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"

namespace oopse {

    class BondOrderParameter : public StaticAnalyser{
        public:
            BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
                 const std::string& sele2, double rCut, int lNumber );
            virtual void process();

        private:

            
            void writeOrderParameter();
                    virtual void initalizeHistogram();
                virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
                virtual void processHistogram();

            Snapshot* currentSnapshot_;

            std::string selectionScript1_;
            SelectionManager seleMan1_;    
            SelectionEvaluator evaluator1_;
            
            std::vector<Vector3d> neighbors_;
            std::vector<std::pair<StuntDouble*, StuntDouble*> > sdPairs_;  /**< each pair is used to define a vector, vector = first - second */
            std::vector<OrderParam> orderParams_;
            
            RealType rCut_;
            int lNumber_;
            int mSize_;
            RealType* Q_l_;
            RealType* W_l_;
            RealType* WHat_l_;
    };
}

#endif

Revision:	3005
Committed:	Mon Sep 18 21:31:23 2006 UTC (17 years, 10 months ago) by chuckv
File size:	3479 byte(s)
Log Message:	Latest Version
#	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	chuckv	2901
48			namespace oopse {
49
50	chuckv	2902	class BondOrderParameter : public StaticAnalyser{
51	chuckv	2901	public:
52	chuckv	2902	BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
53			const std::string& sele2, double rCut, int lNumber );
54	chuckv	2901	virtual void process();
55
56			private:
57
58	chuckv	2925
59			void writeOrderParameter();
60			virtual void initalizeHistogram();
61			virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
62			virtual void processHistogram();
63	chuckv	2901
64			Snapshot* currentSnapshot_;
65
66			std::string selectionScript1_;
67	chuckv	2902	SelectionManager seleMan1_;
68	chuckv	2901	SelectionEvaluator evaluator1_;
69	chuckv	2902
70			std::vector<Vector3d> neighbors_;
71	chuckv	2901	std::vector<std::pair<StuntDouble, StuntDouble> > sdPairs_; /*< each pair is used to define a vector, vector = first - second /
72			std::vector<OrderParam> orderParams_;
73
74	chuckv	2925	RealType rCut_;
75	chuckv	2902	int lNumber_;
76	chuckv	2925	int mSize_;
77	chuckv	3005	RealType* Q_l_;
78			RealType* W_l_;
79			RealType* WHat_l_;
80	chuckv	2901	};
81			}
82
83			#endif
84