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Comparing trunk/src/primitives/DirectionalAtom.hpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# 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{
54 > namespace OpenMD{
55    class DirectionalAtom : public Atom {
56    public:
57      DirectionalAtom(DirectionalAtomType* dAtomType);
# Line 60 | Line 60 | namespace oopse{
60       * @return the inertia tensor of this stuntdouble
61       */
62      virtual Mat3x3d getI();            
63 <
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 <          
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 <
75 >    
76      /**
77       * Sets  the rotation matrix of this stuntdouble in specified snapshot
78       * @param a rotation matrix to be set
# Line 80 | Line 80 | namespace oopse{
80       * @see #getA
81       */        
82      virtual void setA(const RotMat3x3d& a, int snapshotNo);
83 <
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 <
89 >        
90      /**
91       * Returns the gradient of this stuntdouble
92       * @return the gradient of this stuntdouble
93       */
94      virtual std::vector<RealType> getGrad();
95 <
95 >    
96      virtual void accept(BaseVisitor* v);
97 <                
97 >    
98    protected:
99 <    RotMat3x3d electroBodyFrame_;               /**< body fixed standard eletrostatic frame */
100 <  };
101 <
103 < }//namepace oopse
104 <
99 >    RotMat3x3d electroBodyFrame_; // body fixed standard eletrostatic frame
100 >  };  
101 > }//namespace OpenMD
102   #endif //PRIMITIVES_DIRECTIONALATOM_HPP

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