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Comparing trunk/src/brains/Stats.hpp (file contents):
Revision 541 by tim, Sun May 22 21:05:15 2005 UTC vs.
Revision 1402 by chuckv, Fri Jan 8 17:15:27 2010 UTC

# Line 1 | Line 1
1   /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2 > * Copyright (c) 2005, 2009 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
5   * non-exclusive, royalty free, license to use, modify and
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_X,
89 <      PRESSURE_TENSOR_Y,
90 <      PRESSURE_TENSOR_Z,      
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 >      SHADOWH,
103        ENDINDEX  //internal use
104      };
105  
106      Stats();
107 <    const double& operator [](int index) const {
107 >    const RealType& operator [](int index) const {
108        assert(index >=0 && index < ENDINDEX);
109        return data_[index];
110      }
111  
112 <    double& operator [](int index){
112 >    RealType& operator [](int index){
113        assert(index >=0 && index < ENDINDEX);            
114        return data_[index];
115      }
# Line 116 | Line 131 | namespace oopse {
131      void setTau(const Mat3x3d& tau) {
132        tau_ = tau;
133      }
134 <        
134 >
135 >    typedef std::map<std::string, Stats::StatsIndex> StatsMapType;
136 >    static  StatsMapType statsMap;
137 >  
138    private:
139      static void init();
140      static bool isInit_;
141 <    double data_[ENDINDEX - BEGININDEX];
141 >    RealType data_[ENDINDEX - BEGININDEX];
142      static std::string title_[ENDINDEX - BEGININDEX];
143      static std::string units_[ENDINDEX - BEGININDEX];
144      Mat3x3d tau_;
145    };
146  
147 < } //end namespace oopse
147 >
148 >
149 > } //end namespace OpenMD
150   #endif //BRAINS_STATS_HPP

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