| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* 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 |
|
* 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 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 51 |
|
#define PRIMITIVES_DIRECTIONALATOM_HPP |
| 52 |
|
|
| 53 |
|
#include "primitives/Atom.hpp" |
| 54 |
< |
#include "types/DirectionalAtomType.hpp" |
| 55 |
< |
namespace oopse{ |
| 54 |
> |
#include "types/AtomType.hpp" |
| 55 |
> |
namespace OpenMD{ |
| 56 |
|
class DirectionalAtom : public Atom { |
| 57 |
|
public: |
| 58 |
< |
DirectionalAtom(DirectionalAtomType* dAtomType); |
| 58 |
> |
DirectionalAtom(AtomType* dAtomType); |
| 59 |
|
/** |
| 60 |
|
* Returns the inertia tensor of this stuntdouble |
| 61 |
|
* @return the inertia tensor of this stuntdouble |
| 62 |
|
*/ |
| 63 |
|
virtual Mat3x3d getI(); |
| 64 |
< |
|
| 64 |
> |
|
| 65 |
|
/** |
| 66 |
|
* Sets the previous rotation matrix of this stuntdouble |
| 67 |
|
* @param a new rotation matrix |
| 68 |
|
*/ |
| 69 |
|
virtual void setPrevA(const RotMat3x3d& a); |
| 70 |
< |
|
| 70 |
> |
|
| 71 |
|
/** |
| 72 |
|
* Sets the current rotation matrix of this stuntdouble |
| 73 |
|
* @param a new rotation matrix |
| 74 |
|
*/ |
| 75 |
|
virtual void setA(const RotMat3x3d& a); |
| 76 |
< |
|
| 76 |
> |
|
| 77 |
|
/** |
| 78 |
|
* Sets the rotation matrix of this stuntdouble in specified snapshot |
| 79 |
|
* @param a rotation matrix to be set |
| 81 |
|
* @see #getA |
| 82 |
|
*/ |
| 83 |
|
virtual void setA(const RotMat3x3d& a, int snapshotNo); |
| 84 |
< |
|
| 84 |
> |
|
| 85 |
|
/** |
| 86 |
|
* Left multiple rotation matrix by another rotation matrix |
| 87 |
|
* @param m a rotation matrix |
| 88 |
|
*/ |
| 89 |
|
void rotateBy(const RotMat3x3d& m); |
| 90 |
< |
|
| 90 |
< |
|
| 90 |
> |
|
| 91 |
|
/** |
| 92 |
|
* Returns the gradient of this stuntdouble |
| 93 |
|
* @return the gradient of this stuntdouble |
| 94 |
|
*/ |
| 95 |
|
virtual std::vector<RealType> getGrad(); |
| 96 |
< |
|
| 96 |
> |
|
| 97 |
|
virtual void accept(BaseVisitor* v); |
| 98 |
< |
|
| 99 |
< |
protected: |
| 100 |
< |
RotMat3x3d electroBodyFrame_; /**< body fixed standard eletrostatic frame */ |
| 101 |
< |
}; |
| 102 |
< |
|
| 103 |
< |
}//namepace oopse |
| 104 |
< |
|
| 98 |
> |
|
| 99 |
> |
private: |
| 100 |
> |
Mat3x3d I_; |
| 101 |
> |
RotMat3x3d electroBodyFrame_; // body fixed standard eletrostatic frame |
| 102 |
> |
}; |
| 103 |
> |
}//namespace OpenMD |
| 104 |
|
#endif //PRIMITIVES_DIRECTIONALATOM_HPP |
