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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 |
| 15 |
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* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
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* 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 |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
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* |
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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 |
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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 |
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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 |
+ |
* |
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+ |
* [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). |
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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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|
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#include "primitives/Atom.hpp" |
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#include "types/DirectionalAtomType.hpp" |
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namespace oopse{ |
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> |
namespace OpenMD{ |
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class DirectionalAtom : public Atom { |
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public: |
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DirectionalAtom(DirectionalAtomType* dAtomType); |
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* @return the inertia tensor of this stuntdouble |
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*/ |
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virtual Mat3x3d getI(); |
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< |
|
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> |
|
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/** |
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* Sets the previous rotation matrix of this stuntdouble |
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* @param a new rotation matrix |
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*/ |
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virtual void setPrevA(const RotMat3x3d& a); |
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|
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> |
|
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/** |
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* Sets the current rotation matrix of this stuntdouble |
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* @param a new rotation matrix |
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*/ |
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virtual void setA(const RotMat3x3d& a); |
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|
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> |
|
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/** |
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* Sets the rotation matrix of this stuntdouble in specified snapshot |
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* @param a rotation matrix to be set |
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* @see #getA |
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*/ |
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virtual void setA(const RotMat3x3d& a, int snapshotNo); |
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|
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> |
|
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/** |
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* Left multiple rotation matrix by another rotation matrix |
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* @param m a rotation matrix |
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*/ |
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void rotateBy(const RotMat3x3d& m); |
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< |
|
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< |
|
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> |
|
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/** |
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* Returns the gradient of this stuntdouble |
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* @return the gradient of this stuntdouble |
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*/ |
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virtual std::vector<double> getGrad(); |
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< |
|
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> |
virtual std::vector<RealType> getGrad(); |
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> |
|
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virtual void accept(BaseVisitor* v); |
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< |
|
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> |
|
| 98 |
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protected: |
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RotMat3x3d electroBodyFrame_; /**< body fixed standard eletrostatic frame */ |
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< |
}; |
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< |
|
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< |
}//namepace oopse |
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< |
|
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> |
RotMat3x3d electroBodyFrame_; // body fixed standard eletrostatic frame |
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> |
}; |
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> |
}//namespace OpenMD |
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|
#endif //PRIMITIVES_DIRECTIONALATOM_HPP |
