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Comparing:
trunk/src/primitives/RigidBody.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/primitives/RigidBody.hpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 54 | Line 55
55   #include "primitives/StuntDouble.hpp"
56   #include "primitives/DirectionalAtom.hpp"
57   #include "types/AtomStamp.hpp"
58 < namespace oopse{
58 > namespace OpenMD{
59    class RigidBody : public StuntDouble {
60    public:
61  
# Line 95 | Line 96 | namespace oopse{
96       */
97      virtual Mat3x3d getI();
98  
98 –
99 –    /** Sets the internal unit frame of this stuntdouble by three euler angles */
100 –    void setElectroFrameFromEuler(RealType phi, RealType theta, RealType psi);
101 –        
99      /**
100       * Returns the gradient of this stuntdouble
101 <     * @return the inertia tensor of this stuntdouble
105 <     * @see #setI
101 >     * @return the gradient of this stuntdouble
102       */
103      virtual std::vector<RealType> getGrad();
104  
# Line 110 | Line 106 | namespace oopse{
106  
107      void addAtom(Atom* at, AtomStamp* ats);
108  
109 <    /** calculate the reference coordinates */
109 >    /** calculates the reference coordinates */
110      void calcRefCoords();
111  
112 <    /** Convert Atomic forces and torques to total forces and torques */
112 >    /** Converts Atomic forces and torques to total forces and torques */
113      void calcForcesAndTorques();
114  
115 +    /**
116 +        Converts Atomic forces and torques to total forces and torques
117 +        and computes the rigid body contribution to the virial.
118 +        Returns the rigid body contribution to the virial as a 3x3
119 +        matrix.
120 +        */
121 +    Mat3x3d calcForcesAndTorquesAndVirial();
122 +    
123      /** update the positions of atoms belong to this rigidbody */
124      void updateAtoms();
125  
# Line 146 | Line 150 | namespace oopse{
150      /**
151       * Returns the atoms of this rigid body
152       * @return the atoms of this rigid body in a vector
153 <     * @deprecate
153 >     * @deprecated
154       */          
155      std::vector<Atom*> getAtoms() {
156        return atoms_;
# Line 218 | Line 222 | namespace oopse{
222      std::vector<RotMat3x3d> refOrients_;
223    };
224  
225 < }//namepace oopse
225 > }//namespace OpenMD
226  
227   #endif //PRIMITIVES_RIGIDBODY_HPP
228  

Comparing:
trunk/src/primitives/RigidBody.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/primitives/RigidBody.hpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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