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root/OpenMD/trunk/src/applications/dynamicProps/MultipassCorrFunc.hpp
Revision: 2056
Committed: Fri Feb 20 15:12:07 2015 UTC (10 years, 6 months ago) by gezelter
File size: 4743 byte(s)
Log Message:
Fixes to HullFinder (and by extension to RNEMD) for getSurfaceArea() call.
Adding Multipass Correlation Function (unused right now).

File Contents

# User Rev Content
1 gezelter 2056 /*
2     * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3     *
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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, 234107 (2008).
39     * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40     * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41     */
42     #ifndef APPLICATIONS_DYNAMICPROPS_MULTIPASSCORRFUNC_HPP
43     #define APPLICATIONS_DYNAMICPROPS_MULTIPASSCORRFUNC_HPP
44    
45     #include <string>
46     #include <vector>
47    
48     #include "brains/SimInfo.hpp"
49     #include "io/DumpReader.hpp"
50     #include "primitives/StuntDouble.hpp"
51     #include "selection/SelectionEvaluator.hpp"
52     #include "selection/SelectionManager.hpp"
53    
54     namespace OpenMD {
55    
56     /**
57     * @class MultipassCorrFunc MultipassCorrFunc.hpp "applications/dynamicProps/MultipassCorrFunc"
58     * @brief Base class for Correlation function that reads the dump file to pre-process into more manageable data units
59     */
60    
61     class MultipassCorrFunc {
62     public:
63     MultipassCorrFunc(SimInfo* info, const std::string& filename,
64     const std::string& sele1, const std::string& sele2,
65     int storageLayout);
66    
67     virtual ~MultipassCorrFunc(){ }
68     void doCorrelate();
69    
70     void setOutputName(const std::string& filename) {
71     outputFilename_ = filename;
72     }
73    
74     const std::string& getOutputFileName() const {
75     return outputFilename_;
76     }
77    
78     const std::string& getCorrFuncType() const {
79     return corrFuncType_;
80     }
81    
82     void setCorrFuncType(const std::string& type) {
83     corrFuncType_ = type;
84     }
85    
86     void setExtraInfo(const std::string& extra) {
87     extra_ = extra;
88     }
89    
90     protected:
91    
92     virtual void preCorrelate();
93     virtual void correlation();
94     virtual void postCorrelate();
95     virtual void updateFrame(int frame);
96     virtual void computeProperty1(int frame, StuntDouble* sd, int index) = 0;
97     virtual void computeProperty2(int frame, StuntDouble* sd, int index) = 0;
98     virtual RealType calcCorrVal(int frame1, int frame2, int id1, int id2) = 0;
99    
100     int storageLayout_;
101    
102     RealType deltaTime_;
103     int nTimeBins_;
104     int nFrames_;
105     std::vector<RealType> histogram_;
106     std::vector<int> count_;
107     std::vector<RealType> times_;
108    
109     SimInfo* info_;
110     std::string dumpFilename_;
111     SelectionManager seleMan1_;
112     SelectionManager seleMan2_;
113    
114     private:
115     virtual void writeCorrelate();
116     virtual void validateSelection(const SelectionManager& seleMan) {}
117    
118     Snapshot* currentSnapshot_;
119    
120     std::string selectionScript1_;
121     std::string selectionScript2_;
122    
123     SelectionEvaluator evaluator1_;
124     SelectionEvaluator evaluator2_;
125    
126     std::string outputFilename_;
127    
128     std::string corrFuncType_;
129     std::string extra_;
130    
131     std::vector<std::vector<int> > sele1ToIndex_;
132     std::vector<std::vector<int> > sele2ToIndex_;
133    
134     };
135    
136     }
137     #endif

Properties

Name Value
svn:eol-style native
svn:executable *