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Comparing branches/development/src/brains/Snapshot.hpp (file contents):
Revision 1550 by gezelter, Wed Apr 27 21:49:59 2011 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 77 | Line 78 | namespace OpenMD{
78                                    chi_(0.0),
79                                    integralOfChiDt_(0.0),
80                                    eta_(0.0), id_(-1), hasCOM_(false),
81 <                                  hasVolume_(false), volume_(0.0) {
81 >                                  volume_(0.0), hasVolume_(false) {
82  
83      }
84  
# Line 88 | Line 89 | namespace OpenMD{
89                                    currentTime_(0), orthoTolerance_(1e-6),
90                                    orthoRhombic_(0), chi_(0.0),
91                                    integralOfChiDt_(0.0), eta_(0.0), id_(-1),
92 <                                  hasCOM_(false), hasVolume_(false),
93 <                                  volume_(0.0)  {
92 >                                  hasCOM_(false), volume_(0.0),
93 >                                  hasVolume_(false) {
94      }
95      
96      /** Returns the id of this Snapshot */
# Line 149 | 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 207 | Line 212 | namespace OpenMD{
212        hasCOM_ = true;
213      }
214  
210 –    Vector3d getAtomPosByIindex(int iIndex) {
211 – #ifdef IS_MPI
212 –      return atomIData.position[iIndex];
213 – #else
214 –      return atomData.position[iIndex];
215 – #endif
216 –    }
217 –    Vector3d getAtomPosByJindex(int jIndex) {
218 – #ifdef IS_MPI
219 –      return atomJData.position[jIndex];
220 – #else
221 –      return atomData.position[jIndex];
222 – #endif
223 –    }
224 –
225 –    Vector3d getCutoffGroupPosByIindex(int iIndex) {
226 – #ifdef IS_MPI
227 –      return cgIData.position[iIndex];
228 – #else
229 –      return cgData.position[iIndex];
230 – #endif
231 –    }
232 –    Vector3d getCutoffGroupPosByJindex(int jIndex) {
233 – #ifdef IS_MPI
234 –      return cgJData.position[jIndex];
235 – #else
236 –      return cgData.position[jIndex];
237 – #endif
238 –    }
239 –
215      DataStorage atomData;
216      DataStorage rigidbodyData;
217      DataStorage cgData;
218      Stats statData;
219  
245 – #ifdef IS_MPI
246 –    DataStorage atomIData;
247 –    DataStorage atomJData;
248 –    DataStorage cgIData;
249 –    DataStorage cgJData;
250 – #endif
251 –  
252 –            
220    private:
221      RealType currentTime_;
222  

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