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Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1551 by gezelter, Thu Apr 28 18:38:21 2011 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 54 | Line 54
54  
55   #include "brains/DataStorage.hpp"
56   #include "brains/Stats.hpp"
57 – #include "UseTheForce/DarkSide/simulation_interface.h"
57  
58 < namespace oopse{
58 > namespace OpenMD{
59  
60    /**
61     * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
62     * @brief Snapshot class is a repository class for storing dynamic data during
63     *  Simulation
64 <   * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
64 >   * Every snapshot class will contain one DataStorage for atoms and one DataStorage
65     *  for rigid bodies.
66     */
67    class Snapshot {
68    public:
69              
70 <    Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
71 <                                             currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
70 >    Snapshot(int nAtoms, int nRigidbodies,
71 >             int nCutoffGroups) : atomData(nAtoms),
72 >                                  rigidbodyData(nRigidbodies),
73 >                                  cgData(nCutoffGroups, DataStorage::dslPosition),
74 >                                  currentTime_(0),
75 >                                  orthoTolerance_(1e-6),
76 >                                  orthoRhombic_(0),
77 >                                  chi_(0.0),
78 >                                  integralOfChiDt_(0.0),
79 >                                  eta_(0.0), id_(-1), hasCOM_(false),
80 >                                  hasVolume_(false), volume_(0.0) {
81  
82      }
83  
84 <    Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
85 <      : atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
86 <        currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
87 <
88 <      }
89 <            
84 >    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
85 >             int storageLayout) : atomData(nAtoms, storageLayout),
86 >                                  rigidbodyData(nRigidbodies, storageLayout),
87 >                                  cgData(nCutoffGroups, DataStorage::dslPosition),
88 >                                  currentTime_(0), orthoTolerance_(1e-6),
89 >                                  orthoRhombic_(0), chi_(0.0),
90 >                                  integralOfChiDt_(0.0), eta_(0.0), id_(-1),
91 >                                  hasCOM_(false), hasVolume_(false),
92 >                                  volume_(0.0)  {
93 >    }
94 >    
95      /** Returns the id of this Snapshot */
96      int getID() {
97        return id_;
# Line 103 | Line 116 | namespace oopse{
116        return rigidbodyData.getSize();
117      }
118  
119 +    /** Returns the number of rigid bodies */
120 +    int getNumberOfCutoffGroups() {
121 +      return cgData.getSize();
122 +    }
123 +
124      /** Returns the H-Matrix */
125      Mat3x3d getHmat() {
126        return hmat_;
# Line 112 | Line 130 | namespace oopse{
130      void setHmat(const Mat3x3d& m);
131              
132      RealType getVolume() {
133 <      return hmat_.determinant();
133 >      if (hasVolume_){
134 >        return volume_;
135 >      }else{
136 >        return hmat_.determinant();
137 >      }
138      }
139  
140 +    void setVolume(RealType volume){
141 +      hasVolume_=true;
142 +      volume_ = volume;
143 +    }
144 +
145      /** Returns the inverse H-Matrix */
146      Mat3x3d getInvHmat() {
147        return invHmat_;
# Line 122 | Line 149 | namespace oopse{
149  
150      /** Wrapping the vector according to periodic boundary condition*/
151      void wrapVector(Vector3d& v);
152 <
152 >    Vector3d getCOM();
153 >    Vector3d getCOMvel();
154 >    Vector3d getCOMw();
155              
156      RealType getTime() {
157        return currentTime_;
# Line 154 | Line 183 | namespace oopse{
183        integralOfChiDt_ = integralOfChiDt;
184      }
185              
186 +
187 +    void setOrthoTolerance(RealType orthoTolerance) {
188 +      orthoTolerance_ = orthoTolerance;
189 +    }
190 +
191      Mat3x3d getEta() {
192        return eta_;
193      }
# Line 161 | Line 195 | namespace oopse{
195      void setEta(const Mat3x3d& eta) {
196        eta_ = eta;
197      }
198 <            
198 >
199 >    bool hasCOM() {
200 >      return hasCOM_;
201 >    }
202 >
203 >    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
204 >      COM_ = COM;
205 >      COMvel_ = COMvel;
206 >      COMw_ = COMw;
207 >      hasCOM_ = true;
208 >    }
209 >
210      DataStorage atomData;
211      DataStorage rigidbodyData;
212 +    DataStorage cgData;
213      Stats statData;
214 <            
214 >
215    private:
216      RealType currentTime_;
217  
218      Mat3x3d hmat_;
219      Mat3x3d invHmat_;
220 +    RealType orthoTolerance_;
221      int orthoRhombic_;
222 +    RealType volume_;
223  
224      RealType chi_;
225      RealType integralOfChiDt_;
226      Mat3x3d eta_;
227 <            
227 >    Vector3d COM_;
228 >    Vector3d COMvel_;
229 >    Vector3d COMw_;
230      int id_; /**< identification number of the snapshot */
231 +    bool hasCOM_;
232 +    bool hasVolume_;
233 +            
234    };
235  
236    typedef DataStorage (Snapshot::*DataStoragePointer);

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC

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