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Comparing trunk/src/applications/staticProps/RadialDistrFunc.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 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, 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_STATICPROPS_RADIALDISTRFUNC_HPP
43   #define APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
# Line 47 | Line 48
48   #include "selection/SelectionEvaluator.hpp"
49   #include "selection/SelectionManager.hpp"
50   #include "utils/NumericConstant.hpp"
51 < namespace oopse {
51 > #include "applications/staticProps/StaticAnalyser.hpp"
52  
53 + namespace OpenMD {
54 +
55    /**
56     * @class RadialDistrFunc
57     * @brief Radial Distribution Function
58     */
59 <  class RadialDistrFunc {
59 >  class RadialDistrFunc : public StaticAnalyser {
60    public:
61 <    RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);
61 >    RadialDistrFunc(SimInfo* info, const std::string& filename,
62 >                    const std::string& sele1, const std::string& sele2);
63  
64      virtual ~RadialDistrFunc() {}
65          
66      void process();        
67  
64 –    void setOutputName(const std::string& filename) {
65 –      outputFilename_ = filename;
66 –    }
68  
68 –    const std::string& getOutputFileName() const {
69 –      return outputFilename_;
70 –    }
71 –
72 –    void setStep(int step) {
73 –      assert(step > 0);
74 –      step_ =step;    
75 –    }
69          
70    protected:
71  
72      virtual void preProcess() {}
73      virtual void postProcess() {}
74 +    virtual void processNonOverlapping(SelectionManager& sman1,
75 +                                       SelectionManager& sman2);
76 +    virtual void processOverlapping(SelectionManager& sman);
77  
78      int getNPairs() { return nPairs_;}
79          
84 –    SimInfo* info_;
80      Snapshot* currentSnapshot_;
81  
87 –    std::string dumpFilename_;
88 –    std::string outputFilename_;
89 –    int step_;
82      std::string selectionScript1_;
83      std::string selectionScript2_;
84      int nProcessed_;
85 +    SelectionEvaluator evaluator1_;
86 +    SelectionEvaluator evaluator2_;
87 +
88      SelectionManager seleMan1_;
89      SelectionManager seleMan2_;
90 +    SelectionManager sele1_minus_common_;
91 +    SelectionManager sele2_minus_common_;
92 +    SelectionManager common_;        
93          
94    private:
95  
96 <    virtual void initalizeHistogram() {}
96 >    virtual void initializeHistogram() {}
97      virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2) =0;
98      virtual void processHistogram() {}
101 –    void processNonOverlapping(SelectionManager& sman1, SelectionManager& sman2);
102 –    void processOverlapping(SelectionManager& sman);
99  
100      virtual void validateSelection1(SelectionManager& sman) {}
101      virtual void validateSelection2(SelectionManager& sman) {}
102      virtual void writeRdf() = 0;
107 –
103          
109 –    SelectionEvaluator evaluator1_;
110 –    SelectionEvaluator evaluator2_;
111 –
112 –    SelectionManager sele1_minus_common_;
113 –    SelectionManager sele2_minus_common_;
114 –    SelectionManager common_;        
104      int nPairs_;
105    };
106  

Comparing trunk/src/applications/staticProps/RadialDistrFunc.hpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 UTC

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