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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *  Created by J. Daniel Gezelter on 09/26/06
 *  @author  J. Daniel Gezelter 
 *  @version $Id$
 *
 */

#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"

namespace OpenMD {

  /**
   * @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 \f[ Q_{l} \f] and 
   * \f[ \hat{W}_{l} \f] parameters up to \f[ l = 12 \f].  The completed
   * configurational averages of these values as well as the
   * distributions of atomic \f[ q_{l} \f] and \f[ \hat{w}_{l} \f]
   * 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 initializeHistogram();
    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:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	5246 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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	* [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 $Id$
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
55	namespace OpenMD {
56
57	/**
58	* @class BondOrderParameter
59	* @brief Bond Order Parameter
60	*
61	* Computes orientational bond order parameters as outlined in:
62	*
63	* "Bond-orientaional order in liquids and glasses," by
64	* P. J. Steinhart, D. R. Nelson, and M. Ronchetti,
65	* Phys. Rev. B, 28, 784 (1983).
66	*
67	* A somewhat more useful reference which has formulae for these order
68	* parameters for individual atoms is:
69	*
70	* "Numerical calculation of the rate of crystal nucleation in a
71	* Lennard-Jones system at moderate undercooling," by
72	* Pieter Rein ten Wolde, Maria J. Ruiz-Montero, and Daan Frenkel,
73	* J. Chem. Phys. 104, pp. 9932-9947 (1996).
74	*
75	* Note that this version uses a single cutoff radius to decide
76	* membership in the list of neighbors, and does not have use a
77	* distance-dependent weighting as used in the second reference above.
78	*
79	* The selection script can be utilized to look at specific types of
80	* central atoms. A dynamic selector can also be utilized. By
81	* default, this class computes the \f[ Q_{l} \f] and
82	* \f[ \hat{W}_{l} \f] parameters up to \f[ l = 12 \f]. The completed
83	* configurational averages of these values as well as the
84	* distributions of atomic \f[ q_{l} \f] and \f[ \hat{w}_{l} \f]
85	* values 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 initializeHistogram();
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	Snapshot* currentSnapshot_;
103	std::string selectionScript_;
104	SelectionManager seleMan_;
105	SelectionEvaluator evaluator_;
106
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	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
131