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Revision 246 by gezelter, Wed Jan 12 22:41:40 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.
1 > /*
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 < /**
43 <  * @file Stats.hpp
44 <  * @author tlin
45 <  * @date 11/04/2004
46 <  * @time 23:56am
47 <  * @version 1.0
48 <  */
42 > /**
43 > * @file Stats.hpp
44 > * @author tlin
45 > * @date 11/04/2004
46 > * @time 23:56am
47 > * @version 1.0
48 > */
49  
50   #ifndef BRAINS_STATS_HPP
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"
61 < */
62 < class Stats{
63 <    public:
64 <        enum StatsIndex {
65 <            BEGININDEX = 0,  //internal use
66 <            TIME = BEGININDEX,            
67 <            TOTAL_ENERGY,
68 <            POTENTIAL_ENERGY,
69 <            KINETIC_ENERGY,
70 <            TEMPERATURE,
71 <            PRESSURE,
72 <            VOLUME,
73 <            CONSERVED_QUANTITY,            
74 <            TRANSLATIONAL_KINETIC,
75 <            ROTATIONAL_KINETIC,
76 <            LONG_RANGE_POTENTIAL,  
77 <            SHORT_RANGE_POTENTIAL,
78 <            VANDERWAALS_POTENTIAL,
79 <            ELECTROSTATIC_POTENTIAL,
80 <            BOND_POTENTIAL,
81 <            BEND_POTENTIAL,
82 <            DIHEDRAL_POTENTIAL,
83 <            IMPROPER_POTENTIAL,
84 <            VRAW,
85 <            VHARM,
86 <            ENDINDEX  //internal use
87 <        };
59 >  /**
60 >   * @class Stats Stats.hpp "brains/Stats.hpp"
61 >   */
62 >  class Stats{
63 >  public:
64 >    enum StatsIndex {
65 >      BEGININDEX = 0,  //internal use
66 >      TIME = BEGININDEX,            
67 >      TOTAL_ENERGY,
68 >      POTENTIAL_ENERGY,
69 >      KINETIC_ENERGY,
70 >      TEMPERATURE,
71 >      PRESSURE,
72 >      VOLUME,
73 >      HULLVOLUME,
74 >      GYRVOLUME,
75 >      CONSERVED_QUANTITY,            
76 >      TRANSLATIONAL_KINETIC,
77 >      ROTATIONAL_KINETIC,
78 >      LONG_RANGE_POTENTIAL,  
79 >      SHORT_RANGE_POTENTIAL,
80 >      VANDERWAALS_POTENTIAL,
81 >      ELECTROSTATIC_POTENTIAL,
82 >      BOND_POTENTIAL,
83 >      BEND_POTENTIAL,
84 >      DIHEDRAL_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 >      SHADOWH,
103 >      ENDINDEX  //internal use
104 >    };
105  
106 <        Stats();
107 <        const double& operator [](int index) const {
108 <            assert(index >=0 && index < ENDINDEX);
109 <            return data_[index];
110 <        }
106 >    Stats();
107 >    const RealType& operator [](int index) const {
108 >      assert(index >=0 && index < ENDINDEX);
109 >      return data_[index];
110 >    }
111  
112 <        double& operator [](int index){
113 <            assert(index >=0 && index < ENDINDEX);            
114 <            return data_[index];
115 <        }
112 >    RealType& operator [](int index){
113 >      assert(index >=0 && index < ENDINDEX);            
114 >      return data_[index];
115 >    }
116          
117 <        static std::string getTitle(int index) {
118 <            assert(index >=0 && index < ENDINDEX);
119 <            return title_[index];
120 <        }
117 >    static std::string getTitle(int index) {
118 >      assert(index >=0 && index < ENDINDEX);
119 >      return title_[index];
120 >    }
121  
122 <        static std::string getUnits(int index) {
123 <            assert(index >=0 && index < ENDINDEX);
124 <            return units_[index];
125 <        }
122 >    static std::string getUnits(int index) {
123 >      assert(index >=0 && index < ENDINDEX);
124 >      return units_[index];
125 >    }
126  
127 <        Mat3x3d getTau() {
128 <            return tau_;
129 <        }
127 >    Mat3x3d getTau() {
128 >      return tau_;
129 >    }
130          
131 <        void setTau(const Mat3x3d& tau) {
132 <            tau_ = tau;
133 <        }
116 <        
117 <    private:
118 <        static void init();
119 <        static bool isInit_;
120 <        double data_[ENDINDEX - BEGININDEX];
121 <        static std::string title_[ENDINDEX - BEGININDEX];
122 <        static std::string units_[ENDINDEX - BEGININDEX];
123 <        Mat3x3d tau_;
124 < };
131 >    void setTau(const Mat3x3d& tau) {
132 >      tau_ = tau;
133 >    }
134  
135 < } //end namespace oopse
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 >    RealType data_[ENDINDEX - BEGININDEX];
142 >    static std::string title_[ENDINDEX - BEGININDEX];
143 >    static std::string units_[ENDINDEX - BEGININDEX];
144 >    Mat3x3d tau_;
145 >  };
146 >
147 >
148 >
149 > } //end namespace OpenMD
150   #endif //BRAINS_STATS_HPP

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