applications/dynamicProps/CorrelationFunction.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_DYNAMICPROPS_CORRELATIONFUNCTION_HPP
#define APPLICATIONS_DYNAMICPROPS_CORRELATIONFUNCTION_HPP

#include <string>
#include <vector>

#include "brains/SimInfo.hpp"
#include "brains/BlockSnapshotManager.hpp"

#include "primitives/StuntDouble.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"

namespace oopse {

/**
 * @class CorrelationFunction CorrelationFunction.hpp "applications/dynamicProps/CorrelationFunction"
 * @brief Base class for Correlation function
 */
 
class CorrelationFunction {
    public:
        CorrelationFunction(SimInfo* info, const std::string& filename, 
            const std::string& sele1, const std::string& sele2, int storageLayout);
        
        void doCorrelate();


        void setOutputName(const std::string& filename) {
            outputFilename_ = filename;
        }

        const std::string& getOutputFileName() const {
            return outputFilename_;
        }


        const std::string& getCorrFuncType() const {
            return corrFuncType_;
        }

        void setCorrFuncType(const std::string& type) {
            corrFuncType_ = type;
        }

        void setExtraInfo(const std::string& extra) {
            extra_ = extra;
        }
            
    protected:
        
        virtual void preCorrelate();        
        virtual void postCorrelate();

        double deltaTime_;
        int nTimeBins_;
        std::vector<double> histogram_;
        std::vector<int> count_;
        
    private:

        void correlateBlocks(SnapshotBlock* block1, SnapshotBlock* block2);
        void correlateFrames(int frame1, int frame2);
        void updateFrame(int frame);
        
        virtual void writeCorrelate();

        virtual double calcCorrVal(StuntDouble* sd1, int frame1, StuntDouble* sd2, int frame2) = 0;

        virtual void validateSelection(const SelectionManager& seleMan) {}

        SimInfo* info_;
        int storageLayout_;
        std::string dumpFilename_;
        std::string selectionScript1_;
        std::string selectionScript2_;
        
        SelectionEvaluator evaluator1_;
        SelectionEvaluator evaluator2_;
        SelectionManager seleMan1_;
        SelectionManager seleMan2_;        

        BlockSnapshotManager* bsMan_;        


        std::string outputFilename_;

        std::string corrFuncType_;
        std::string extra_;
};

}
#endif
Revision:	2006
Committed:	Sun Feb 13 08:05:33 2005 UTC (19 years, 6 months ago) by tim
File size:	4501 byte(s)
Log Message:	more work in dynamicProps
#	User	Rev	Content
1	tim	2002	/*
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_DYNAMICPROPS_CORRELATIONFUNCTION_HPP
42			#define APPLICATIONS_DYNAMICPROPS_CORRELATIONFUNCTION_HPP
43
44	tim	2006	#include <string>
45			#include <vector>
46
47			#include "brains/SimInfo.hpp"
48			#include "brains/BlockSnapshotManager.hpp"
49
50			#include "primitives/StuntDouble.hpp"
51			#include "selection/SelectionEvaluator.hpp"
52			#include "selection/SelectionManager.hpp"
53
54	tim	2002	namespace oopse {
55
56			/**
57			* @class CorrelationFunction CorrelationFunction.hpp "applications/dynamicProps/CorrelationFunction"
58			* @brief Base class for Correlation function
59			*/
60
61			class CorrelationFunction {
62			public:
63			CorrelationFunction(SimInfo* info, const std::string& filename,
64			const std::string& sele1, const std::string& sele2, int storageLayout);
65
66			void doCorrelate();
67
68
69			void setOutputName(const std::string& filename) {
70			outputFilename_ = filename;
71			}
72
73			const std::string& getOutputFileName() const {
74			return outputFilename_;
75			}
76
77
78			const std::string& getCorrFuncType() const {
79			return corrFuncType_;
80			}
81
82			void setCorrFuncType(const std::string& type) {
83			corrFuncType_ = type;
84			}
85
86			void setExtraInfo(const std::string& extra) {
87			extra_ = extra;
88			}
89
90			protected:
91
92			virtual void preCorrelate();
93			virtual void postCorrelate();
94
95			double deltaTime_;
96			int nTimeBins_;
97			std::vector<double> histogram_;
98			std::vector<int> count_;
99
100			private:
101
102			void correlateBlocks(SnapshotBlock* block1, SnapshotBlock* block2);
103			void correlateFrames(int frame1, int frame2);
104			void updateFrame(int frame);
105
106			virtual void writeCorrelate();
107
108			virtual double calcCorrVal(StuntDouble* sd1, int frame1, StuntDouble* sd2, int frame2) = 0;
109
110			virtual void validateSelection(const SelectionManager& seleMan) {}
111
112			SimInfo* info_;
113			int storageLayout_;
114			std::string dumpFilename_;
115			std::string selectionScript1_;
116			std::string selectionScript2_;
117
118			SelectionEvaluator evaluator1_;
119			SelectionEvaluator evaluator2_;
120			SelectionManager seleMan1_;
121			SelectionManager seleMan2_;
122
123			BlockSnapshotManager* bsMan_;
124
125
126			std::string outputFilename_;
127
128			std::string corrFuncType_;
129			std::string extra_;
130			};
131
132			}
133			#endif