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root/OpenMD/branches/development/src/primitives/DirectionalAtom.hpp

Comparing:
trunk/src/primitives/DirectionalAtom.hpp (file contents), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/primitives/DirectionalAtom.hpp (file contents), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
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.
#	Line 37 | Line 28
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		/**
#	Line 50 | Line 51
51		#define PRIMITIVES_DIRECTIONALATOM_HPP
52
53		#include "primitives/Atom.hpp"
54	<	#include "types/DirectionalAtomType.hpp"
55	<	namespace oopse{
56	<	class DirectionalAtom : public Atom {
57	<	public:
58	<	DirectionalAtom(DirectionalAtomType* dAtomType);
59	<	/**
60	<	* Returns the inertia tensor of this stuntdouble
61	<	* @return the inertia tensor of this stuntdouble
62	<	*/
63	<	virtual Mat3x3d getI();
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	<
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	<
77	<	/**
78	<	* Sets  the rotation matrix of this stuntdouble in specified snapshot
79	<	* @param a rotation matrix to be set
80	<	* @param snapshotNo
81	<	* @see #getA
82	<	*/
83	<	virtual void setA(const RotMat3x3d& a, int snapshotNo);
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	<
91	<
92	<	/**
93	<	* Returns the gradient of this stuntdouble
94	<	* @return the gradient of this stuntdouble
95	<	*/
96	<	virtual std::vector<double> getGrad();
97	<
98	<	virtual void accept(BaseVisitor* v);
99	<
100	<	protected:
101	<	RotMat3x3d electroBodyFrame_;               /**< body fixed standard eletrostatic frame */
102	<	};
103	<
103	<	}//namepace oopse
104	<
54	>	#include "types/AtomType.hpp"
55	>	namespace OpenMD{
56	>	class DirectionalAtom : public Atom {
57	>	public:
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	>
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	>
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	>
77	>	/**
78	>	* Sets  the rotation matrix of this stuntdouble in specified snapshot
79	>	* @param a rotation matrix to be set
80	>	* @param snapshotNo
81	>	* @see #getA
82	>	*/
83	>	virtual void setA(const RotMat3x3d& a, int snapshotNo);
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	>
91	>	/**
92	>	* Returns the gradient of this stuntdouble
93	>	* @return the gradient of this stuntdouble
94	>	*/
95	>	virtual std::vector<RealType> getGrad();
96	>
97	>	virtual void accept(BaseVisitor* v);
98	>
99	>	private:
100	>	Mat3x3d I_;
101	>	RotMat3x3d electroBodyFrame_; // body fixed standard eletrostatic frame
102	>	};
103	>	}//namespace OpenMD
104		#endif //PRIMITIVES_DIRECTIONALATOM_HPP

Comparing:
trunk/src/primitives/DirectionalAtom.hpp (property svn:keywords), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/primitives/DirectionalAtom.hpp (property svn:keywords), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

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