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Comparing trunk/src/applications/staticProps/GofRAngle.hpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 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_GOFRANGLE_HPP
43   #define APPLICATIONS_STATICPROPS_GOFRANGLE_HPP
44  
45   #include "applications/staticProps/RadialDistrFunc.hpp"
46 < namespace oopse {
46 > namespace OpenMD {
47  
48    class GofRAngle : public RadialDistrFunc {
49      
50    public:
51 <    GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins);
51 >    GofRAngle(SimInfo* info, const std::string& filename,
52 >              const std::string& sele1, const std::string& sele2,
53 >              RealType len, int nrbins, int nangleBins);
54 >    GofRAngle(SimInfo* info, const std::string& filename,
55 >              const std::string& sele1, const std::string& sele2,
56 >              const std::string& sele3,
57 >              RealType len, int nrbins, int nangleBins);
58  
59      int getNRBins() {
60        return nRBins_;
# Line 62 | Line 69 | namespace oopse {
69    private:
70  
71      virtual void preProcess();
72 <    virtual void initalizeHistogram();
73 <    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
74 <    virtual void processHistogram();
72 >    virtual void processNonOverlapping( SelectionManager& sman1,
73 >                                        SelectionManager& sman2);
74 >    virtual void processOverlapping( SelectionManager& sman );
75  
76 +    virtual void initializeHistogram();
77 +    virtual void processHistogram();
78 +    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
79 +    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2,
80 +                                  StuntDouble* sd3);
81      virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
82 <
82 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
83 >                                   StuntDouble* sd3) = 0;
84      virtual void writeRdf();
85  
86 +
87      RealType deltaCosAngle_;
88      int nAngleBins_;
89      RealType len_;
90      int nRBins_;
91      RealType deltaR_;
92 +
93 +    bool doSele3_;
94 +    std::string selectionScript3_;
95 +    SelectionManager seleMan3_;
96 +    SelectionEvaluator evaluator3_;
97          
98      std::vector<std::vector<int> > histogram_;
99      std::vector<std::vector<RealType> > avgGofr_;
# Line 84 | Line 103 | namespace oopse {
103  
104    class GofRTheta : public GofRAngle {
105    public:
106 <    GofRTheta(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins)
106 >    GofRTheta(SimInfo* info, const std::string& filename,
107 >              const std::string& sele1, const std::string& sele2,
108 >              RealType len, int nrbins, int nangleBins)
109        : GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
110          setOutputName(getPrefix(filename) + ".gofrt");
111        }
112 +    GofRTheta(SimInfo* info, const std::string& filename,
113 +              const std::string& sele1, const std::string& sele2,
114 +              const std::string& sele3,
115 +              RealType len, int nrbins, int nangleBins)
116 +      : GofRAngle (info, filename, sele1, sele2, sele3, len, nrbins,
117 +                   nangleBins) {
118 +        setOutputName(getPrefix(filename) + ".gofrt");
119 +      }
120          
121    private:
122  
123      virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
124 +    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
125 +                                   StuntDouble* sd3);        
126    };
127  
128  
129    class GofROmega : public GofRAngle {
130    public:
131 <    GofROmega(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins)
131 >    GofROmega(SimInfo* info, const std::string& filename,
132 >              const std::string& sele1, const std::string& sele2,
133 >              RealType len, int nrbins, int nangleBins)
134        : GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
135          setOutputName(getPrefix(filename) + ".gofro");
136        }
137 +    GofROmega(SimInfo* info, const std::string& filename,
138 +              const std::string& sele1, const std::string& sele2,
139 +              const std::string& sele3,
140 +              RealType len, int nrbins, int nangleBins)
141 +      : GofRAngle (info, filename, sele1, sele2, sele3, len, nrbins,
142 +                   nangleBins) {
143 +        setOutputName(getPrefix(filename) + ".gofro");
144 +      }
145      
146    private:
147 <    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
147 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);    
148 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
149 >                                   StuntDouble* sd3);        
150 >  
151    };
152  
153   }

Comparing trunk/src/applications/staticProps/GofRAngle.hpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 UTC

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