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Comparing trunk/src/brains/Snapshot.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 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 56 | Line 56
56   #include "brains/Stats.hpp"
57   #include "UseTheForce/DarkSide/simulation_interface.h"
58  
59 – namespace oopse{
59  
60 + namespace OpenMD{
61 +
62    /**
63     * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
64     * @brief Snapshot class is a repository class for storing dynamic data during
# Line 68 | Line 69 | namespace oopse{
69    class Snapshot {
70    public:
71              
72 <    Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
73 <                                             currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
72 >    Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms),
73 >                                             rigidbodyData(nRigidbodies),
74 >                                             currentTime_(0),
75 >                                             orthoTolerance_(1e-6),
76 >                                             orthoRhombic_(0),
77 >                                             chi_(0.0),
78 >                                             integralOfChiDt_(0.0),
79 >                                             eta_(0.0), id_(-1),
80 >                                             hasCOM_(false), 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) {
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), hasVolume_(false),volume_(0.0)  {
89  
90        }
91              
# Line 111 | Line 121 | namespace oopse{
121      /** Sets the H-Matrix */
122      void setHmat(const Mat3x3d& m);
123              
124 <    double getVolume() {
125 <      return hmat_.determinant();
124 >    RealType getVolume() {
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 122 | Line 141 | namespace oopse{
141  
142      /** Wrapping the vector according to periodic boundary condition*/
143      void wrapVector(Vector3d& v);
144 <
144 >    Vector3d getCOM();
145 >    Vector3d getCOMvel();
146 >    Vector3d getCOMw();
147              
148 <    double getTime() {
148 >    RealType getTime() {
149        return currentTime_;
150      }
151  
152 <    void increaseTime(double dt) {
152 >    void increaseTime(RealType dt) {
153        setTime(getTime() + dt);
154      }
155  
156 <    void setTime(double time) {
156 >    void setTime(RealType time) {
157        currentTime_ =time;
158        //time at statData is redundant
159        statData[Stats::TIME] = currentTime_;
160      }
161  
162 <    double getChi() {
162 >    RealType getChi() {
163        return chi_;
164      }
165  
166 <    void setChi(double chi) {
166 >    void setChi(RealType chi) {
167        chi_ = chi;
168      }
169  
170 <    double getIntegralOfChiDt() {
170 >    RealType getIntegralOfChiDt() {
171        return integralOfChiDt_;
172      }
173  
174 <    void setIntegralOfChiDt(double integralOfChiDt) {
174 >    void setIntegralOfChiDt(RealType integralOfChiDt) {
175        integralOfChiDt_ = integralOfChiDt;
176      }
177              
178 +
179 +    void setOrthoTolerance(RealType orthoTolerance) {
180 +      orthoTolerance_ = orthoTolerance;
181 +    }
182 +
183      Mat3x3d getEta() {
184        return eta_;
185      }
# Line 161 | Line 187 | namespace oopse{
187      void setEta(const Mat3x3d& eta) {
188        eta_ = eta;
189      }
190 <            
190 >
191 >    bool hasCOM() {
192 >      return hasCOM_;
193 >    }
194 >
195 >    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
196 >      COM_ = COM;
197 >      COMvel_ = COMvel;
198 >      COMw_ = COMw;
199 >      hasCOM_ = true;
200 >    }
201 >                  
202      DataStorage atomData;
203      DataStorage rigidbodyData;
204      Stats statData;
205              
206    private:
207 <    double currentTime_;
207 >    RealType currentTime_;
208  
209      Mat3x3d hmat_;
210      Mat3x3d invHmat_;
211 +    RealType orthoTolerance_;
212      int orthoRhombic_;
213 +    RealType volume_;
214  
215 <    double chi_;
216 <    double integralOfChiDt_;
215 >    RealType chi_;
216 >    RealType integralOfChiDt_;
217      Mat3x3d eta_;
218 <            
218 >    Vector3d COM_;
219 >    Vector3d COMvel_;
220 >    Vector3d COMw_;
221      int id_; /**< identification number of the snapshot */
222 +    bool hasCOM_;
223 +    bool hasVolume_;
224 +            
225    };
226  
227    typedef DataStorage (Snapshot::*DataStoragePointer);

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