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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: |
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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 |
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* the article in which the program was described (Matthew |
| 13 |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
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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 |
< |
* |
| 18 |
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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 |
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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. |
| 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 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* 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). |
| 40 |
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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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/** |
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|
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#include "integrators/NVE.hpp" |
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#include "primitives/Molecule.hpp" |
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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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|
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NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){ |
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mass = integrableObject->getMass(); |
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|
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// velocity half step |
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vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc; |
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> |
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
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|
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// position whole step |
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pos += dt * vel; |
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|
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ji = integrableObject->getJ(); |
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|
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< |
ji += (dt2 * OOPSEConstant::energyConvert) * Tb; |
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> |
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
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|
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rotAlgo->rotate(integrableObject, ji, dt); |
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|
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mass = integrableObject->getMass(); |
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|
|
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// velocity half step |
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< |
vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc; |
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> |
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
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|
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< |
integrableObject->setVel(vel); |
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> |
integrableObject->setVel(vel); |
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|
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|
if (integrableObject->isDirectional()){ |
| 142 |
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|
| 148 |
|
|
| 149 |
|
ji = integrableObject->getJ(); |
| 150 |
|
|
| 151 |
< |
ji += (dt2 * OOPSEConstant::energyConvert) * Tb; |
| 151 |
> |
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
| 152 |
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|
| 153 |
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integrableObject->setJ(ji); |
| 154 |
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} |
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|
| 165 |
|
|
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RealType NVE::calcConservedQuantity() { |
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return thermo.getTotalE(); |
| 167 |
> |
return thermo.getTotalE() ; |
| 168 |
|
} |
| 169 |
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|
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< |
} //end namespace oopse |
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> |
} //end namespace OpenMD |
