applications/staticProps/BOPofR.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_BOPOFR_HPP
#define APPLICATIONS_STATICPROPS_BOPOFR_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 BOPofR : public StaticAnalyser{
  public:
    BOPofR(SimInfo* info, const std::string& filename, 
                       const std::string& sele, double rCut, int nbins, RealType len);
    
    virtual ~BOPofR();
    virtual void process();
    
  private:
    virtual void initializeHistogram();
    virtual void collectHistogram(std::vector<RealType> q, 
                                  std::vector<ComplexType> what, RealType distCOM);    
    void writeOrderParameter();

    Snapshot* currentSnapshot_;
    std::string selectionScript_;
    SelectionManager seleMan_;    
    SelectionEvaluator evaluator_;           
            
    RealType rCut_;
    static const int lMax_ = 6;
    int frameCounter_;
    int nBins_;
    RealType len_;
    RealType deltaR_;
    
    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;
   
    std::vector<int> RCount_;
    std::vector<int>  WofR_;
    std::vector<int> QofR_;
  };
}

#endif

Revision:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	4979 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	User	Rev	Content
1	chuckv	1128	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1128	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1128	* 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	gezelter	1390	* 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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	chuckv	1128	* Created by J. Daniel Gezelter on 09/26/06
42			* @author J. Daniel Gezelter
43	gezelter	1442	* @version $Id$
44	chuckv	1128	*
45			*/
46
47			#ifndef APPLICATIONS_STATICPROPS_BOPOFR_HPP
48			#define APPLICATIONS_STATICPROPS_BOPOFR_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	gezelter	1390	namespace OpenMD {
56	chuckv	1128
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	gezelter	1808	* A somewhat more useful reference which has formulae for these
68			* order parameters for individual atoms is:
69	chuckv	1128	*
70			* "Numerical calculation of the rate of crystal nucleation in a
71	gezelter	1808	* Lennard-Jones system at moderate undercooling," by Pieter Rein
72			* ten Wolde, Maria J. Ruiz-Montero, and Daan Frenkel,
73	chuckv	1128	* J. Chem. Phys. 104, pp. 9932-9947 (1996).
74			*
75	gezelter	1808	* Note that this version uses a single cutoff radius to decide
76	chuckv	1128	* membership in the list of neighbors, and does not have use a
77	gezelter	1808	* distance-dependent weighting as used in the second reference
78			* above.
79	chuckv	1128	*
80			* The selection script can be utilized to look at specific types of
81	gezelter	1808	* central atoms. A dynamic selector can also be utilized. By
82			* default, this class computes the \f[ Q_{l} \f] and
83			* \f[ \hat{W}_{l} \f] parameters up to \f[ l = 12 \f]. The
84			* completed configurational averages of these values as well as the
85			* distributions of atomic \f[ q_{l} \f] and \f[ \hat{w}_{l} \f]
86			* values are then placed in .boq and .bow files.
87	chuckv	1128	*/
88			class BOPofR : public StaticAnalyser{
89			public:
90			BOPofR(SimInfo* info, const std::string& filename,
91			const std::string& sele, double rCut, int nbins, RealType len);
92
93			virtual ~BOPofR();
94			virtual void process();
95
96			private:
97	gezelter	1794	virtual void initializeHistogram();
98	chuckv	1128	virtual void collectHistogram(std::vector<RealType> q,
99			std::vector<ComplexType> what, RealType distCOM);
100			void writeOrderParameter();
101
102			Snapshot* currentSnapshot_;
103			std::string selectionScript_;
104			SelectionManager seleMan_;
105			SelectionEvaluator evaluator_;
106
107			RealType rCut_;
108	chuckv	1137	static const int lMax_ = 6;
109	chuckv	1128	int frameCounter_;
110			int nBins_;
111	gezelter	1808	RealType len_;
112			RealType deltaR_;
113	chuckv	1128
114			std::map<std::pair<int,int>,int> m2Min;
115			std::map<std::pair<int,int>,int> m2Max;
116			std::map<std::pair<int,int>,std::vector<RealType> > w3j;
117
118	chuckv	1137	std::vector<int> RCount_;
119			std::vector<int> WofR_;
120			std::vector<int> QofR_;
121	chuckv	1128	};
122			}
123
124			#endif
125