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Comparing trunk/src/applications/staticProps/GofRAngle.hpp (file contents):
Revision 353 by tim, Wed Feb 16 19:36:30 2005 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 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]  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 {
48 >  class GofRAngle : public RadialDistrFunc {
49      
50 <    public:
51 <        GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);
50 >  public:
51 >    GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins);
52  
53 <        void setNRBins(int nbins) {
54 <            assert(nbins > 0);
55 <            nRBins_ = nbins;
55 <            deltaR_ = len_ / nRBins_;
56 <            for (int i = 0 ; i < nRBins_; ++i) {
57 <                histogram_[i].resize(nAngleBins_);
58 <                avgGofr_[i].resize(nAngleBins_);
59 <            }            
60 <        }
53 >    int getNRBins() {
54 >      return nRBins_;
55 >    }
56  
57 <        int getNRBins() {
58 <            return nRBins_;
59 <        }
57 >    RealType getLength() {
58 >      return len_;
59 >    }
60  
61 <        void setLength(double len) {
67 <            len_ = len;
68 <            deltaR_ = len_ /nRBins_;                
69 <        }
70 <
71 <        double getLength() {
72 <            return len_;
73 <        }
61 >    int getNAngleBins() {return nAngleBins_;}
62          
63 <        void setNAngleBins(int nbins) {
76 <            assert(nbins >0);
77 <            nAngleBins_ = nbins;
78 <            deltaCosAngle_ = 2.0 / nAngleBins_;
79 <            for (int i = 0 ; i < nRBins_; ++i) {
80 <                histogram_[i].resize(nAngleBins_);
81 <                avgGofr_[i].resize(nAngleBins_);
82 <            }
83 <        }
84 <        
85 <        int getNAngleBins() {return nAngleBins_;}
86 <        
87 <    private:
63 >  private:
64  
65 <        virtual void preProcess();
66 <        virtual void initalizeHistogram();
67 <        virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
68 <        virtual void processHistogram();
65 >    virtual void preProcess();
66 >    virtual void initializeHistogram();
67 >    virtual void processHistogram();
68 >    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
69  
70 <        virtual double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
70 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
71  
72 <        virtual void writeRdf();
72 >    virtual void writeRdf();
73  
74 <        double deltaCosAngle_;
75 <        int nAngleBins_;
76 <        double len_;
77 <        int nRBins_;
78 <        double deltaR_;
74 >    RealType deltaCosAngle_;
75 >    int nAngleBins_;
76 >    RealType len_;
77 >    int nRBins_;
78 >    RealType deltaR_;
79          
80 <        std::vector<std::vector<int> > histogram_;
81 <        std::vector<std::vector<double> > avgGofr_;
82 <        int npairs_;
83 < };
80 >    std::vector<std::vector<int> > histogram_;
81 >    std::vector<std::vector<RealType> > avgGofr_;
82 >    int npairs_;
83 >  };
84  
85  
86 < class GofRTheta : public GofRAngle {
87 <    public:
88 <        GofRTheta(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
89 <            : GofRAngle (info, filename, sele1, sele2) {
90 <                setOutputName(getPrefix(filename) + ".gofrt");
91 <        }
86 >  class GofRTheta : public GofRAngle {
87 >  public:
88 >    GofRTheta(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins)
89 >      : GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
90 >        setOutputName(getPrefix(filename) + ".gofrt");
91 >      }
92          
93 <    private:
93 >  private:
94  
95 <        virtual double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
96 < };
95 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
96 >  };
97  
98  
99 < class GofROmega : public GofRAngle {
100 <    public:
101 <        GofROmega(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
102 <            : GofRAngle (info, filename, sele1, sele2) {
103 <                setOutputName(getPrefix(filename) + ".gofrw");
104 <        }
99 >  class GofROmega : public GofRAngle {
100 >  public:
101 >    GofROmega(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins)
102 >      : GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
103 >        setOutputName(getPrefix(filename) + ".gofro");
104 >      }
105      
106 <    private:
107 <        virtual double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
108 < };
106 >  private:
107 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
108 >  };
109  
110   }
111   #endif

Comparing trunk/src/applications/staticProps/GofRAngle.hpp (property svn:keywords):
Revision 353 by tim, Wed Feb 16 19:36:30 2005 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

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