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Comparing trunk/src/applications/staticProps/BOPofR.hpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1992 by gezelter, Thu Apr 24 17:30:00 2014 UTC

# Line 35 | Line 35
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 < *
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 > * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41   *  Created by J. Daniel Gezelter on 09/26/06
42   *  @author  J. Daniel Gezelter
43 < *  @version $Id: BOPofR.hpp,v 1.3 2009-11-25 20:01:59 gezelter Exp $
43 > *  @version $Id$
44   *
45   */
46  
# Line 51 | Line 51
51   #include "applications/staticProps/StaticAnalyser.hpp"
52   #include "math/Vector3.hpp"
53   #include "math/SphericalHarmonic.hpp"
54 – #include "math/Wigner3jm_interface.h"
54  
55   namespace OpenMD {
56  
58 –  /**
59 –   * @class BondOrderParameter
60 –   * @brief Bond Order Parameter
61 –   *
62 –   * Computes orientational bond order parameters as outlined in:
63 –   *
64 –   *   "Bond-orientaional order in liquids and glasses," by
65 –   *    P. J. Steinhart, D. R. Nelson, and M. Ronchetti,
66 –   *    Phys. Rev. B, 28, 784 (1983).
67 –   *
68 –   * A somewhat more useful reference which has formulae for these order
69 –   * parameters for individual atoms is:
70 –   *
71 –   *   "Numerical calculation of the rate of crystal nucleation in a
72 –   *    Lennard-Jones system at moderate undercooling," by
73 –   *    Pieter Rein ten Wolde, Maria J. Ruiz-Montero, and Daan Frenkel,
74 –   *    J. Chem. Phys. 104, pp. 9932-9947 (1996).
75 –   *
76 –   * Note that this version uses a single cutoff radius to decide
77 –   * membership in the list of neighbors, and does not have use a
78 –   * distance-dependent weighting as used in the second reference above.
79 –   *
80 –   * The selection script can be utilized to look at specific types of
81 –   * central atoms.  A dynamic selector can also be utilized.  By default,
82 –   * this class computes the Q_{l} and \hat{W}_{l} parameters up to l = 12.
83 –   * The completed configurational averages of these values as
84 –   * well as the distributions of atomic q_{l} and \hat{w}_{l} values
85 –   * are then placed in .boq and .bow files.
86 –   */
57    class BOPofR : public StaticAnalyser{
58    public:
59      BOPofR(SimInfo* info, const std::string& filename,
60 <                       const std::string& sele, double rCut, int nbins, RealType len);
60 >           const std::string& sele, double rCut, int nbins, RealType len);
61      
62      virtual ~BOPofR();
63      virtual void process();
64      
65 <  private:
66 <    virtual void initalizeHistogram();
65 >  protected:
66 >    virtual void initializeHistogram();
67      virtual void collectHistogram(std::vector<RealType> q,
68 <                                  std::vector<ComplexType> what, RealType distCOM);    
69 <    void writeOrderParameter();
68 >                                  std::vector<ComplexType> what,
69 >                                  RealType distCOM) = 0;
70 >    virtual void writeOrderParameter() = 0;
71  
72      Snapshot* currentSnapshot_;
73      std::string selectionScript_;
# Line 107 | Line 78 | namespace OpenMD {
78      static const int lMax_ = 6;
79      int frameCounter_;
80      int nBins_;
81 <        RealType len_;
82 <        RealType deltaR_;
81 >    RealType len_;
82 >    RealType deltaR_;
83      
84      std::map<std::pair<int,int>,int> m2Min;
85      std::map<std::pair<int,int>,int> m2Max;
86      std::map<std::pair<int,int>,std::vector<RealType> > w3j;
87    
88      std::vector<int> RCount_;
89 <    std::vector<int>  WofR_;
89 >    std::vector<int> WofR_;
90      std::vector<int> QofR_;
91    };
92 +
93 +
94 +  class IcosahedralOfR : public BOPofR {
95 +  public:
96 +    IcosahedralOfR(SimInfo* info, const std::string& filename,
97 +                   const std::string& sele, double rCut, int nbins,
98 +                   RealType len);
99 +
100 +    virtual void collectHistogram(std::vector<RealType> q,
101 +                                  std::vector<ComplexType> what,
102 +                                  RealType distCOM);
103 +    virtual void writeOrderParameter();
104 +  };
105 +
106 +  class FCCOfR : public BOPofR {
107 +  public:
108 +    FCCOfR(SimInfo* info, const std::string& filename,
109 +           const std::string& sele, double rCut, int nbins, RealType len);
110 +
111 +    virtual void collectHistogram(std::vector<RealType> q,
112 +                                  std::vector<ComplexType> what,
113 +                                  RealType distCOM);
114 +    virtual void writeOrderParameter();
115 +  };  
116   }
117  
118   #endif

Comparing trunk/src/applications/staticProps/BOPofR.hpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1992 by gezelter, Thu Apr 24 17:30:00 2014 UTC

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