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Comparing trunk/src/applications/staticProps/RadialDistrFunc.hpp (file contents):
Revision 306 by tim, Wed Feb 9 17:08:22 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
43  
44 + #include <string>
45   #include <vector>
46  
47   #include "selection/SelectionEvaluator.hpp"
48   #include "selection/SelectionManager.hpp"
49 < namespace oopse {
49 > #include "utils/NumericConstant.hpp"
50 > #include "applications/staticProps/StaticAnalyser.hpp"
51  
52 < /**
51 < * @class RadialDistrFunc
52 < * @brief Radial Distribution Function
53 < */
54 < class RadialDistrFunc {
55 <    public:
56 <        RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2. double len);
52 > namespace OpenMD {
53  
54 <        void process();        
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 <        void setNBins(int nbins) {
61 <            assert(nbins > 0);
62 <            nbins_ = nbins;
63 <            delta_ = len_ / nbins_;
64 <        }
65 <
66 <        int getNBins() {
67 <            return nbins_;
68 <        }
62 >    virtual ~RadialDistrFunc() {}
63          
64 <        void setOutputName(const std::string& filename) {
71 <            outputFilename_ = filename;
72 <        }
64 >    void process();        
65  
74 –        const std::string& getOutputFileName() const {
75 –            return outputFilename_;
76 –        }
66  
78 –        void setStep(int step) {
79 –            assert(step > 0);
80 –            step_ =step;    
81 –        }
67          
68 <    protected:
68 >  protected:
69  
70 <        virtual void preProcess() {}
71 <        virtual void postProcess() {}
70 >    virtual void preProcess() {}
71 >    virtual void postProcess() {}
72  
73 <        SimInfo* info_;
89 <        Snapshot* currentSnapshot_;
90 <        double len_;
91 <        int nbins_;
92 <        double delta_;
93 <        std::string dumpFilename_;
94 <        std::string outputFilename_;
95 <        int step_;
96 <        std::string selectionScript1_;
97 <        std::string selectionScript2_;
73 >    int getNPairs() { return nPairs_;}
74          
75 <    private:
75 >    Snapshot* currentSnapshot_;
76  
77 <        virtual void initalizeHistogram() {}
78 <        virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2) =0;
79 <        virtual void processHistogram() = 0;
77 >    std::string selectionScript1_;
78 >    std::string selectionScript2_;
79 >    int nProcessed_;
80 >    SelectionManager seleMan1_;
81 >    SelectionManager seleMan2_;
82 >        
83 >  private:
84  
85 <        virtual void writeRdf() = 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 validateSelection1(SelectionManager& sman) {}
92 +    virtual void validateSelection2(SelectionManager& sman) {}
93 +    virtual void writeRdf() = 0;
94 +
95          
96 <        SelectionEvaluator evaluator1_;
97 <        SelectionEvaluator evaluator2_;
110 <        SelectionManager seleMan1_;
111 <        SelectionManager seleMan2_;
112 <        
113 < };
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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