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Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 1104 by gezelter, Fri Dec 29 21:43:18 2006 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1709 by gezelter, Tue May 15 13:04:08 2012 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]  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 < namespace oopse{
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), rigidbodyData(nRigidbodies),
72 <                                             currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
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), rigidbodyData(nRigidbodies, storageLayout),
87 <        currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
88 <
89 <      }
90 <            
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 103 | Line 117 | namespace oopse{
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 112 | Line 131 | namespace oopse{
131      void setHmat(const Mat3x3d& m);
132              
133      RealType getVolume() {
134 <      return hmat_.determinant();
134 >      if (hasVolume_){
135 >        return volume_;
136 >      }else{
137 >        return hmat_.determinant();
138 >      }
139      }
140  
141 +    void setVolume(RealType volume){
142 +      hasVolume_=true;
143 +      volume_ = volume;
144 +    }
145 +
146      /** Returns the inverse H-Matrix */
147      Mat3x3d getInvHmat() {
148        return invHmat_;
# Line 122 | Line 150 | namespace oopse{
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 169 | Line 201 | namespace oopse{
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 179 | Line 219 | namespace oopse{
219        COMw_ = COMw;
220        hasCOM_ = true;
221      }
222 <                  
222 >
223      DataStorage atomData;
224      DataStorage rigidbodyData;
225 +    DataStorage cgData;
226      Stats statData;
227 <            
227 >
228    private:
229      RealType currentTime_;
230  
# Line 191 | Line 232 | namespace oopse{
232      Mat3x3d invHmat_;
233      RealType orthoTolerance_;
234      int orthoRhombic_;
235 +    RealType volume_;
236  
237      RealType chi_;
238      RealType integralOfChiDt_;
# Line 198 | Line 240 | namespace oopse{
240      Vector3d COM_;
241      Vector3d COMvel_;
242      Vector3d COMw_;
201 –    bool hasCOM_;
202 –            
243      int id_; /**< identification number of the snapshot */
244 +    bool hasCOM_;
245 +    bool hasVolume_;
246 +    Mat3x3d tau_;
247    };
248  
249    typedef DataStorage (Snapshot::*DataStoragePointer);

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 1104 by gezelter, Fri Dec 29 21:43:18 2006 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1709 by gezelter, Tue May 15 13:04:08 2012 UTC

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