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root/OpenMD/trunk/src/primitives/DirectionalAtom.hpp
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Comparing trunk/src/primitives/DirectionalAtom.hpp (file contents):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# Line 51 | Line 51
51  
52   #include "primitives/Atom.hpp"
53   #include "types/DirectionalAtomType.hpp"
54 < namespace oopse{
55 <    class DirectionalAtom : public Atom {
56 <        public:
57 <            DirectionalAtom(DirectionalAtomType* dAtomType);
58 <            /**
59 <             * Returns the inertia tensor of this stuntdouble
60 <             * @return the inertia tensor of this stuntdouble
61 <             */
62 <            virtual Mat3x3d getI();            
63 <
64 <           /**
65 <             * Sets  the previous rotation matrix of this stuntdouble
66 <             * @param a  new rotation matrix
67 <             */        
68 <           virtual void setPrevA(const RotMat3x3d& a);
69 <          
70 <           /**
71 <             * Sets  the current rotation matrix of this stuntdouble
72 <             * @param a  new rotation matrix
73 <             */        
74 <            virtual void setA(const RotMat3x3d& a);
75 <
76 <           /**
77 <             * Sets  the rotation matrix of this stuntdouble in specified snapshot
78 <             * @param a rotation matrix to be set
79 <             * @param snapshotNo
80 <             * @see #getA
81 <             */        
82 <            virtual void setA(const RotMat3x3d& a, int snapshotNo);
83 <
84 <            /**
85 <             * Left multiple rotation matrix by another rotation matrix
86 <             * @param m a rotation matrix
87 <             */
88 <            void rotateBy(const RotMat3x3d& m);
89 <            
90 <
91 <            /**
92 <             * Returns the gradient of this stuntdouble
93 <             * @return the gradient of this stuntdouble
94 <             */
95 <            virtual std::vector<double> getGrad();
96 <
97 <            virtual void accept(BaseVisitor* v);
98 <                
99 <        protected:
100 <            RotMat3x3d electroBodyFrame_;               /**< body fixed standard eletrostatic frame */
101 <    };
102 <
103 < }//namepace oopse
104 <
54 > namespace OpenMD{
55 >  class DirectionalAtom : public Atom {
56 >  public:
57 >    DirectionalAtom(DirectionalAtomType* dAtomType);
58 >    /**
59 >     * Returns the inertia tensor of this stuntdouble
60 >     * @return the inertia tensor of this stuntdouble
61 >     */
62 >    virtual Mat3x3d getI();            
63 >    
64 >    /**
65 >     * Sets  the previous rotation matrix of this stuntdouble
66 >     * @param a  new rotation matrix
67 >     */        
68 >    virtual void setPrevA(const RotMat3x3d& a);
69 >    
70 >    /**
71 >     * Sets  the current rotation matrix of this stuntdouble
72 >     * @param a  new rotation matrix
73 >     */        
74 >    virtual void setA(const RotMat3x3d& a);
75 >    
76 >    /**
77 >     * Sets  the rotation matrix of this stuntdouble in specified snapshot
78 >     * @param a rotation matrix to be set
79 >     * @param snapshotNo
80 >     * @see #getA
81 >     */        
82 >    virtual void setA(const RotMat3x3d& a, int snapshotNo);
83 >    
84 >    /**
85 >     * Left multiple rotation matrix by another rotation matrix
86 >     * @param m a rotation matrix
87 >     */
88 >    void rotateBy(const RotMat3x3d& m);
89 >        
90 >    /**
91 >     * Returns the gradient of this stuntdouble
92 >     * @return the gradient of this stuntdouble
93 >     */
94 >    virtual std::vector<RealType> getGrad();
95 >    
96 >    virtual void accept(BaseVisitor* v);
97 >    
98 >  protected:
99 >    RotMat3x3d electroBodyFrame_; // body fixed standard eletrostatic frame
100 >  };  
101 > }//namespace OpenMD
102   #endif //PRIMITIVES_DIRECTIONALATOM_HPP

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