applications/staticProps/GofXyz.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
#ifndef APPLICATIONS_STATICPROPS_GOFXYZ_HPP
#define APPLICATIONS_STATICPROPS_GOFXYZ_HPP

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

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

        int getNRBins() {
            return nRBins_;
        }
        
        double getLength() {
            return len_;
        }
        
    private:

        virtual void preProcess();
        void initalizeHistogram();
        virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
        virtual void writeRdf();

        Vector3d getMolCom(StuntDouble* sd);
        
        //virtual void validateSelection1(SelectionManager& sman);
        
        double len_;
        double halfLen_;
        int nRBins_;
        double deltaR_;
        
        std::vector<std::vector<std::vector<int> > > histogram_;

        struct CoorSet {
            Vector3d xaxis;
            Vector3d yaxis;
            Vector3d zaxis;
        };

        std::map<int, CoorSet> coorSets_;
        std::vector<Molecule*> atom2Mol_;
};


}
#endif

Revision:	2048
Committed:	Thu Feb 17 19:50:30 2005 UTC (19 years, 5 months ago) by tim
File size:	3287 byte(s)
Log Message:	fix a bug in GofXyz
#	User	Rev	Content
1	tim	1994	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#ifndef APPLICATIONS_STATICPROPS_GOFXYZ_HPP
42			#define APPLICATIONS_STATICPROPS_GOFXYZ_HPP
43
44	tim	1995	#include "applications/staticProps/RadialDistrFunc.hpp"
45	tim	1994	namespace oopse {
46
47			class GofXyz : public RadialDistrFunc {
48
49			public:
50	tim	2038	GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins);
51	tim	1994
52	tim	1995	int getNRBins() {
53			return nRBins_;
54			}
55	tim	1994
56	tim	1995	double getLength() {
57			return len_;
58			}
59
60	tim	1994	private:
61
62			virtual void preProcess();
63	tim	1995	void initalizeHistogram();
64	tim	1994	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
65			virtual void writeRdf();
66
67	tim	2045	Vector3d getMolCom(StuntDouble* sd);
68
69			//virtual void validateSelection1(SelectionManager& sman);
70
71	tim	1994	double len_;
72	tim	2048	double halfLen_;
73	tim	1994	int nRBins_;
74			double deltaR_;
75
76			std::vector<std::vector<std::vector<int> > > histogram_;
77
78	tim	2045	struct CoorSet {
79			Vector3d xaxis;
80			Vector3d yaxis;
81			Vector3d zaxis;
82			};
83
84			std::map<int, CoorSet> coorSets_;
85			std::vector<Molecule*> atom2Mol_;
86	tim	1994	};
87
88
89			}
90			#endif
91