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rotAlgo->rotate(integrableObject, ji, dt); |
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|
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integrableObject->setJ(ji); |
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Vector3d ji; |
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Vector3d vel; |
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Vector3d frc; |
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< |
double mass; |
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< |
double instTemp; |
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> |
RealType mass; |
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> |
RealType instTemp; |
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int index; |
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// Set things up for the iteration: |
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|
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< |
double chi = currentSnapshot_->getChi(); |
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< |
double oldChi = chi; |
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< |
double prevChi; |
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< |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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> |
RealType chi = currentSnapshot_->getChi(); |
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> |
RealType oldChi = chi; |
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> |
RealType prevChi; |
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> |
RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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|
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index = 0; |
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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|
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// velocity half step |
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//for(j = 0; j < 3; j++) |
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< |
// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi); |
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< |
vel = oldVel_[index] + dt2/mass*OOPSEConstant::energyConvert * frc - dt2*chi*oldVel_[index]; |
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> |
// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - oldVel_[3*i + j]*chi); |
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> |
vel = oldVel_[index] + dt2/mass*PhysicalConstants::energyConvert * frc - dt2*chi*oldVel_[index]; |
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|
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integrableObject->setVel(vel); |
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|
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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|
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//for(j = 0; j < 3; j++) |
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< |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi); |
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< |
ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index]; |
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> |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi_[3*i+j]*chi); |
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> |
ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *oldJi_[index]; |
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|
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integrableObject->setJ(ji); |
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} |
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currentSnapshot_->setIntegralOfChiDt(0.0); |
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} |
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|
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< |
double NVT::calcConservedQuantity() { |
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> |
RealType NVT::calcConservedQuantity() { |
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|
|
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< |
double chi = currentSnapshot_->getChi(); |
| 260 |
< |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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< |
double conservedQuantity; |
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< |
double fkBT; |
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< |
double Energy; |
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< |
double thermostat_kinetic; |
| 265 |
< |
double thermostat_potential; |
| 259 |
> |
RealType chi = currentSnapshot_->getChi(); |
| 260 |
> |
RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 261 |
> |
RealType conservedQuantity; |
| 262 |
> |
RealType fkBT; |
| 263 |
> |
RealType Energy; |
| 264 |
> |
RealType thermostat_kinetic; |
| 265 |
> |
RealType thermostat_potential; |
| 266 |
|
|
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< |
fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_; |
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> |
fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_; |
| 268 |
|
|
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|
Energy = thermo.getTotalE(); |
| 270 |
|
|
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< |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
| 271 |
> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * PhysicalConstants::energyConvert); |
| 272 |
|
|
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< |
thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert; |
| 273 |
> |
thermostat_potential = fkBT * integralOfChidt / PhysicalConstants::energyConvert; |
| 274 |
|
|
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|
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 276 |
|
|
| 278 |
|
} |
| 279 |
|
|
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|
|
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< |
}//end namespace oopse |
| 281 |
> |
}//end namespace OpenMD |
