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
#	User	Rev	Content
1	chuckv	1128	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1128	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1128	* 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	gezelter	1390	* 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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	chuckv	1128	* Created by J. Daniel Gezelter on 09/26/06
42			* @author J. Daniel Gezelter
43	gezelter	1442	* @version $Id$
44	chuckv	1128	*
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	gezelter	1390	namespace OpenMD {
56	chuckv	1128
57			class BOPofR : public StaticAnalyser{
58			public:
59			BOPofR(SimInfo* info, const std::string& filename,
60	gezelter	1992	const std::string& sele, double rCut, int nbins, RealType len);
61	chuckv	1128
62			virtual ~BOPofR();
63			virtual void process();
64
65	gezelter	1992	protected:
66	jmichalk	1785	virtual void initializeHistogram();
67	chuckv	1128	virtual void collectHistogram(std::vector<RealType> q,
68	gezelter	1992	std::vector<ComplexType> what,
69			RealType distCOM) = 0;
70			virtual void writeOrderParameter() = 0;
71	chuckv	1128
72			Snapshot* currentSnapshot_;
73			std::string selectionScript_;
74			SelectionManager seleMan_;
75			SelectionEvaluator evaluator_;
76
77			RealType rCut_;
78	chuckv	1137	static const int lMax_ = 6;
79	chuckv	1128	int frameCounter_;
80			int nBins_;
81	gezelter	1879	RealType len_;
82			RealType deltaR_;
83	chuckv	1128
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	chuckv	1137	std::vector<int> RCount_;
89	gezelter	1992	std::vector<int> WofR_;
90	chuckv	1137	std::vector<int> QofR_;
91	chuckv	1128	};
92	gezelter	1992
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	chuckv	1128	}
117
118			#endif
119