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Comparing trunk/src/brains/Stats.cpp (file contents):
Revision 1341 by skuang, Fri May 8 19:47:05 2009 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 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 88 | Line 88 | namespace oopse {
88      Stats::title_[INVERSION_POTENTIAL] = "Inversion Potential";
89      Stats::title_[VRAW] = "Raw Potential";
90      Stats::title_[VHARM] = "Harmonic Potential";
91 +    Stats::title_[SHADOWH] = "Shadow Hamiltonian";
92      Stats::title_[PRESSURE_TENSOR_XX] = "P_xx";
93      Stats::title_[PRESSURE_TENSOR_XY] = "P_xy";
94      Stats::title_[PRESSURE_TENSOR_XZ] = "P_xz";
# Line 101 | Line 102 | namespace oopse {
102      Stats::title_[BOX_DIPOLE_Y] = "box dipole y";
103      Stats::title_[BOX_DIPOLE_Z] = "box dipole z";
104      Stats::title_[TAGGED_PAIR_DISTANCE] = "Tagged_Pair_Distance";
105 <    Stats::title_[RNEMD_SWAP_TOTAL] = "RNEMD_exchange_total";
105 >    Stats::title_[RNEMD_EXCHANGE_TOTAL] = "RNEMD_exchange_total";
106      
107      Stats::units_[TIME] = "fs";
108      Stats::units_[TOTAL_ENERGY] = "kcal/mol";
# Line 125 | Line 126 | namespace oopse {
126      Stats::units_[INVERSION_POTENTIAL] = "kcal/mol";
127      Stats::units_[VRAW] = "kcal/mol";
128      Stats::units_[VHARM] = "kcal/mol";
129 +    Stats::units_[SHADOWH] = "kcal/mol";
130      Stats::units_[PRESSURE_TENSOR_XX] = "amu*fs^-2*Ang^-1";
131      Stats::units_[PRESSURE_TENSOR_XY] = "amu*fs^-2*Ang^-1";
132      Stats::units_[PRESSURE_TENSOR_XZ] = "amu*fs^-2*Ang^-1";
# Line 138 | Line 140 | namespace oopse {
140      Stats::units_[BOX_DIPOLE_Y] = "C*m";
141      Stats::units_[BOX_DIPOLE_Z] = "C*m";
142      Stats::units_[TAGGED_PAIR_DISTANCE] = "Ang";
143 <    Stats::units_[RNEMD_SWAP_TOTAL] = "Variable";
143 >    Stats::units_[RNEMD_EXCHANGE_TOTAL] = "Variable";
144  
145      Stats::statsMap.insert(StatsMapType::value_type("TIME", TIME));
146      Stats::statsMap.insert(StatsMapType::value_type("TOTAL_ENERGY", TOTAL_ENERGY));
# Line 175 | Line 177 | namespace oopse {
177      Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Y", BOX_DIPOLE_Y));    
178      Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Z", BOX_DIPOLE_Z));    
179      Stats::statsMap.insert(StatsMapType::value_type("TAGGED_PAIR_DISTANCE", TAGGED_PAIR_DISTANCE));    
180 <    Stats::statsMap.insert(StatsMapType::value_type("RNEMD_SWAP_TOTAL", RNEMD_SWAP_TOTAL));    
180 >    Stats::statsMap.insert(StatsMapType::value_type("RNEMD_EXCHANGE_TOTAL", RNEMD_EXCHANGE_TOTAL));    
181 >    Stats::statsMap.insert(StatsMapType::value_type("SHADOWH", SHADOWH));    
182    }
183  
184   }

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