| 6 |
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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: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* 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 |
< |
* |
| 18 |
< |
* 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 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
|
* 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 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 42 |
|
|
| 43 |
|
/** |
| 52 |
|
#define PRIMITIVES_BEND_HPP |
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#include "primitives/Atom.hpp" |
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|
#include "types/BendType.hpp" |
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< |
namespace oopse { |
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< |
struct BendData { |
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> |
namespace OpenMD { |
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> |
struct BendData { |
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|
RealType angle; |
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|
RealType potential; |
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< |
}; |
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< |
|
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< |
struct BendDataSet { |
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> |
}; |
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> |
|
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> |
struct BendDataSet { |
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|
RealType deltaV; |
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|
BendData prev; |
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BendData curr; |
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< |
}; |
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< |
|
| 65 |
> |
}; |
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> |
|
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|
class Bend { |
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public: |
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|
Bend(Atom* atom1, Atom* atom2, Atom* atom3, BendType* bt) |
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: atom1_(atom1), atom2_(atom2), atom3_(atom3), bendType_(bt) {} |
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< |
|
| 71 |
> |
|
| 72 |
|
virtual ~Bend() {} |
| 73 |
< |
virtual void calcForce(RealType& angle); |
| 74 |
< |
|
| 73 |
> |
virtual void calcForce(RealType& angle, bool doParticlePot); |
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> |
|
| 75 |
|
RealType getPotential() { |
| 76 |
|
return potential_; |
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|
} |
| 78 |
< |
|
| 78 |
> |
|
| 79 |
|
Atom* getAtomA() { |
| 80 |
|
return atom1_; |
| 81 |
|
} |
| 82 |
< |
|
| 82 |
> |
|
| 83 |
|
Atom* getAtomB() { |
| 84 |
|
return atom2_; |
| 85 |
|
} |
| 86 |
< |
|
| 86 |
> |
|
| 87 |
|
Atom* getAtomC() { |
| 88 |
|
return atom3_; |
| 89 |
|
} |
| 90 |
< |
|
| 90 |
> |
|
| 91 |
|
BendType * getBendType() { |
| 92 |
|
return bendType_; |
| 93 |
|
} |
| 94 |
< |
|
| 94 |
> |
|
| 95 |
|
protected: |
| 96 |
< |
|
| 96 |
> |
|
| 97 |
|
RealType potential_; |
| 98 |
|
Atom* atom1_; |
| 99 |
|
Atom* atom2_; |
| 100 |
|
Atom* atom3_; |
| 101 |
|
BendType* bendType_; /**< bend type */ |
| 102 |
< |
|
| 102 |
> |
|
| 103 |
|
}; |
| 104 |
< |
|
| 104 |
< |
|
| 105 |
< |
|
| 106 |
< |
} //end namespace oopse |
| 104 |
> |
} //end namespace OpenMD |
| 105 |
|
#endif //PRIMITIVES_BEND_HPP |
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|
|
