applications/staticProps/BondOrderParameter.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 *  BondOrderParameter.hpp
 *  OOPSE-4
 *
 *  Created by J. Daniel Gezelter on 09/26/06
 *  @author  J. Daniel Gezelter 
 *  @version $Id: BondOrderParameter.hpp,v 1.14 2006-09-26 16:08:44 gezelter Exp $
 *
 */

#ifndef APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
#define APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "applications/staticProps/StaticAnalyser.hpp"
#include "math/Vector3.hpp"
#include "math/SphericalHarmonic.hpp"
#include "math/Wigner3jm_interface.h"

namespace oopse {

  /**
   * @class BondOrderParameter
   * @brief Bond Order Parameter
   *
   * Computes orientational bond order parameters as outlined in:
   *
   *   "Bond-orientaional order in liquids and glasses," by
   *    P. J. Steinhart, D. R. Nelson, and M. Ronchetti, 
   *    Phys. Rev. B, 28, 784 (1983).
   *
   * A somewhat more useful reference which has formulae for these order
   * parameters for individual atoms is:
   *
   *   "Numerical calculation of the rate of crystal nucleation in a
   *    Lennard-Jones system at moderate undercooling," by
   *    Pieter Rein ten Wolde, Maria J. Ruiz-Montero, and Daan Frenkel,
   *    J. Chem. Phys. 104, pp. 9932-9947 (1996).
   *
   * Note that this version uses a single cutoff radius to decide 
   * membership in the list of neighbors, and does not have use a
   * distance-dependent weighting as used in the second reference above.
   *
   * The selection script can be utilized to look at specific types of
   * central atoms.  A dynamic selector can also be utilized.  By default, 
   * this class computes the Q_{l} and \hat{W}_{l} parameters up to l = 12.
   * The completed configurational averages of these values as
   * well as the distributions of atomic q_{l} and \hat{w}_{l} values
   * are then placed in .boq and .bow files.
   */
  class BondOrderParameter : public StaticAnalyser{
  public:
    BondOrderParameter(SimInfo* info, const std::string& filename, 
                       const std::string& sele, double rCut, int nbins);
    
    virtual ~BondOrderParameter();
    virtual void process();
    
  private:
    virtual void initalizeHistogram();
    virtual void collectHistogram(std::vector<RealType> q, 
                                  std::vector<ComplexType> what);    
    void writeOrderParameter(std::vector<RealType> Q, 
                             std::vector<ComplexType> What);

    Snapshot* currentSnapshot_;
    std::string selectionScript_;
    SelectionManager seleMan_;    
    SelectionEvaluator evaluator_;           
            
    RealType rCut_;
    static const int lMax_ = 12;
    int frameCounter_;
    int nBins_;
    
    std::map<std::pair<int,int>,int> m2Min;
    std::map<std::pair<int,int>,int> m2Max;
    std::map<std::pair<int,int>,std::vector<RealType> > w3j;
   
    RealType MinQ_;
    RealType MaxQ_;
    RealType deltaQ_;
    std::vector<int> Qcount_;
    std::map<std::pair<int,int>,int> Q_histogram_;

    RealType MinW_;
    RealType MaxW_;
    RealType deltaW_;
    std::vector<int> Wcount_;
    std::map<std::pair<int,int>,int> W_histogram_;
  };
}

#endif

Revision:	3026
Committed:	Tue Sep 26 16:08:44 2006 UTC (17 years, 9 months ago) by gezelter
File size:	5247 byte(s)
Log Message:	Cleaned up the code for BondOrderParameter and added a bunch of comments. Fixed a memory leak or ten.
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
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
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*
41	* BondOrderParameter.hpp
42	* OOPSE-4
43	*
44	* Created by J. Daniel Gezelter on 09/26/06
45	* @author J. Daniel Gezelter
46	* @version $Id: BondOrderParameter.hpp,v 1.14 2006-09-26 16:08:44 gezelter Exp $
47	*
48	*/
49
50	#ifndef APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
51	#define APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
52	#include "selection/SelectionEvaluator.hpp"
53	#include "selection/SelectionManager.hpp"
54	#include "applications/staticProps/StaticAnalyser.hpp"
55	#include "math/Vector3.hpp"
56	#include "math/SphericalHarmonic.hpp"
57	#include "math/Wigner3jm_interface.h"
58
59	namespace oopse {
60
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	*/
90	class BondOrderParameter : public StaticAnalyser{
91	public:
92	BondOrderParameter(SimInfo* info, const std::string& filename,
93	const std::string& sele, double rCut, int nbins);
94
95	virtual ~BondOrderParameter();
96	virtual void process();
97
98	private:
99	virtual void initalizeHistogram();
100	virtual void collectHistogram(std::vector<RealType> q,
101	std::vector<ComplexType> what);
102	void writeOrderParameter(std::vector<RealType> Q,
103	std::vector<ComplexType> What);
104
105	Snapshot* currentSnapshot_;
106	std::string selectionScript_;
107	SelectionManager seleMan_;
108	SelectionEvaluator evaluator_;
109
110	RealType rCut_;
111	static const int lMax_ = 12;
112	int frameCounter_;
113	int nBins_;
114
115	std::map<std::pair<int,int>,int> m2Min;
116	std::map<std::pair<int,int>,int> m2Max;
117	std::map<std::pair<int,int>,std::vector<RealType> > w3j;
118
119	RealType MinQ_;
120	RealType MaxQ_;
121	RealType deltaQ_;
122	std::vector<int> Qcount_;
123	std::map<std::pair<int,int>,int> Q_histogram_;
124
125	RealType MinW_;
126	RealType MaxW_;
127	RealType deltaW_;
128	std::vector<int> Wcount_;
129	std::map<std::pair<int,int>,int> W_histogram_;
130	};
131	}
132
133	#endif
134