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Comparing trunk/src/brains/Snapshot.hpp (file contents):
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
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).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41    
42   /**
# Line 57 | Line 57
57   #include "UseTheForce/DarkSide/simulation_interface.h"
58  
59  
60 < namespace oopse{
60 > namespace OpenMD{
61  
62    /**
63     * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
# Line 77 | Line 77 | namespace oopse{
77                                               chi_(0.0),
78                                               integralOfChiDt_(0.0),
79                                               eta_(0.0), id_(-1),
80 <                                             hasCOM_(false) {
80 >                                             hasCOM_(false), hasVolume_(false), volume_(0.0) {
81  
82      }
83  
# Line 85 | Line 85 | namespace oopse{
85        : atomData(nAtoms, storageLayout),
86          rigidbodyData(nRigidbodies, storageLayout),
87          currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0),
88 <        integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false)  {
88 >        integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false), hasVolume_(false),volume_(0.0)  {
89  
90        }
91              
# Line 122 | Line 122 | namespace oopse{
122      void setHmat(const Mat3x3d& m);
123              
124      RealType getVolume() {
125 <      return hmat_.determinant();
125 >      if (hasVolume_){
126 >        return volume_;
127 >      }else{
128 >        return hmat_.determinant();
129 >      }
130      }
131  
132 +    void setVolume(RealType volume){
133 +      hasVolume_=true;
134 +      volume_ = volume;
135 +    }
136 +
137      /** Returns the inverse H-Matrix */
138      Mat3x3d getInvHmat() {
139        return invHmat_;
# Line 201 | Line 210 | namespace oopse{
210      Mat3x3d invHmat_;
211      RealType orthoTolerance_;
212      int orthoRhombic_;
213 +    RealType volume_;
214  
215      RealType chi_;
216      RealType integralOfChiDt_;
# Line 208 | Line 218 | namespace oopse{
218      Vector3d COM_;
219      Vector3d COMvel_;
220      Vector3d COMw_;
221 +    int id_; /**< identification number of the snapshot */
222      bool hasCOM_;
223 +    bool hasVolume_;
224              
213 –    int id_; /**< identification number of the snapshot */
225    };
226  
227    typedef DataStorage (Snapshot::*DataStoragePointer);

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