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Comparing trunk/src/applications/staticProps/BOPofR.hpp (file contents):
Revision 1128 by chuckv, Wed Apr 11 23:27:20 2007 UTC vs.
Revision 1992 by gezelter, Thu Apr 24 17:30:00 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 38 | Line 29
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31   *
32 < *  BondOrderParameter.hpp
33 < *  OOPSE-4
34 < *
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 > * [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 1.1 2007-04-11 23:27:20 chuckv Exp $
43 > *  @version $Id$
44   *
45   */
46  
# Line 54 | Line 51
51   #include "applications/staticProps/StaticAnalyser.hpp"
52   #include "math/Vector3.hpp"
53   #include "math/SphericalHarmonic.hpp"
57 – #include "math/Wigner3jm_interface.h"
54  
55 < namespace oopse {
55 > namespace OpenMD {
56  
61 –  /**
62 –   * @class BondOrderParameter
63 –   * @brief Bond Order Parameter
64 –   *
65 –   * Computes orientational bond order parameters as outlined in:
66 –   *
67 –   *   "Bond-orientaional order in liquids and glasses," by
68 –   *    P. J. Steinhart, D. R. Nelson, and M. Ronchetti,
69 –   *    Phys. Rev. B, 28, 784 (1983).
70 –   *
71 –   * A somewhat more useful reference which has formulae for these order
72 –   * parameters for individual atoms is:
73 –   *
74 –   *   "Numerical calculation of the rate of crystal nucleation in a
75 –   *    Lennard-Jones system at moderate undercooling," by
76 –   *    Pieter Rein ten Wolde, Maria J. Ruiz-Montero, and Daan Frenkel,
77 –   *    J. Chem. Phys. 104, pp. 9932-9947 (1996).
78 –   *
79 –   * Note that this version uses a single cutoff radius to decide
80 –   * membership in the list of neighbors, and does not have use a
81 –   * distance-dependent weighting as used in the second reference above.
82 –   *
83 –   * The selection script can be utilized to look at specific types of
84 –   * central atoms.  A dynamic selector can also be utilized.  By default,
85 –   * this class computes the Q_{l} and \hat{W}_{l} parameters up to l = 12.
86 –   * The completed configurational averages of these values as
87 –   * well as the distributions of atomic q_{l} and \hat{w}_{l} values
88 –   * are then placed in .boq and .bow files.
89 –   */
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 75 | namespace oopse {
75      SelectionEvaluator evaluator_;          
76              
77      RealType rCut_;
78 <    static const int lMax_ = 12;
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<std::vector<int> > RCount_;
89 <    std::vector<std::vector<RealType> > WofR_;
90 <    std::vector<std::vector<RealType> > QofR_;
88 >    std::vector<int> RCount_;
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 1128 by chuckv, Wed Apr 11 23:27:20 2007 UTC vs.
Revision 1992 by gezelter, Thu Apr 24 17:30:00 2014 UTC

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