applications/staticProps/RadialDistrFunc.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, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#ifndef APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
#define APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP

#include <string>
#include <vector>

#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "utils/NumericConstant.hpp"
#include "applications/staticProps/StaticAnalyser.hpp"

namespace OpenMD {

  /**
   * @class RadialDistrFunc
   * @brief Radial Distribution Function
   */
  class RadialDistrFunc : public StaticAnalyser {
  public:
    RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);

    virtual ~RadialDistrFunc() {}
        
    void process();        


  protected:

    virtual void preProcess() {}
    virtual void postProcess() {}

    int getNPairs() { return nPairs_;}
        
    Snapshot* currentSnapshot_;

    std::string selectionScript1_;
    std::string selectionScript2_;
    int nProcessed_;
    SelectionManager seleMan1_;
    SelectionManager seleMan2_;
        
  private:

    virtual void initializeHistogram() {}
    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2) =0;
    virtual void processHistogram() {}
    void processNonOverlapping(SelectionManager& sman1, SelectionManager& sman2);
    void processOverlapping(SelectionManager& sman);

    virtual void validateSelection1(SelectionManager& sman) {}
    virtual void validateSelection2(SelectionManager& sman) {}
    virtual void writeRdf() = 0;

        
    SelectionEvaluator evaluator1_;
    SelectionEvaluator evaluator2_;

    SelectionManager sele1_minus_common_;
    SelectionManager sele2_minus_common_;
    SelectionManager common_;        
    int nPairs_;
  };


}
#endif
Revision:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	3892 byte(s)
Log Message:	Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
#	User	Rev	Content
1	tim	306	/*
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	tim	306	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	306	* 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	gezelter	1390	*
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	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	306	*/
42			#ifndef APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
43			#define APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
44
45	tim	307	#include <string>
46	tim	306	#include <vector>
47
48			#include "selection/SelectionEvaluator.hpp"
49			#include "selection/SelectionManager.hpp"
50	tim	311	#include "utils/NumericConstant.hpp"
51	tim	543	#include "applications/staticProps/StaticAnalyser.hpp"
52
53	gezelter	1390	namespace OpenMD {
54	tim	306
55	gezelter	507	/**
56			* @class RadialDistrFunc
57			* @brief Radial Distribution Function
58			*/
59	tim	543	class RadialDistrFunc : public StaticAnalyser {
60	gezelter	507	public:
61			RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);
62	tim	306
63	gezelter	507	virtual ~RadialDistrFunc() {}
64	tim	310
65	gezelter	507	void process();
66	tim	306
67
68
69	gezelter	507	protected:
70	tim	306
71	gezelter	507	virtual void preProcess() {}
72			virtual void postProcess() {}
73	tim	306
74	gezelter	507	int getNPairs() { return nPairs_;}
75	tim	347
76	gezelter	507	Snapshot* currentSnapshot_;
77	tim	310
78	gezelter	507	std::string selectionScript1_;
79			std::string selectionScript2_;
80			int nProcessed_;
81			SelectionManager seleMan1_;
82			SelectionManager seleMan2_;
83	tim	347
84	gezelter	507	private:
85	tim	306
86	jmichalk	1785	virtual void initializeHistogram() {}
87	gezelter	507	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2) =0;
88			virtual void processHistogram() {}
89			void processNonOverlapping(SelectionManager& sman1, SelectionManager& sman2);
90			void processOverlapping(SelectionManager& sman);
91	tim	306
92	gezelter	507	virtual void validateSelection1(SelectionManager& sman) {}
93			virtual void validateSelection2(SelectionManager& sman) {}
94			virtual void writeRdf() = 0;
95	tim	306
96
97	gezelter	507	SelectionEvaluator evaluator1_;
98			SelectionEvaluator evaluator2_;
99	tim	361
100	gezelter	507	SelectionManager sele1_minus_common_;
101			SelectionManager sele2_minus_common_;
102			SelectionManager common_;
103			int nPairs_;
104			};
105	tim	306
106
107			}
108			#endif