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Comparing trunk/src/brains/Snapshot.hpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1966 by gezelter, Fri Jan 24 14:17:42 2014 UTC

# Line 35 | Line 35
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 62 | Line 62 | namespace OpenMD{
62      RealType currentTime;         /**< current time */
63      Mat3x3d  hmat;                /**< axes of the periodic box in matrix form */
64      Mat3x3d  invHmat;             /**< the inverse of the Hmat matrix */
65 +    Mat3x3d  bBox;                /**< axes of a bounding box in matrix form */
66 +    Mat3x3d  invBbox;             /**< the inverse of the bounding box */
67      bool     orthoRhombic;        /**< is this an orthorhombic periodic box? */
68      RealType totalEnergy;         /**< total energy of this frame */
69      RealType translationalKinetic; /**< translational kinetic energy of this frame */
# Line 70 | Line 72 | namespace OpenMD{
72      RealType potentialEnergy;     /**< potential energy of this frame */
73      RealType shortRangePotential; /**< short-range contributions to the potential*/
74      RealType longRangePotential;  /**< long-range contributions to the potential */
75 +    RealType reciprocalPotential; /**< reciprocal-space contributions to the potential */
76      RealType bondPotential;       /**< bonded contribution to the potential */
77      RealType bendPotential;       /**< angle-bending contribution to the potential */
78      RealType torsionPotential;    /**< dihedral (torsion angle) contribution to the potential */
# Line 128 | Line 131 | namespace OpenMD{
131      int      getNumberOfRigidBodies();
132      /** Returns the number of rigid bodies */
133      int      getNumberOfCutoffGroups();
134 +    /** Returns the number of bytes in a FrameData structure */
135 +    static int getFrameDataSize();
136  
137      /** Returns the H-Matrix */
138      Mat3x3d  getHmat();
# Line 135 | Line 140 | namespace OpenMD{
140      void     setHmat(const Mat3x3d& m);
141      /** Returns the inverse H-Matrix */
142      Mat3x3d  getInvHmat();
143 +
144 +    /** Returns the Bounding Box */
145 +    Mat3x3d  getBoundingBox();
146 +    /** Sets the Bounding Box */
147 +    void     setBoundingBox(const Mat3x3d& m);
148 +    /** Returns the inverse Bounding Box*/
149 +    Mat3x3d  getInvBoundingBox();
150              
151      RealType getVolume();
152      RealType getXYarea();
# Line 173 | Line 185 | namespace OpenMD{
185      RealType getLongRangePotential();
186      potVec   getLongRangePotentials();
187  
188 +    void     setReciprocalPotential(const RealType rp);
189 +    RealType getReciprocalPotential();
190 +    
191      void     setExcludedPotentials(const potVec exPot);
192      potVec   getExcludedPotentials();
193    
# Line 264 | Line 279 | namespace OpenMD{
279      bool hasGyrationalVolume;
280      bool hasHullVolume;
281      bool hasConservedQuantity;
282 +    bool hasBoundingBox;
283  
284    private:
285      RealType orthoTolerance_;

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