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Comparing branches/development/src/brains/Snapshot.hpp (file contents):
Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC vs.
Revision 1858 by gezelter, Wed Apr 3 21:32:13 2013 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 78 | Line 80 | namespace OpenMD{
80      potVec   excludedPotentials;  /**< breakdown of excluded potentials by family */
81      RealType restraintPotential;  /**< potential energy of restraints */
82      RealType rawPotential;        /**< unrestrained potential energy (when restraints are applied) */
83 +    RealType xyArea;              /**< XY area of this frame */
84      RealType volume;              /**< total volume of this frame */
85      RealType pressure;            /**< pressure of this frame */
86      RealType temperature;         /**< temperature of this frame */
# Line 134 | Line 137 | namespace OpenMD{
137      void     setHmat(const Mat3x3d& m);
138      /** Returns the inverse H-Matrix */
139      Mat3x3d  getInvHmat();
140 +
141 +    /** Returns the Bounding Box */
142 +    Mat3x3d  getBoundingBox();
143 +    /** Sets the Bounding Box */
144 +    void     setBoundingBox(const Mat3x3d& m);
145 +    /** Returns the inverse Bounding Box*/
146 +    Mat3x3d  getInvBoundingBox();
147              
148      RealType getVolume();
149 +    RealType getXYarea();
150      void     setVolume(const RealType vol);
151  
152      /** Wrapping the vector according to periodic boundary condition*/
# Line 246 | Line 257 | namespace OpenMD{
257      bool hasKineticEnergy;    
258      bool hasShortRangePotential;
259      bool hasLongRangePotential;
260 <    bool hasPotentialEnergy;    
260 >    bool hasPotentialEnergy;    
261 >    bool hasXYarea;
262      bool hasVolume;        
263      bool hasPressure;      
264      bool hasTemperature;    
# Line 261 | Line 273 | namespace OpenMD{
273      bool hasGyrationalVolume;
274      bool hasHullVolume;
275      bool hasConservedQuantity;
276 +    bool hasBoundingBox;
277  
278    private:
279      RealType orthoTolerance_;

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