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.
 */
#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/Wigner3jm_interface.h"

namespace oopse {
  
  class BondOrderParameter : public StaticAnalyser{
  public:
    BondOrderParameter(SimInfo* info, const std::string& filename, 
                       const std::string& sele, double rCut, int lNumber, int nbins);

    virtual ~BondOrderParameter();
    virtual void process();

  private:
    
    void writeOrderParameter(RealType Q_l, RealType W_l_hat);
    virtual void initalizeHistogram();
    virtual void collectHistogram(RealType q_l, RealType w_l);

    Snapshot* currentSnapshot_;

    std::string selectionScript_;
    SelectionManager seleMan_;    
    SelectionEvaluator evaluator_;           
            
    RealType rCut_;
    int lNumber_;
    int mSize_;    
    int frameCounter_;

    RealType MinQ_;
    RealType MaxQ_;
    RealType deltaQ_;
    RealType sumQ_;
    RealType sumQ2_;
    int Qcount_;
    std::vector<int> Q_histogram_;

    RealType MinW_;
    RealType MaxW_;
    RealType deltaW_;
    RealType sumW_;
    RealType sumW2_;
    int Wcount_;
    std::vector<int> W_histogram_;
  };
}

#endif

Revision:	3017
Committed:	Fri Sep 22 01:36:27 2006 UTC (17 years, 10 months ago) by gezelter
File size:	3447 byte(s)
Log Message:	Following Rein ten Wolde article
#	User	Rev	Content
1	chuckv	2901	/*
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	chuckv	2902	#ifndef APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
42			#define APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
43	chuckv	2901	#include "selection/SelectionEvaluator.hpp"
44			#include "selection/SelectionManager.hpp"
45			#include "applications/staticProps/StaticAnalyser.hpp"
46	chuckv	2902	#include "math/Vector3.hpp"
47	gezelter	3008	#include "math/Wigner3jm_interface.h"
48	chuckv	2901
49			namespace oopse {
50	gezelter	3007
51			class BondOrderParameter : public StaticAnalyser{
52			public:
53			BondOrderParameter(SimInfo* info, const std::string& filename,
54			const std::string& sele, double rCut, int lNumber, int nbins);
55	chuckv	2901
56	gezelter	3007	virtual ~BondOrderParameter();
57			virtual void process();
58	chuckv	2901
59	gezelter	3007	private:
60	gezelter	3017
61			void writeOrderParameter(RealType Q_l, RealType W_l_hat);
62			virtual void initalizeHistogram();
63			virtual void collectHistogram(RealType q_l, RealType w_l);
64	chuckv	2901
65	gezelter	3007	Snapshot* currentSnapshot_;
66
67			std::string selectionScript_;
68			SelectionManager seleMan_;
69			SelectionEvaluator evaluator_;
70	chuckv	2925
71	gezelter	3007	RealType rCut_;
72			int lNumber_;
73			int mSize_;
74	gezelter	3009	int frameCounter_;
75	gezelter	3017
76			RealType MinQ_;
77			RealType MaxQ_;
78			RealType deltaQ_;
79			RealType sumQ_;
80			RealType sumQ2_;
81			int Qcount_;
82			std::vector<int> Q_histogram_;
83
84			RealType MinW_;
85			RealType MaxW_;
86			RealType deltaW_;
87			RealType sumW_;
88			RealType sumW2_;
89			int Wcount_;
90			std::vector<int> W_histogram_;
91	gezelter	3007	};
92	chuckv	2901	}
93
94			#endif
95