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root/OpenMD/trunk/src/applications/staticProps/RadialDistrFunc.hpp
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Comparing trunk/src/applications/staticProps/RadialDistrFunc.hpp (file contents):
Revision 347 by tim, Tue Feb 15 17:11:35 2005 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   #ifndef APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
42   #define APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
# Line 47 | Line 47
47   #include "selection/SelectionEvaluator.hpp"
48   #include "selection/SelectionManager.hpp"
49   #include "utils/NumericConstant.hpp"
50 < namespace oopse {
50 > #include "applications/staticProps/StaticAnalyser.hpp"
51  
52 < /**
53 < * @class RadialDistrFunc
54 < * @brief Radial Distribution Function
55 < */
56 < class RadialDistrFunc {
57 <    public:
58 <        RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);
52 > namespace OpenMD {
53  
54 <        virtual ~RadialDistrFunc() {}
54 >  /**
55 >   * @class RadialDistrFunc
56 >   * @brief Radial Distribution Function
57 >   */
58 >  class RadialDistrFunc : public StaticAnalyser {
59 >  public:
60 >    RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);
61 >
62 >    virtual ~RadialDistrFunc() {}
63          
64 <        void process();        
64 >    void process();        
65  
64 –        void setOutputName(const std::string& filename) {
65 –            outputFilename_ = filename;
66 –        }
66  
68 –        const std::string& getOutputFileName() const {
69 –            return outputFilename_;
70 –        }
71 –
72 –        void setStep(int step) {
73 –            assert(step > 0);
74 –            step_ =step;    
75 –        }
67          
68 <    protected:
68 >  protected:
69  
70 <        virtual void preProcess() {}
71 <        virtual void postProcess() {}
70 >    virtual void preProcess() {}
71 >    virtual void postProcess() {}
72  
73 <        int getNRealPairs() { return nRealPairs_; }
73 >    int getNPairs() { return nPairs_;}
74          
75 <        SimInfo* info_;
85 <        Snapshot* currentSnapshot_;
75 >    Snapshot* currentSnapshot_;
76  
77 <        std::string dumpFilename_;
78 <        std::string outputFilename_;
79 <        int step_;
80 <        std::string selectionScript1_;
81 <        std::string selectionScript2_;
92 <        int nProcessed_;
77 >    std::string selectionScript1_;
78 >    std::string selectionScript2_;
79 >    int nProcessed_;
80 >    SelectionManager seleMan1_;
81 >    SelectionManager seleMan2_;
82          
83 <    private:
83 >  private:
84  
85 <        virtual void initalizeHistogram() {}
86 <        virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2) =0;
87 <        virtual void processHistogram() = 0;
85 >    virtual void initalizeHistogram() {}
86 >    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2) =0;
87 >    virtual void processHistogram() {}
88 >    void processNonOverlapping(SelectionManager& sman1, SelectionManager& sman2);
89 >    void processOverlapping(SelectionManager& sman);
90  
91 <        virtual void writeRdf() = 0;
91 >    virtual void validateSelection1(SelectionManager& sman) {}
92 >    virtual void validateSelection2(SelectionManager& sman) {}
93 >    virtual void writeRdf() = 0;
94  
95          
96 <        SelectionEvaluator evaluator1_;
97 <        SelectionEvaluator evaluator2_;
105 <        SelectionManager seleMan1_;
106 <        SelectionManager seleMan2_;
107 <        int nRealPairs_;
108 < };
96 >    SelectionEvaluator evaluator1_;
97 >    SelectionEvaluator evaluator2_;
98  
99 +    SelectionManager sele1_minus_common_;
100 +    SelectionManager sele2_minus_common_;
101 +    SelectionManager common_;        
102 +    int nPairs_;
103 +  };
104  
105 +
106   }
107   #endif

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