applications/staticProps/DensityPlot.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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#ifndef APPLICATIONS_STATICPROPS_DENSITYPLOT_HPP
#define APPLICATIONS_STATICPROPS_DENSITYPLOT_HPP
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "applications/staticProps/StaticAnalyser.hpp"

namespace OpenMD {

    class DensityPlot : public StaticAnalyser{
        public:
            DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele,RealType len, int nrbins);
            virtual void process();

            int getNRBins() {
              return nRBins_; 
            }
            
            RealType getLength() {
              return len_;
            }
        

        private:
            Vector3d calcNewOrigin();
            
            void writeDensity();            

            Snapshot* currentSnapshot_;
            RealType len_;
            RealType halfLen_;
            int nRBins_;
            RealType deltaR_;                
            std::vector<int> histogram_; 
            std::vector<RealType> density_; 

            std::string selectionScript_;
            SelectionManager seleMan_;
            SelectionEvaluator evaluator_;
            std::string cmSelectionScript_;
            SelectionManager cmSeleMan_;
            SelectionEvaluator cmEvaluator_;

            
    };
}

#endif


Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	3521 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	tim	545	/*
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	545	* 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	545	* 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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	545	*/
42			#ifndef APPLICATIONS_STATICPROPS_DENSITYPLOT_HPP
43			#define APPLICATIONS_STATICPROPS_DENSITYPLOT_HPP
44			#include "selection/SelectionEvaluator.hpp"
45			#include "selection/SelectionManager.hpp"
46			#include "applications/staticProps/StaticAnalyser.hpp"
47
48	gezelter	1390	namespace OpenMD {
49	tim	545
50			class DensityPlot : public StaticAnalyser{
51			public:
52	tim	963	DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele,RealType len, int nrbins);
53	tim	545	virtual void process();
54
55			int getNRBins() {
56			return nRBins_;
57			}
58
59	tim	963	RealType getLength() {
60	tim	545	return len_;
61			}
62
63
64			private:
65	tim	558	Vector3d calcNewOrigin();
66
67	tim	545	void writeDensity();
68	tim	558
69	tim	545	Snapshot* currentSnapshot_;
70	tim	963	RealType len_;
71			RealType halfLen_;
72	tim	545	int nRBins_;
73	tim	963	RealType deltaR_;
74	tim	545	std::vector<int> histogram_;
75	tim	963	std::vector<RealType> density_;
76	tim	545
77			std::string selectionScript_;
78			SelectionManager seleMan_;
79	tim	558	SelectionEvaluator evaluator_;
80			std::string cmSelectionScript_;
81			SelectionManager cmSeleMan_;
82			SelectionEvaluator cmEvaluator_;
83
84
85	tim	545	};
86			}
87
88			#endif
89
90
91