applications/staticProps/TwoDGofR.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_TWODGOFR_HPP
#define APPLICATIONS_STATICPROPS_TWODGOFR_HPP

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

  class TwoDGofR : public RadialDistrFunc {
    
  public:
    TwoDGofR(SimInfo* info, const std::string& filename, const std::string& sele1, 
           const std::string& sele2, RealType len, RealType dz, 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_;
    RealType deltaZ_;
    
    std::vector<int> histogram_;
    std::vector<RealType> avgTwoDGofR_;
  };

}
#endif
Revision:	1794
Committed:	Thu Sep 6 19:44:06 2012 UTC (12 years, 7 months ago) by gezelter
File size:	3095 byte(s)
Log Message:	Merging some of the trunk changes back to the development branch, cleaning up a datastorage bug
#	User	Rev	Content
1	gezelter	1454	/*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1454	*/
42			#ifndef APPLICATIONS_STATICPROPS_TWODGOFR_HPP
43			#define APPLICATIONS_STATICPROPS_TWODGOFR_HPP
44
45			#include "applications/staticProps/RadialDistrFunc.hpp"
46			namespace OpenMD {
47
48			class TwoDGofR : public RadialDistrFunc {
49
50			public:
51			TwoDGofR(SimInfo* info, const std::string& filename, const std::string& sele1,
52			const std::string& sele2, RealType len, RealType dz, int nrbins);
53
54			int getNRBins() {
55			return nRBins_;
56			}
57
58			RealType getLength() {
59			return len_;
60			}
61
62			private:
63
64			virtual void preProcess();
65	gezelter	1794	virtual void initializeHistogram();
66	gezelter	1454	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
67			virtual void processHistogram();
68
69			virtual void writeRdf();
70
71			RealType len_;
72			int nRBins_;
73			RealType deltaR_;
74			RealType deltaZ_;
75
76			std::vector<int> histogram_;
77			std::vector<RealType> avgTwoDGofR_;
78			};
79
80			}
81			#endif