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Comparing trunk/src/applications/staticProps/GofRAngle.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 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_GOFRANGLE_HPP
42   #define APPLICATIONS_STATICPROPS_GOFRANGLE_HPP
43  
44   #include "applications/staticProps/RadialDistrFunc.hpp"
45 < namespace oopse {
45 > namespace OpenMD {
46  
47    class GofRAngle : public RadialDistrFunc {
48      
49    public:
50 <    GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins, int nangleBins);
50 >    GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins);
51  
52      int getNRBins() {
53        return nRBins_;
54      }
55  
56 <    double getLength() {
56 >    RealType getLength() {
57        return len_;
58      }
59  
# Line 63 | Line 63 | namespace oopse {
63  
64      virtual void preProcess();
65      virtual void initalizeHistogram();
66 –    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
66      virtual void processHistogram();
67 +    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
68  
69 <    virtual double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
69 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
70  
71      virtual void writeRdf();
72  
73 <    double deltaCosAngle_;
73 >    RealType deltaCosAngle_;
74      int nAngleBins_;
75 <    double len_;
75 >    RealType len_;
76      int nRBins_;
77 <    double deltaR_;
77 >    RealType deltaR_;
78          
79      std::vector<std::vector<int> > histogram_;
80 <    std::vector<std::vector<double> > avgGofr_;
80 >    std::vector<std::vector<RealType> > avgGofr_;
81      int npairs_;
82    };
83  
84  
85    class GofRTheta : public GofRAngle {
86    public:
87 <    GofRTheta(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins, int nangleBins)
87 >    GofRTheta(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins)
88        : GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
89          setOutputName(getPrefix(filename) + ".gofrt");
90        }
91          
92    private:
93  
94 <    virtual double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
94 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
95    };
96  
97  
98    class GofROmega : public GofRAngle {
99    public:
100 <    GofROmega(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins, int nangleBins)
100 >    GofROmega(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins)
101        : GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
102          setOutputName(getPrefix(filename) + ".gofro");
103        }
104      
105    private:
106 <    virtual double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
106 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
107    };
108  
109   }

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