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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 2022 by gezelter, Fri Sep 26 22:22:28 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 95 | Line 98 | namespace OpenMD{
98      Mat3x3d  stressTensor;        /**< stress tensor */
99      Mat3x3d  pressureTensor;      /**< pressure tensor */
100      Vector3d systemDipole;        /**< total system dipole moment */
101 +    Mat3x3d  systemQuadrupole;    /**< total system quadrupole moment */
102      Vector3d conductiveHeatFlux;  /**< heat flux vector (conductive only) */
103      Vector3d convectiveHeatFlux;  /**< heat flux vector (convective only) */
104      RealType conservedQuantity;   /**< anything conserved by the integrator */
# Line 128 | Line 132 | namespace OpenMD{
132      int      getNumberOfRigidBodies();
133      /** Returns the number of rigid bodies */
134      int      getNumberOfCutoffGroups();
135 +    /** Returns the number of bytes in a FrameData structure */
136 +    static int getFrameDataSize();
137  
138      /** Returns the H-Matrix */
139      Mat3x3d  getHmat();
# Line 135 | Line 141 | namespace OpenMD{
141      void     setHmat(const Mat3x3d& m);
142      /** Returns the inverse H-Matrix */
143      Mat3x3d  getInvHmat();
144 +
145 +    /** Returns the Bounding Box */
146 +    Mat3x3d  getBoundingBox();
147 +    /** Sets the Bounding Box */
148 +    void     setBoundingBox(const Mat3x3d& m);
149 +    /** Returns the inverse Bounding Box*/
150 +    Mat3x3d  getInvBoundingBox();
151              
152      RealType getVolume();
153      RealType getXYarea();
# Line 173 | Line 186 | namespace OpenMD{
186      RealType getLongRangePotential();
187      potVec   getLongRangePotentials();
188  
189 +    void     setReciprocalPotential(const RealType rp);
190 +    RealType getReciprocalPotential();
191 +    
192      void     setExcludedPotentials(const potVec exPot);
193      potVec   getExcludedPotentials();
194    
# Line 217 | Line 233 | namespace OpenMD{
233      Vector3d getSystemDipole();
234      void     setSystemDipole(const Vector3d& bd);
235  
236 +    Mat3x3d  getSystemQuadrupole();
237 +    void     setSystemQuadrupole(const Mat3x3d& bq);
238 +
239      pair<RealType, RealType> getThermostat();
240      void setThermostat(const pair<RealType, RealType>& thermostat);
241  
# Line 258 | Line 277 | namespace OpenMD{
277      bool hasCOMvel;
278      bool hasCOMw;
279      bool hasPressureTensor;    
280 <    bool hasSystemDipole;    
280 >    bool hasSystemDipole;
281 >    bool hasSystemQuadrupole;
282      bool hasConvectiveHeatFlux;
283      bool hasInertiaTensor;
284      bool hasGyrationalVolume;
285      bool hasHullVolume;
286      bool hasConservedQuantity;
287 +    bool hasBoundingBox;
288  
289    private:
290      RealType orthoTolerance_;

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