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Comparing trunk/src/integrators/RNEMD.hpp (file contents):
Revision 1331 by gezelter, Thu Apr 2 16:04:52 2009 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 53 | Line 53
53   #include "math/RandNumGen.hpp"
54   #include "selection/SelectionEvaluator.hpp"
55   #include "selection/SelectionManager.hpp"
56 + #include <iostream>
57  
58 < namespace oopse {
58 > namespace OpenMD {
59  
60    /**
61     * @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
# Line 64 | Line 65 | namespace oopse {
65    public:
66      RNEMD(SimInfo* info);
67      virtual ~RNEMD();
68 <        
68 >    
69 >    void doRNEMD();
70      void doSwap();
71 <    void set_RNEMD_swapTime(RealType swapTime) { swapTime_ = swapTime; }
71 >    void doScale();
72 >    void collectData();
73 >    void getStarted();
74 >    void getStatus();
75 >    void set_RNEMD_exchange_time(RealType exchangeTime) {
76 >      exchangeTime_ = exchangeTime;
77 >    }
78      void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
79      RealType get_RNEMD_exchange_total() { return exchangeSum_; }
80 <    void set_RNEMD_exchange_total(RealType et) {exchangeSum_ = et;}
80 >    void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
81 >    void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
82  
83    private:
84  
85      enum RNEMDTypeEnum {
86 <      rnemdKinetic,
86 >      rnemdKineticSwap,
87 >      rnemdKineticScale,
88 >      rnemdPxScale,
89 >      rnemdPyScale,
90 >      rnemdPzScale,
91        rnemdPx,
92        rnemdPy,
93        rnemdPz,
94        rnemdUnknown
95      };
96 <    
96 >    
97      SimInfo* info_;
98      RandNumGen* randNumGen_;
86 –    int nBins_;  
87 –    RealType swapTime_;
88 –    RealType exchangeSum_;
89 –    RNEMDTypeEnum rnemdType_;
99      std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
100 +    RNEMDTypeEnum rnemdType_;
101      std::string rnemdObjectSelection_;
92 –    SelectionManager seleMan_;
102      SelectionEvaluator evaluator_;
103 +    SelectionManager seleMan_;
104      bool usePeriodicBoundaryConditions_;
105 <
105 >    int nBins_;
106 >    int midBin_;
107 >    int rnemdLogWidth_;
108 >    RealType exchangeTime_;
109 >    RealType targetFlux_;
110 >    RealType exchangeSum_;
111 >    int failTrialCount_;
112 >    int failRootCount_;
113 >    std::ofstream rnemdLog_;
114 >    // keeps track of what's being averaged
115 >    std::vector<RealType> valueHist_;
116 >    std::vector<int> valueCount_;
117 >    // keeps track of the number of degrees of freedom being averaged
118 >    std::vector<RealType> xTempHist_, yTempHist_, zTempHist_;
119 >    std::ofstream xTempLog_, yTempLog_, zTempLog_;
120    };
121  
122   }
123 < #endif //INTEGRATORS_VELOCITIZER_HPP
123 > #endif //INTEGRATORS_RNEMD_HPP

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