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/SphericalHarmonic.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 lMax, int nbins);

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

  private:
    
    void writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What);
    virtual void initalizeHistogram();
    virtual void collectHistogram(std::vector<RealType> q);

    Snapshot* currentSnapshot_;

    std::string selectionScript_;
    SelectionManager seleMan_;    
    SelectionEvaluator evaluator_;           
            
    RealType rCut_;
    int lMax_;
    int frameCounter_;
    int nBins_;

    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:	3021
Committed:	Mon Sep 25 22:08:33 2006 UTC (17 years, 9 months ago) by gezelter
File size:	3472 byte(s)
Log Message:	fixing bond order parameter code
#	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	3021	#include "math/SphericalHarmonic.hpp"
48	gezelter	3008	#include "math/Wigner3jm_interface.h"
49	chuckv	2901
50			namespace oopse {
51	gezelter	3007
52			class BondOrderParameter : public StaticAnalyser{
53			public:
54			BondOrderParameter(SimInfo* info, const std::string& filename,
55	gezelter	3021	const std::string& sele, double rCut, int lMax, int nbins);
56	chuckv	2901
57	gezelter	3007	virtual ~BondOrderParameter();
58			virtual void process();
59	chuckv	2901
60	gezelter	3007	private:
61	gezelter	3017
62	gezelter	3021	void writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What);
63	gezelter	3017	virtual void initalizeHistogram();
64	gezelter	3021	virtual void collectHistogram(std::vector<RealType> q);
65	chuckv	2901
66	gezelter	3007	Snapshot* currentSnapshot_;
67
68			std::string selectionScript_;
69			SelectionManager seleMan_;
70			SelectionEvaluator evaluator_;
71	chuckv	2925
72	gezelter	3007	RealType rCut_;
73	gezelter	3021	int lMax_;
74	gezelter	3009	int frameCounter_;
75	gezelter	3021	int nBins_;
76	gezelter	3017
77			RealType MinQ_;
78			RealType MaxQ_;
79			RealType deltaQ_;
80	gezelter	3021	std::vector<int> Qcount_;
81			std::map<std::pair<int,int>,int> Q_histogram_;
82	gezelter	3017
83			RealType MinW_;
84			RealType MaxW_;
85			RealType deltaW_;
86	gezelter	3021	std::vector<int> Wcount_;
87			std::map<std::pair<int,int>,int> W_histogram_;
88	gezelter	3007	};
89	chuckv	2901	}
90
91			#endif
92