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Comparing trunk/src/brains/Stats.cpp (file contents):
Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 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 49 | Line 49
49  
50   #include "brains/Stats.hpp"
51  
52 < namespace oopse {
52 > namespace OpenMD {
53  
54    bool Stats::isInit_ = false;
55    std::string Stats::title_[Stats::ENDINDEX - Stats::BEGININDEX];
# Line 73 | Line 73 | namespace oopse {
73      Stats::title_[TEMPERATURE] = "Temperature";
74      Stats::title_[PRESSURE] = "Pressure";
75      Stats::title_[VOLUME] = "Volume";
76 +    Stats::title_[HULLVOLUME] = "Hull Volume";
77 +    Stats::title_[GYRVOLUME] = "Gyrational Volume";
78      Stats::title_[CONSERVED_QUANTITY] = "Conserved Quantity";            
79      Stats::title_[TRANSLATIONAL_KINETIC] = "Translational Kinetic";
80      Stats::title_[ROTATIONAL_KINETIC] = "Rotational Kinetic";
# Line 83 | Line 85 | namespace oopse {
85      Stats::title_[BOND_POTENTIAL] = "Bond Potential";
86      Stats::title_[BEND_POTENTIAL] = "Bend Potential";
87      Stats::title_[DIHEDRAL_POTENTIAL] = "Dihedral Potential";
88 <    Stats::title_[IMPROPER_POTENTIAL] = "Improper Potential";
88 >    Stats::title_[INVERSION_POTENTIAL] = "Inversion Potential";
89      Stats::title_[VRAW] = "Raw Potential";
90      Stats::title_[VHARM] = "Harmonic Potential";
91      Stats::title_[PRESSURE_TENSOR_XX] = "P_xx";
# Line 98 | Line 100 | namespace oopse {
100      Stats::title_[BOX_DIPOLE_X] = "box dipole x";
101      Stats::title_[BOX_DIPOLE_Y] = "box dipole y";
102      Stats::title_[BOX_DIPOLE_Z] = "box dipole z";
103 <
103 >    Stats::title_[TAGGED_PAIR_DISTANCE] = "Tagged_Pair_Distance";
104 >    Stats::title_[RNEMD_EXCHANGE_TOTAL] = "RNEMD_exchange_total";
105 >    
106      Stats::units_[TIME] = "fs";
107      Stats::units_[TOTAL_ENERGY] = "kcal/mol";
108      Stats::units_[POTENTIAL_ENERGY] = "kcal/mol";
# Line 106 | Line 110 | namespace oopse {
110      Stats::units_[TEMPERATURE] = "K";
111      Stats::units_[PRESSURE] = "atm";
112      Stats::units_[VOLUME] = "A^3";
113 +    Stats::units_[HULLVOLUME] = "A^3";
114 +    Stats::units_[GYRVOLUME] = "A^3";
115      Stats::units_[CONSERVED_QUANTITY] = "kcal/mol";            
116      Stats::units_[TRANSLATIONAL_KINETIC] = "kcal/mol";
117      Stats::units_[ROTATIONAL_KINETIC] = "kcal/mol";
# Line 116 | Line 122 | namespace oopse {
122      Stats::units_[BOND_POTENTIAL] = "kcal/mol";
123      Stats::units_[BEND_POTENTIAL] = "kcal/mol";
124      Stats::units_[DIHEDRAL_POTENTIAL] = "kcal/mol";
125 <    Stats::units_[IMPROPER_POTENTIAL] = "kcal/mol";
125 >    Stats::units_[INVERSION_POTENTIAL] = "kcal/mol";
126      Stats::units_[VRAW] = "kcal/mol";
127      Stats::units_[VHARM] = "kcal/mol";
128      Stats::units_[PRESSURE_TENSOR_XX] = "amu*fs^-2*Ang^-1";
# Line 131 | Line 137 | namespace oopse {
137      Stats::units_[BOX_DIPOLE_X] = "C*m";
138      Stats::units_[BOX_DIPOLE_Y] = "C*m";
139      Stats::units_[BOX_DIPOLE_Z] = "C*m";
140 +    Stats::units_[TAGGED_PAIR_DISTANCE] = "Ang";
141 +    Stats::units_[RNEMD_EXCHANGE_TOTAL] = "Variable";
142  
143      Stats::statsMap.insert(StatsMapType::value_type("TIME", TIME));
144      Stats::statsMap.insert(StatsMapType::value_type("TOTAL_ENERGY", TOTAL_ENERGY));
# Line 139 | Line 147 | namespace oopse {
147      Stats::statsMap.insert(StatsMapType::value_type("TEMPERATURE", TEMPERATURE));
148      Stats::statsMap.insert(StatsMapType::value_type("PRESSURE", PRESSURE));
149      Stats::statsMap.insert(StatsMapType::value_type("VOLUME", VOLUME));
150 +    Stats::statsMap.insert(StatsMapType::value_type("HULLVOLUME", HULLVOLUME));
151 +    Stats::statsMap.insert(StatsMapType::value_type("GYRVOLUME", GYRVOLUME));
152      Stats::statsMap.insert(StatsMapType::value_type("CONSERVED_QUANTITY", CONSERVED_QUANTITY));
153      Stats::statsMap.insert(StatsMapType::value_type("TRANSLATIONAL_KINETIC", TRANSLATIONAL_KINETIC));
154      Stats::statsMap.insert(StatsMapType::value_type("ROTATIONAL_KINETIC", ROTATIONAL_KINETIC));
# Line 149 | Line 159 | namespace oopse {
159      Stats::statsMap.insert(StatsMapType::value_type("BOND_POTENTIAL", BOND_POTENTIAL));
160      Stats::statsMap.insert(StatsMapType::value_type("BEND_POTENTIAL", BEND_POTENTIAL));
161      Stats::statsMap.insert(StatsMapType::value_type("DIHEDRAL_POTENTIAL", DIHEDRAL_POTENTIAL));
162 <    Stats::statsMap.insert(StatsMapType::value_type("IMPROPER_POTENTIAL", IMPROPER_POTENTIAL));
162 >    Stats::statsMap.insert(StatsMapType::value_type("INVERSION_POTENTIAL", INVERSION_POTENTIAL));
163      Stats::statsMap.insert(StatsMapType::value_type("VRAW", VRAW));    
164      Stats::statsMap.insert(StatsMapType::value_type("VHARM", VHARM));    
165      Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XX", PRESSURE_TENSOR_XX));    
# Line 164 | Line 174 | namespace oopse {
174      Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_X", BOX_DIPOLE_X));    
175      Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Y", BOX_DIPOLE_Y));    
176      Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Z", BOX_DIPOLE_Z));    
177 +    Stats::statsMap.insert(StatsMapType::value_type("TAGGED_PAIR_DISTANCE", TAGGED_PAIR_DISTANCE));    
178 +    Stats::statsMap.insert(StatsMapType::value_type("RNEMD_EXCHANGE_TOTAL", RNEMD_EXCHANGE_TOTAL));    
179    }
180  
181   }

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