applications/staticProps/BOPofR.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, 234107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *  Created by J. Daniel Gezelter on 09/26/06
 *  @author  J. Daniel Gezelter 
 *  @version $Id$
 *
 */

#ifndef APPLICATIONS_STATICPROPS_BOPOFR_HPP
#define APPLICATIONS_STATICPROPS_BOPOFR_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 BOPofR : public StaticAnalyser{
  public:
    BOPofR(SimInfo* info, const std::string& filename, 
           const std::string& sele, double rCut, int nbins, RealType len);
    
    virtual ~BOPofR();
    virtual void process();
    
  protected:
    virtual void initializeHistogram();
    virtual void collectHistogram(std::vector<RealType> q, 
                                  std::vector<ComplexType> what, 
                                  RealType distCOM) = 0;
    virtual void writeOrderParameter() = 0;

    Snapshot* currentSnapshot_;
    std::string selectionScript_;
    SelectionManager seleMan_;    
    SelectionEvaluator evaluator_;           
            
    RealType rCut_;
    static const int lMax_ = 6;
    int frameCounter_;
    int nBins_;
    RealType len_;
    RealType deltaR_;
    
    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;
   
    std::vector<int> RCount_;
    std::vector<int> WofR_;
    std::vector<int> QofR_;
  };


  class IcosahedralOfR : public BOPofR {
  public:
    IcosahedralOfR(SimInfo* info, const std::string& filename, 
                   const std::string& sele, double rCut, int nbins, 
                   RealType len);

    virtual void collectHistogram(std::vector<RealType> q, 
                                  std::vector<ComplexType> what, 
                                  RealType distCOM);
    virtual void writeOrderParameter();
  };

  class FCCOfR : public BOPofR {
  public:
    FCCOfR(SimInfo* info, const std::string& filename, 
           const std::string& sele, double rCut, int nbins, RealType len);

    virtual void collectHistogram(std::vector<RealType> q, 
                                  std::vector<ComplexType> what, 
                                  RealType distCOM);
    virtual void writeOrderParameter();
  };  
}

#endif

Revision:	1992
Committed:	Thu Apr 24 17:30:00 2014 UTC (11 years ago) by gezelter
File size:	4513 byte(s)
Log Message:	Added FCCOfR and IcosahedralOfR analyzers to staticProps
#	Content
1	/*
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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
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	*
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, 234107 (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_BOPOFR_HPP
48	#define APPLICATIONS_STATICPROPS_BOPOFR_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 OpenMD {
56
57	class BOPofR : public StaticAnalyser{
58	public:
59	BOPofR(SimInfo* info, const std::string& filename,
60	const std::string& sele, double rCut, int nbins, RealType len);
61
62	virtual ~BOPofR();
63	virtual void process();
64
65	protected:
66	virtual void initializeHistogram();
67	virtual void collectHistogram(std::vector<RealType> q,
68	std::vector<ComplexType> what,
69	RealType distCOM) = 0;
70	virtual void writeOrderParameter() = 0;
71
72	Snapshot* currentSnapshot_;
73	std::string selectionScript_;
74	SelectionManager seleMan_;
75	SelectionEvaluator evaluator_;
76
77	RealType rCut_;
78	static const int lMax_ = 6;
79	int frameCounter_;
80	int nBins_;
81	RealType len_;
82	RealType deltaR_;
83
84	std::map<std::pair<int,int>,int> m2Min;
85	std::map<std::pair<int,int>,int> m2Max;
86	std::map<std::pair<int,int>,std::vector<RealType> > w3j;
87
88	std::vector<int> RCount_;
89	std::vector<int> WofR_;
90	std::vector<int> QofR_;
91	};
92
93
94	class IcosahedralOfR : public BOPofR {
95	public:
96	IcosahedralOfR(SimInfo* info, const std::string& filename,
97	const std::string& sele, double rCut, int nbins,
98	RealType len);
99
100	virtual void collectHistogram(std::vector<RealType> q,
101	std::vector<ComplexType> what,
102	RealType distCOM);
103	virtual void writeOrderParameter();
104	};
105
106	class FCCOfR : public BOPofR {
107	public:
108	FCCOfR(SimInfo* info, const std::string& filename,
109	const std::string& sele, double rCut, int nbins, RealType len);
110
111	virtual void collectHistogram(std::vector<RealType> q,
112	std::vector<ComplexType> what,
113	RealType distCOM);
114	virtual void writeOrderParameter();
115	};
116	}
117
118	#endif
119