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Comparing trunk/src/applications/staticProps/BondOrderParameter.hpp (file contents):
Revision 1038 by chuckv, Mon Sep 18 21:31:23 2006 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 + *  Created by J. Daniel Gezelter on 09/26/06
42 + *  @author  J. Daniel Gezelter
43 + *  @version $Id: BondOrderParameter.hpp,v 1.15 2009-11-25 20:01:59 gezelter Exp $
44 + *
45   */
46 +
47   #ifndef APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
48   #define APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
49   #include "selection/SelectionEvaluator.hpp"
50   #include "selection/SelectionManager.hpp"
51   #include "applications/staticProps/StaticAnalyser.hpp"
52   #include "math/Vector3.hpp"
53 + #include "math/SphericalHarmonic.hpp"
54 + #include "math/Wigner3jm_interface.h"
55  
56 < namespace oopse {
56 > namespace OpenMD {
57  
58 <    class BondOrderParameter : public StaticAnalyser{
59 <        public:
60 <            BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
61 <                 const std::string& sele2, double rCut, int lNumber );
62 <            virtual void process();
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 >   */
87 >  class BondOrderParameter : public StaticAnalyser{
88 >  public:
89 >    BondOrderParameter(SimInfo* info, const std::string& filename,
90 >                       const std::string& sele, double rCut, int nbins);
91 >    
92 >    virtual ~BondOrderParameter();
93 >    virtual void process();
94 >    
95 >  private:
96 >    virtual void initalizeHistogram();
97 >    virtual void collectHistogram(std::vector<RealType> q,
98 >                                  std::vector<ComplexType> what);    
99 >    void writeOrderParameter(std::vector<RealType> Q,
100 >                             std::vector<ComplexType> What);
101  
102 <        private:
103 <
102 >    Snapshot* currentSnapshot_;
103 >    std::string selectionScript_;
104 >    SelectionManager seleMan_;    
105 >    SelectionEvaluator evaluator_;          
106              
107 <            void writeOrderParameter();
108 <                    virtual void initalizeHistogram();
109 <                virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
110 <                virtual void processHistogram();
107 >    RealType rCut_;
108 >    static const int lMax_ = 12;
109 >    int frameCounter_;
110 >    int nBins_;
111 >    
112 >    std::map<std::pair<int,int>,int> m2Min;
113 >    std::map<std::pair<int,int>,int> m2Max;
114 >    std::map<std::pair<int,int>,std::vector<RealType> > w3j;
115 >  
116 >    RealType MinQ_;
117 >    RealType MaxQ_;
118 >    RealType deltaQ_;
119 >    std::vector<int> Qcount_;
120 >    std::map<std::pair<int,int>,int> Q_histogram_;
121  
122 <            Snapshot* currentSnapshot_;
123 <
124 <            std::string selectionScript1_;
125 <            SelectionManager seleMan1_;    
126 <            SelectionEvaluator evaluator1_;
127 <            
70 <            std::vector<Vector3d> neighbors_;
71 <            std::vector<std::pair<StuntDouble*, StuntDouble*> > sdPairs_;  /**< each pair is used to define a vector, vector = first - second */
72 <            std::vector<OrderParam> orderParams_;
73 <            
74 <            RealType rCut_;
75 <            int lNumber_;
76 <            int mSize_;
77 <            RealType* Q_l_;
78 <            RealType* W_l_;
79 <            RealType* WHat_l_;
80 <    };
122 >    RealType MinW_;
123 >    RealType MaxW_;
124 >    RealType deltaW_;
125 >    std::vector<int> Wcount_;
126 >    std::map<std::pair<int,int>,int> W_histogram_;
127 >  };
128   }
129  
130   #endif

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