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Comparing trunk/src/applications/staticProps/BondOrderParameter.hpp (file contents):
Revision 1038 by chuckv, Mon Sep 18 21:31:23 2006 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
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	+	* 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] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	+	*  Created by J. Daniel Gezelter on 09/26/06
42	+	*  @author  J. Daniel Gezelter
43	+	*  @version $Id$
44	+	*
45		*/
46	+
47		#ifndef APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
48		#define APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_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	<	namespace oopse {
55	>	namespace OpenMD {
56
57	<	class BondOrderParameter : public StaticAnalyser{
58	<	public:
59	<	BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
60	<	const std::string& sele2, double rCut, int lNumber );
61	<	virtual void process();
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	>	class BondOrderParameter : public StaticAnalyser{
87	>	public:
88	>	BondOrderParameter(SimInfo* info, const std::string& filename,
89	>	const std::string& sele, double rCut, int nbins);
90	>
91	>	virtual ~BondOrderParameter();
92	>	virtual void process();
93	>
94	>	private:
95	>	virtual void initializeHistogram();
96	>	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
101	<	private:
102	<
101	>	Snapshot* currentSnapshot_;
102	>	std::string selectionScript_;
103	>	SelectionManager seleMan_;
104	>	SelectionEvaluator evaluator_;
105
106	<	void writeOrderParameter();
107	<	virtual void initalizeHistogram();
108	<	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
109	<	virtual void processHistogram();
106	>	RealType rCut_;
107	>	static const int lMax_ = 12;
108	>	int frameCounter_;
109	>	int nBins_;
110	>
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	>	RealType MinQ_;
116	>	RealType MaxQ_;
117	>	RealType deltaQ_;
118	>	std::vector<int> Qcount_;
119	>	std::map<std::pair<int,int>,int> Q_histogram_;
120
121	<	Snapshot* currentSnapshot_;
122	<
123	<	std::string selectionScript1_;
124	<	SelectionManager seleMan1_;
125	<	SelectionEvaluator evaluator1_;
126	<
70	<	std::vector<Vector3d> neighbors_;
71	<	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	<	RealType rCut_;
75	<	int lNumber_;
76	<	int mSize_;
77	<	RealType* Q_l_;
78	<	RealType* W_l_;
79	<	RealType* WHat_l_;
80	<	};
121	>	RealType MinW_;
122	>	RealType MaxW_;
123	>	RealType deltaW_;
124	>	std::vector<int> Wcount_;
125	>	std::map<std::pair<int,int>,int> W_histogram_;
126	>	};
127		}
128
129		#endif

Comparing trunk/src/applications/staticProps/BondOrderParameter.hpp (property svn:keywords):
Revision 1038 by chuckv, Mon Sep 18 21:31:23 2006 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

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