applications/staticProps/GofR.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_GOFR_HPP
#define APPLICATIONS_STATICPROPS_GOFR_HPP

#include "applications/staticProps/RadialDistrFunc.hpp"
namespace OpenMD {

  class GofR : public RadialDistrFunc {
    
  public:
    GofR(SimInfo* info, const std::string& filename, const std::string& sele1, 
         const std::string& sele2, RealType len, int nrbins);

    int getNRBins() {
      return nRBins_; 
    }

    RealType getLength() {
      return len_;
    }
        
  private:

    virtual void preProcess();
    virtual void initializeHistogram();
    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
    virtual void processHistogram();

    virtual void writeRdf();

    RealType len_;
    int nRBins_;
    RealType deltaR_;
        
    std::vector<int> histogram_;
    std::vector<RealType> avgGofr_;
  };

}
#endif
Revision:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	3019 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_GOFR_HPP
43			#define APPLICATIONS_STATICPROPS_GOFR_HPP
44
45	tim	311	#include "applications/staticProps/RadialDistrFunc.hpp"
46	gezelter	1390	namespace OpenMD {
47	tim	306
48	gezelter	507	class GofR : public RadialDistrFunc {
49	tim	306
50	gezelter	507	public:
51			GofR(SimInfo* info, const std::string& filename, const std::string& sele1,
52	tim	963	const std::string& sele2, RealType len, int nrbins);
53	tim	306
54	gezelter	507	int getNRBins() {
55			return nRBins_;
56			}
57	tim	311
58	tim	963	RealType getLength() {
59	gezelter	507	return len_;
60			}
61	tim	310
62	gezelter	507	private:
63	tim	306
64	gezelter	507	virtual void preProcess();
65	jmichalk	1785	virtual void initializeHistogram();
66	gezelter	507	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
67			virtual void processHistogram();
68	tim	306
69	gezelter	507	virtual void writeRdf();
70	tim	310
71	tim	963	RealType len_;
72	gezelter	507	int nRBins_;
73	tim	963	RealType deltaR_;
74	tim	306
75	gezelter	507	std::vector<int> histogram_;
76	tim	963	std::vector<RealType> avgGofr_;
77	gezelter	507	};
78	tim	306
79			}
80			#endif