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:	1794
Committed:	Thu Sep 6 19:44:06 2012 UTC (12 years, 7 months ago) by gezelter
File size:	3892 byte(s)
Log Message:	Merging some of the trunk changes back to the development branch, cleaning up a datastorage bug
#	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, 24107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42	#ifndef APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
43	#define APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
44
45	#include <string>
46	#include <vector>
47
48	#include "selection/SelectionEvaluator.hpp"
49	#include "selection/SelectionManager.hpp"
50	#include "utils/NumericConstant.hpp"
51	#include "applications/staticProps/StaticAnalyser.hpp"
52
53	namespace OpenMD {
54
55	/**
56	* @class RadialDistrFunc
57	* @brief Radial Distribution Function
58	*/
59	class RadialDistrFunc : public StaticAnalyser {
60	public:
61	RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);
62
63	virtual ~RadialDistrFunc() {}
64
65	void process();
66
67
68
69	protected:
70
71	virtual void preProcess() {}
72	virtual void postProcess() {}
73
74	int getNPairs() { return nPairs_;}
75
76	Snapshot* currentSnapshot_;
77
78	std::string selectionScript1_;
79	std::string selectionScript2_;
80	int nProcessed_;
81	SelectionManager seleMan1_;
82	SelectionManager seleMan2_;
83
84	private:
85
86	virtual void initializeHistogram() {}
87	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
92	virtual void validateSelection1(SelectionManager& sman) {}
93	virtual void validateSelection2(SelectionManager& sman) {}
94	virtual void writeRdf() = 0;
95
96
97	SelectionEvaluator evaluator1_;
98	SelectionEvaluator evaluator2_;
99
100	SelectionManager sele1_minus_common_;
101	SelectionManager sele2_minus_common_;
102	SelectionManager common_;
103	int nPairs_;
104	};
105
106
107	}
108	#endif