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Comparing trunk/src/integrators/RNEMD.hpp (file contents):
Revision 1368 by skuang, Mon Oct 19 13:39:04 2009 UTC vs.
Revision 1561 by gezelter, Wed May 11 19:04:40 2011 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 55 | Line 55
55   #include "selection/SelectionManager.hpp"
56   #include <iostream>
57  
58 < namespace oopse {
58 > using namespace std;
59 > namespace OpenMD {
60  
61    /**
62     * @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
# Line 76 | Line 77 | namespace oopse {
77        exchangeTime_ = exchangeTime;
78      }
79      void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
80 <    RealType get_RNEMD_exchange_total() { return exchangeSum_; }
80 >    void set_RNEMD_logWidth(int logWidth) { rnemdLogWidth_ = logWidth; }
81      void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
82      void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
83 +    RealType get_RNEMD_exchange_total() { return exchangeSum_; }
84  
85    private:
86  
# Line 96 | Line 98 | namespace oopse {
98      
99      SimInfo* info_;
100      RandNumGen* randNumGen_;
101 <    std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
101 >    map<string, RNEMDTypeEnum> stringToEnumMap_;
102      RNEMDTypeEnum rnemdType_;
103 <    std::string rnemdObjectSelection_;
103 >    string rnemdObjectSelection_;
104      SelectionEvaluator evaluator_;
105      SelectionManager seleMan_;
106      bool usePeriodicBoundaryConditions_;
107 +    bool output3DTemp_;
108      int nBins_;
109      int midBin_;
110      int rnemdLogWidth_;
111 +    RealType zShift_;
112      RealType exchangeTime_;
113      RealType targetFlux_;
114      RealType exchangeSum_;
115      int failTrialCount_;
116      int failRootCount_;
117 <    std::ofstream rnemdLog_;
117 >    ofstream rnemdLog_;
118      // keeps track of what's being averaged
119 <    std::vector<RealType> valueHist_;
120 <    std::vector<int> valueCount_;
119 >    vector<RealType> valueHist_;
120 >    vector<int> valueCount_, xyzTempCount_;
121      // keeps track of the number of degrees of freedom being averaged
122 <    std::vector<RealType> xTempHist_, yTempHist_, zTempHist_;
123 <    std::ofstream xTempLog_, yTempLog_, zTempLog_;
122 >    vector<RealType> xTempHist_, yTempHist_, zTempHist_;
123 >    ofstream xTempLog_, yTempLog_, zTempLog_;
124    };
125  
126   }

Comparing trunk/src/integrators/RNEMD.hpp (property svn:keywords):
Revision 1368 by skuang, Mon Oct 19 13:39:04 2009 UTC vs.
Revision 1561 by gezelter, Wed May 11 19:04:40 2011 UTC

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