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]  Vardeman & Gezelter, in progress (2009).                        
 *
 *  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 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:	1600
Committed:	Wed Aug 3 20:20:37 2011 UTC (13 years, 9 months ago) by gezelter
File size:	5144 byte(s)
Log Message:	Completing the Fortran removal project. Fixes for compilation with clang / llvm, debugging, removing code that we'd never used.
#	User	Rev	Content
1	chuckv	994	/*
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	994	* 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	994	* 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	gezelter	1054	*
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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	1054	*
41			* Created by J. Daniel Gezelter on 09/26/06
42			* @author J. Daniel Gezelter
43	gezelter	1442	* @version $Id$
44	gezelter	1054	*
45	chuckv	994	*/
46	gezelter	1054
47	chuckv	995	#ifndef APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
48			#define APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
49	chuckv	994	#include "selection/SelectionEvaluator.hpp"
50			#include "selection/SelectionManager.hpp"
51			#include "applications/staticProps/StaticAnalyser.hpp"
52	chuckv	995	#include "math/Vector3.hpp"
53	gezelter	1051	#include "math/SphericalHarmonic.hpp"
54	chuckv	994
55	gezelter	1390	namespace OpenMD {
56	gezelter	1054
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 default,
81			* this class computes the Q_{l} and \hat{W}_{l} parameters up to l = 12.
82			* The completed configurational averages of these values as
83			* well as the distributions of atomic q_{l} and \hat{w}_{l} values
84			* are then placed in .boq and .bow files.
85			*/
86	gezelter	1039	class BondOrderParameter : public StaticAnalyser{
87			public:
88			BondOrderParameter(SimInfo* info, const std::string& filename,
89	gezelter	1052	const std::string& sele, double rCut, int nbins);
90	gezelter	1054
91	gezelter	1039	virtual ~BondOrderParameter();
92			virtual void process();
93	gezelter	1054
94	gezelter	1039	private:
95	gezelter	1048	virtual void initalizeHistogram();
96	gezelter	1054	virtual void collectHistogram(std::vector<RealType> q,
97			std::vector<ComplexType> what);
98			void writeOrderParameter(std::vector<RealType> Q,
99			std::vector<ComplexType> What);
100	chuckv	994
101	gezelter	1039	Snapshot* currentSnapshot_;
102			std::string selectionScript_;
103			SelectionManager seleMan_;
104			SelectionEvaluator evaluator_;
105	chuckv	1001
106	gezelter	1039	RealType rCut_;
107	gezelter	1052	static const int lMax_ = 12;
108	gezelter	1041	int frameCounter_;
109	gezelter	1051	int nBins_;
110	gezelter	1053
111			std::map<std::pair<int,int>,int> m2Min;
112			std::map<std::pair<int,int>,int> m2Max;
113			std::map<std::pair<int,int>,std::vector<RealType> > w3j;
114
115	gezelter	1048	RealType MinQ_;
116			RealType MaxQ_;
117			RealType deltaQ_;
118	gezelter	1051	std::vector<int> Qcount_;
119			std::map<std::pair<int,int>,int> Q_histogram_;
120	gezelter	1048
121			RealType MinW_;
122			RealType MaxW_;
123			RealType deltaW_;
124	gezelter	1051	std::vector<int> Wcount_;
125			std::map<std::pair<int,int>,int> W_histogram_;
126	gezelter	1039	};
127	chuckv	994	}
128
129			#endif
130