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Comparing trunk/src/brains/Stats.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 51 | Line 51
51   #define BRAINS_STATS_HPP
52  
53   #include <string>
54 + #include <map>
55  
56   #include "math/SquareMatrix3.hpp"
57 < namespace oopse {
57 > namespace OpenMD {
58  
59    /**
60     * @class Stats Stats.hpp "brains/Stats.hpp"
# Line 69 | Line 70 | namespace oopse {
70        TEMPERATURE,
71        PRESSURE,
72        VOLUME,
73 +      HULLVOLUME,
74 +      GYRVOLUME,
75        CONSERVED_QUANTITY,            
76        TRANSLATIONAL_KINETIC,
77        ROTATIONAL_KINETIC,
# Line 79 | Line 82 | namespace oopse {
82        BOND_POTENTIAL,
83        BEND_POTENTIAL,
84        DIHEDRAL_POTENTIAL,
85 <      IMPROPER_POTENTIAL,
85 >      INVERSION_POTENTIAL,
86        VRAW,
87        VHARM,
88 +      PRESSURE_TENSOR_XX,
89 +      PRESSURE_TENSOR_XY,
90 +      PRESSURE_TENSOR_XZ,
91 +      PRESSURE_TENSOR_YX,
92 +      PRESSURE_TENSOR_YY,
93 +      PRESSURE_TENSOR_YZ,
94 +      PRESSURE_TENSOR_ZX,
95 +      PRESSURE_TENSOR_ZY,
96 +      PRESSURE_TENSOR_ZZ,
97 +      BOX_DIPOLE_X,
98 +      BOX_DIPOLE_Y,
99 +      BOX_DIPOLE_Z,
100 +      TAGGED_PAIR_DISTANCE,
101 +      RNEMD_EXCHANGE_TOTAL,
102        ENDINDEX  //internal use
103      };
104  
105      Stats();
106 <    const double& operator [](int index) const {
106 >    const RealType& operator [](int index) const {
107        assert(index >=0 && index < ENDINDEX);
108        return data_[index];
109      }
110  
111 <    double& operator [](int index){
111 >    RealType& operator [](int index){
112        assert(index >=0 && index < ENDINDEX);            
113        return data_[index];
114      }
# Line 113 | Line 130 | namespace oopse {
130      void setTau(const Mat3x3d& tau) {
131        tau_ = tau;
132      }
133 <        
133 >
134 >    typedef std::map<std::string, Stats::StatsIndex> StatsMapType;
135 >    static  StatsMapType statsMap;
136 >  
137    private:
138      static void init();
139      static bool isInit_;
140 <    double data_[ENDINDEX - BEGININDEX];
140 >    RealType data_[ENDINDEX - BEGININDEX];
141      static std::string title_[ENDINDEX - BEGININDEX];
142      static std::string units_[ENDINDEX - BEGININDEX];
143      Mat3x3d tau_;
144    };
145  
146 < } //end namespace oopse
146 >
147 >
148 > } //end namespace OpenMD
149   #endif //BRAINS_STATS_HPP

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