ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/applications/staticProps/GofRAngle.hpp
(Generate patch)

Comparing trunk/src/applications/staticProps/GofRAngle.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 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 {
49      
50    public:
51 <    GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins, int nangleBins);
51 >    GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins);
52  
53      int getNRBins() {
54        return nRBins_;
55      }
56  
57 <    double getLength() {
57 >    RealType getLength() {
58        return len_;
59      }
60  
# Line 62 | Line 63 | namespace oopse {
63    private:
64  
65      virtual void preProcess();
66 <    virtual void initalizeHistogram();
66 <    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
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();
73  
74 <    double deltaCosAngle_;
74 >    RealType deltaCosAngle_;
75      int nAngleBins_;
76 <    double len_;
76 >    RealType len_;
77      int nRBins_;
78 <    double deltaR_;
78 >    RealType deltaR_;
79          
80      std::vector<std::vector<int> > histogram_;
81 <    std::vector<std::vector<double> > avgGofr_;
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, double len, int nrbins, int nangleBins)
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:
94  
95 <    virtual double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
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, double len, int nrbins, int nangleBins)
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);        
107 >    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
108    };
109  
110   }

Comparing trunk/src/applications/staticProps/GofRAngle.hpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines