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Comparing branches/development/src/brains/Snapshot.hpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1708 by gezelter, Tue May 15 13:02:10 2012 UTC

# Line 36 | Line 36
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).                        
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  
56   #include "brains/DataStorage.hpp"
57   #include "brains/Stats.hpp"
57 – #include "UseTheForce/DarkSide/simulation_interface.h"
58  
59 –
59   namespace OpenMD{
60  
61    /**
62     * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
63     * @brief Snapshot class is a repository class for storing dynamic data during
64     *  Simulation
65 <   * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
65 >   * Every snapshot class will contain one DataStorage for atoms and one DataStorage
66     *  for rigid bodies.
67     */
68    class Snapshot {
69    public:
70              
71 <    Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms),
72 <                                             rigidbodyData(nRigidbodies),
73 <                                             currentTime_(0),
74 <                                             orthoTolerance_(1e-6),
75 <                                             orthoRhombic_(0),
76 <                                             chi_(0.0),
77 <                                             integralOfChiDt_(0.0),
78 <                                             eta_(0.0), id_(-1),
79 <                                             hasCOM_(false), hasVolume_(false), volume_(0.0) {
71 >    Snapshot(int nAtoms, int nRigidbodies,
72 >             int nCutoffGroups) : atomData(nAtoms),
73 >                                  rigidbodyData(nRigidbodies),
74 >                                  cgData(nCutoffGroups, DataStorage::dslPosition),
75 >                                  currentTime_(0),
76 >                                  orthoTolerance_(1e-6),
77 >                                  orthoRhombic_(0),
78 >                                  chi_(0.0),
79 >                                  integralOfChiDt_(0.0),
80 >                                  eta_(0.0), id_(-1), hasCOM_(false),
81 >                                  volume_(0.0), hasVolume_(false) {
82  
83      }
84  
85 <    Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
86 <      : atomData(nAtoms, storageLayout),
87 <        rigidbodyData(nRigidbodies, storageLayout),
88 <        currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0),
89 <        integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false), hasVolume_(false),volume_(0.0)  {
90 <
91 <      }
92 <            
85 >    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
86 >             int storageLayout) : atomData(nAtoms, storageLayout),
87 >                                  rigidbodyData(nRigidbodies, storageLayout),
88 >                                  cgData(nCutoffGroups, DataStorage::dslPosition),
89 >                                  currentTime_(0), orthoTolerance_(1e-6),
90 >                                  orthoRhombic_(0), chi_(0.0),
91 >                                  integralOfChiDt_(0.0), eta_(0.0), id_(-1),
92 >                                  hasCOM_(false), volume_(0.0),
93 >                                  hasVolume_(false) {
94 >    }
95 >    
96      /** Returns the id of this Snapshot */
97      int getID() {
98        return id_;
# Line 113 | Line 117 | namespace OpenMD{
117        return rigidbodyData.getSize();
118      }
119  
120 +    /** Returns the number of rigid bodies */
121 +    int getNumberOfCutoffGroups() {
122 +      return cgData.getSize();
123 +    }
124 +
125      /** Returns the H-Matrix */
126      Mat3x3d getHmat() {
127        return hmat_;
# Line 141 | Line 150 | namespace OpenMD{
150  
151      /** Wrapping the vector according to periodic boundary condition*/
152      void wrapVector(Vector3d& v);
153 +    /** Scaling a vector to multiples of the periodic box */
154 +    Vector3d scaleVector(Vector3d &v);
155 +
156 +
157      Vector3d getCOM();
158      Vector3d getCOMvel();
159      Vector3d getCOMw();
# Line 198 | Line 211 | namespace OpenMD{
211        COMw_ = COMw;
212        hasCOM_ = true;
213      }
214 <                  
214 >
215      DataStorage atomData;
216      DataStorage rigidbodyData;
217 +    DataStorage cgData;
218      Stats statData;
219 <            
219 >
220    private:
221      RealType currentTime_;
222  

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