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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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* |
| 9 |
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* 1. Acknowledgement of the program authors must be made in any |
| 10 |
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* 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 |
| 13 |
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* 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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* |
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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 |
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* such damages. |
| 31 |
+ |
* |
| 32 |
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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 |
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* work. Good starting points are: |
| 35 |
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* |
| 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, 234107 (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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+ |
#include "config.h" |
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#include <cmath> |
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|
#include "primitives/Bend.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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/**@todo still a lot left to improve*/ |
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void Bend::calcForce(RealType& angle) { |
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Vector3d pos1 = atom1_->getPos(); |
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< |
Vector3d pos2 = atom2_->getPos(); |
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< |
Vector3d pos3 = atom3_->getPos(); |
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> |
void Bend::calcForce(RealType& angle, bool doParticlePot) { |
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> |
Vector3d pos1 = atoms_[0]->getPos(); |
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> |
Vector3d pos2 = atoms_[1]->getPos(); |
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> |
Vector3d pos3 = atoms_[2]->getPos(); |
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|
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Vector3d r21 = pos1 - pos2; |
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RealType d21 = r21.length(); |
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|
Vector3d force2 = force1 + force3; |
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force2 *= -1.0; |
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|
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atom1_->addFrc(force1); |
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< |
atom2_->addFrc(force2); |
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< |
atom3_->addFrc(force3); |
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|
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> |
atoms_[0]->addFrc(force1); |
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> |
atoms_[1]->addFrc(force2); |
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> |
atoms_[2]->addFrc(force3); |
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> |
|
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> |
if (doParticlePot) { |
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> |
atoms_[0]->addParticlePot(potential_); |
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> |
atoms_[1]->addParticlePot(potential_); |
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> |
atoms_[2]->addParticlePot(potential_); |
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> |
} |
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> |
|
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|
angle = theta /M_PI * 180.0; |
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|
} |
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|
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< |
} //end namespace oopse |
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> |
} //end namespace OpenMD |
