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Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC vs.
Revision 1709 by gezelter, Tue May 15 13:04:08 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    /**
# Line 79 | 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 90 | 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 151 | 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 201 | namespace OpenMD{
201        eta_ = eta;
202      }
203  
204 +    Mat3x3d getTau() {
205 +      return tau_;
206 +    }
207 +        
208 +    void setTau(const Mat3x3d& tau) {
209 +      tau_ = tau;
210 +    }
211 +
212      bool hasCOM() {
213        return hasCOM_;
214      }
# Line 209 | Line 220 | namespace OpenMD{
220        hasCOM_ = true;
221      }
222  
212 –    Vector3d getAtomPosByIindex(int iIndex) {
213 – #ifdef IS_MPI
214 –      return atomIData.position[iIndex];
215 – #else
216 –      return atomData.position[iIndex];
217 – #endif
218 –    }
219 –    Vector3d getAtomPosByJindex(int jIndex) {
220 – #ifdef IS_MPI
221 –      return atomJData.position[jIndex];
222 – #else
223 –      return atomData.position[jIndex];
224 – #endif
225 –    }
226 –
227 –    Vector3d getCutoffGroupPosByIindex(int iIndex) {
228 – #ifdef IS_MPI
229 –      return cgIData.position[iIndex];
230 – #else
231 –      return cgData.position[iIndex];
232 – #endif
233 –    }
234 –    Vector3d getCutoffGroupPosByJindex(int jIndex) {
235 – #ifdef IS_MPI
236 –      return cgJData.position[jIndex];
237 – #else
238 –      return cgData.position[jIndex];
239 – #endif
240 –    }
241 –
223      DataStorage atomData;
224      DataStorage rigidbodyData;
225      DataStorage cgData;
226      Stats statData;
227  
247 – #ifdef IS_MPI
248 –    DataStorage atomIData;
249 –    DataStorage atomJData;
250 –    DataStorage cgIData;
251 –    DataStorage cgJData;
252 – #endif
253 –  
254 –            
228    private:
229      RealType currentTime_;
230  
# Line 270 | Line 243 | namespace OpenMD{
243      int id_; /**< identification number of the snapshot */
244      bool hasCOM_;
245      bool hasVolume_;
246 <            
246 >    Mat3x3d tau_;
247    };
248  
249    typedef DataStorage (Snapshot::*DataStoragePointer);

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